Repository: SpatialTranscriptomicsResearch/st_pipeline (language: python)

Issue:
Merge from base



Discussion / hints:

Fix patch:
diff --git a/CHANGELOG b/CHANGELOG
index 40d0d2e..6c39024 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -489,4 +489,7 @@ file is present
 
 Version 1.8.0
 * Improved the unit-tests
-* Make input data a positional arguments in extra scripts
\ No newline at end of file
+* Make input data a positional arguments in extra scripts
+
+Version 1.8.1
+* Fix a small bug when having the UMI before the BARCODE
\ No newline at end of file
diff --git a/README_SHORT b/README_SHORT
index 4644e44..dcdc393 100644
--- a/README_SHORT
+++ b/README_SHORT
@@ -53,6 +53,4 @@ Basically what the ST pipeline does is:
 You can see a graphical more detailed description of the workflow in the documents workflow.pdf and workflow_extended.pdf
 
 The output will be a matrix of counts (genes as columns, spots as rows),
-a BED file containing the transcripts (Read name, coordinate, gene, etc..), and a JSON
-file with useful stats.
-The ST pipeline will also output a log file with useful information.
+The ST pipeline will also output a log file with useful information and stats.
diff --git a/docs/_sources/changes.rst.txt b/docs/_sources/changes.rst.txt
new file mode 100644
index 0000000..1a404c8
--- /dev/null
+++ b/docs/_sources/changes.rst.txt
@@ -0,0 +1,578 @@
+Changes
+-------
+
+**Version 1.7.8**
+
+* Updated docs
+* Added flags to skip (trimming, mapping and annotation)
+* Fixed a bug in the compute saturation option
+* Restored the unittests
+* Improvements when dealing with ambiguous and no_feature genes
+
+**Version 1.7.6**
+
+* Ported to Python 3
+
+**Version 1.7.3**
+
+* Fixed a small bug when soring the output of taggd
+* Improved the st_qa.py script
+
+**Version 1.7.2**
+
+* Removed parallel code for un-necessary parts
+* Added option to provide saturation points
+
+**Version 1.6.2**
+
+* Fixed a error in the parameters
+
+**Version 1.6.1**
+
+* Added option to disable the barcode demultiplexing step
+* Added option to disable the UMI filtering step
+
+**Version 1.6.0**
+
+* Made the parsing of unique UMIs gene by gene and parallel
+* AdjacentBi is now the default method for UMI counting
+* Made the trimming function output the trimmed R2 in BAM format with the barcode and UMI
+* Made the mapping function works with a BAM file as input (latest STAR release)
+* Made the annotation function parallel
+* Made the quality step parallel
+* Improvements in speed and memory (constant memory use)
+* The STAR genome loading strategy can be now set
+* Added an affinity based method to cluster UMIs
+* Added option to set the STAR BAM sort memory limit
+
+**Version 1.5.1**
+
+* Fixed a bug that will output the matrix of counts inverted
+
+**Version 1.5.0**
+
+* st_qa.py generate expression heatmap plots
+* Fixed a minor bug in the computation of the saturation curves
+* adjust_matrix_coordinates now does not update the coordinates by default
+* adjust_matrix_coordiantes works with the latest ST Spot detector format
+* small updates in the fastq merging script
+* relaxed a bit the restriction checks for some parameters
+
+**Version 1.4.5**
+
+* Added extra scripts:
+	- merge_bcl : merge BCL files based in patterns
+	- filter_gene_type_matrix : filter gene in output data based on Ensembl gene types
+* Bumped Pysam and HTSeq 
+
+**Version 1.4.1**
+
+* Small update to make the PIP installation more robust
+
+**Version 1.4.0**
+
+* Small update to make the PIP installation more robust
+
+**Version 1.3.5**
+
+* Optimized the counting of UMIs by strand, start-pos and offset
+
+**Version 1.3.4**
+
+* Fixed a typo in one of the parameter that caused the pipeline to not run
+
+**Version 1.3.3**
+
+* Disabled spliced alignments by default
+
+**Version 1.3.2**
+
+* Optimized the mapping and annotation steps
+
+**Version 1.3.1**
+
+* Homopolymer miss-matches is a parameter now
+* Removing now also PolyNs (parameter)
+
+**Version 1.3.0**
+
+* Added more methods to cluster UMIs
+* Optimized the UMI counting algorithm
+* Optimized the memory use
+
+**Version 1.2.6**
+
+* Take into account soft-clipped bases when computing start/end positions
+
+**Version 1.2.5**
+* Changed the limit range of some parameters
+
+**Version 1.2.4**
+
+* Fixed small bugs
+* Small improvements in st_qa.py and convertEnsemblToNames.py
+
+**Version 1.2.3**
+
+* Bumped TaggD version
+* Added more stats to the dataset output
+* Added scripts to compute stats
+* Added new option for TaggD
+
+**Version 1.2.2**
+
+* Fixed bugs in convertEnsemblToNames
+* Added some parameters for TaggD demultiplexing
+* Bumped version of TaggD
+
+**Version 1.2.1**
+
+* Made homopolymers filters enabled by default
+* Added a test dataset to the docs
+
+
+**Version 1.2.0**
+
+* Fixed a small bug in the deletion of the tmp folder
+
+**Version 1.1.7**
+
+* Make sure to remove tmp files even if an error happens
+
+**Version 1.1.6**
+
+* Fixed bug that would leave some files in /tmp
+* Allowed mis-matches when removing adaptors is now 2
+
+**Version 1.1.5**
+
+* Removed some un-necessary parameters
+
+**Version 1.1.1**
+
+* Simplified the two pass mode
+
+**Version 1.1.0**
+
+* Added flag to discard reads mapping to anti-sense strand
+* Parameters for GC content filter instead of using the same value as AT content filter
+* Fixed a small bug in the logging of some parameters
+
+**Version 1.0.4**
+
+* When removing adaptors (homopolymers streches) allow to up to 3 missmatches
+* Added GC content filter (same % as AT content)
+
+**Version 1.0.3**
+
+* Fixed a minor bug in the counting of UMIs or - strand
+
+**Version 1.0.2**
+
+* If no temp folder is given a new unique one is created on top of the execution folder
+* integrate createDataset.py into the code of the pipeline
+* Adjusted some parameters names and descriptions (no UMI is default)
+* Added sliding window when counting unique molecules
+* Added support for bzip
+
+**Version 1.0.1**
+
+* Fixed small bug in the parsing of the umi quality parameter
+
+**Version 1.0.0**
+
+* Added option to check for UMI quality
+* Optimized the UMI template check code
+* Optimized how the unique molecules are counted
+* Better stats for the quality filter step
+* Updated convertEnsemblToNames script
+* Updated stringdocs
+
+**Version 0.9.9**
+
+* Small bug fixes
+
+**Version 0.9.6**
+
+* Fixed a bug with the non ambiguous option
+* Fix a bug in the saturation computation
+
+**Version 0.9.5**
+
+* When a R2 is trimmed its correspondant R1 is trimmed as well
+
+**Version 0.9.4**
+
+* Fixed a stupid bug in the compute saturation option
+
+**Version 0.9.3**
+
+* Changed the rRNA filter so the BAM output does not need to be sorted
+
+**Version 0.9.2**
+
+* Fixed a bug in the parsing of parameters
+
+**Version 0.9.1**
+
+* Fixed a small bug with the location of discarded files
+
+**Version 0.9.0**
+
+* Replaced JSON for data frame in the output format
+* Replaced python gzip for system call (faster)
+* Changed the logic of how the filenames are stored and handled
+
+**Version 0.8.9**
+
+* Improved the error messages and error handling
+
+**Version 0.8.8**
+
+* Removed barcodes IDs from the output file
+
+**Version 0.8.7**
+
+* Updated comments, manual and license
+* Small improvements
+
+**Version 0.8.5**
+
+* Fixed a bug in the computation of saturation curves
+
+**Version 0.8.4**
+
+* Added a normal hash with INT keys to increase speed and reduce memory
+* Using the gene_id for annotation again
+
+**Version 0.8.3**
+
+* Added parameter for strandness in annotation (yes by default)
+* Simplified a bit the quality trimming step (do not account for user input trimmed bases)
+
+**Version 0.8.2**
+
+* Added stats for annotated reads
+* Replaced shelve dict for sqldict
+* Fixed some small bugs in the annotation
+
+**Version 0.8.1**
+
+* Removed the pair mode keep option
+* Removed un-neccessary pair mode and mapped checks after alignment
+
+**Version 0.8.0**
+
+* Added option to do the STAR 2 pass mode
+* Removed option to run pipeline without IDs
+* Speed improvements
+* Perform demultiplex after mapping
+* No attaching the barcode to reverse reads
+* Removing some parameters
+* Some improvements in stDataPlotter
+* Option to use BAM format
+* Removed annotation filtering step
+* Removed forward trimming parameters
+* Output gene names even with ENSEMBL
+
+**Version 0.7.7**
+
+* Small memory improvements
+* Updates in plotting script
+
+**Version 0.7.6**
+
+* End coordinates now contain the whole read length
+* Make annotation strand aware (reverse)
+* Updated to STAR 2.5
+
+**Version 0.7.5**
+
+* Fixed a small bug
+
+**Version 0.7.4**
+
+* Added some memory improvements
+
+**Version 0.7.3**
+
+* Added parameters for inverse trimming
+* Memory and speed optimizations in createDatasets
+* Added option for low_memory use
+
+**Version 0.7.2**
+
+* Added unique genes to saturation points
+* Added option to keep non-annotated reads
+
+**Version 0.7.1**
+
+* Fixed some small bugs
+
+**Version 0.7.0**
+
+* Fixed a bug in the saturation points
+* Removed counttrie as option for clustering
+* Updated and improved CTTS scripts
+* Updated datfa plotter color list
+
+**Version 0.6.9**
+
+* Fixed a bug in the saturation points
+
+**Version 0.6.8**
+
+* Improved speed and memory in createDatasets
+* Changed saturation points to fixed values that grow exp
+* Improved speed in computation of saturation points
+* Small bug fixes
+* Upgraded json2Scatter with many improvements
+* Rename json2scatter to stDataPlotter
+
+**Version 0.6.7**
+
+* Fixed a bug in the hierarchical clustering
+* Added the input parameter to qa_stats
+* Append experiment name to output files
+* Added option to compute saturation points
+* Added tool to plot stdata and clusters with aligned image
+
+**Version 0.6.6**
+
+* Fixed a bug in the hierarchical clustering
+* Fixed a bug in the printed stats
+
+**Version 0.6.5**
+
+* Fixed a bug in retrieving the version of the software
+* Added time stamps in different steps
+* Added a UMI template quality filter
+
+**Version 0.6.4**
+
+* Fixed a bug in counttrie clustering method
+* Improved sorting of molecular barcodes prior clustering
+* Added hiearachical clustering option
+
+**Version 0.6.3**
+
+* Removed reads.json
+* Added qa_stats.json to the output
+* Restored old versioning system
+* Removed hadoop related stuff
+* Added support for gziped input files
+
+**Version 0.6.2**
+
+* Improved the log a bit
+* Added parameters for max,min intron size and max gap size
+
+**Version 0.6.1**
+
+* Fixed some bugs in the prefix tree
+
+**Version 0.5.9**
+
+* Added an option to find molecular barcodes clusters using a prefix tree
+
+**Version 0.5.8**
+
+* Fixed a bug in the function to retrieve the pipeline version
+
+**Version 0.5.7**
+
+* Fixed a bug with --disable-multimap option
+
+**Version 0.5.6**
+
+* Fixed a typo in a parameter
+* Fixed a bug that caused some parameters to not work
+
+**Version 0.5.5**
+
+* Added some extra debugging info in createDatasets
+* Output the read name in the BED output file
+* Changed --allowed-kimera for --allowed-kmer
+* Added version as parameter and log message
+
+**Version 0.5.4**
+
+* Added parameter to disable soft clipping in mapping
+* Disable softclipping in rRNA filter
+* Make sure that discarded reads after rRNA filter are replaced by Ns
+* Improved stats info a bit
+
+**Version 0.5.3**
+
+* Bumped Taggd to 0.2.2
+
+**Version 0.5.2**
+
+* Fixed a bug in the rRNA filter that would cause to not discard rRNA mapped reads
+
+**Version 0.5.1**
+
+* Added check when UMI is the same as barcode
+* Added more stats
+* Added percentiles distributiosn stats for createDAtaset
+* Added support for BAM and SAM (not functional now)
+* Added option to disable multiple aligned reads
+* Fixed a bug in the bed file
+
+**Version 0.5.0**
+
+* Added AT content filter in quality trimming
+* Added min mapped length filter after mapping
+* Make sure one of the multiple aligned reads is set as not multiple aligned so it can be annotated
+* Discard the other multiple aligned reads after mapping
+* Disable sorting
+* Restored back to use gene_id as column for annotation
+
+**Version 0.4.9**
+
+* Changed naming convention
+* Added support for normal RNA analysis
+
+**Version 0.4.8**
+
+* Improved STAR configuration
+* Added mapping post processing to filter out and adjust reversed reads
+* Changed to use gene_name for annotation
+* Fixed some bugs and some improvements
+* Fixed bugs in the trimming
+
+**Version 0.4.7**
+
+* Improved stats
+* Fixed a bug that would remove original input files
+* Added a script to convert ENSEMBL ids to gene names
+
+**Version 0.4.6**
+
+* Fixed a bug that would not compute the number of discarded reads when using molecular barcodes
+
+**Version 0.4.5**
+
+* Fixed a bug in the barcodes JSON output
+
+**Version 0.4.4**
+
+* Fixed a bug in the molecular barcodes algorithm
+* Fixed a bug that would keep the original fastq reads in the system
+* Update taggd version
+
+**Version 0.4.3**
+
+* Small improvements with error checking and log in the mapping
+* Fixed a bug that would remove the file after filtering annoted reads
+* Make the sorting by name instead by position due to a bug in htseq-count
+
+**Version 0.4.2**
+
+* Fixed a bug in the capture of parameters
+
+**Version 0.4.1**
+
+* Improved the logs
+* Fixed few bugs
+
+**Version 0.4.0**
+
+* Added back taggd
+* Added BED file to output
+* Added STAR
+* Optimized workflow
+* do rRNA filter first
+* Optimized annotation
+* Optimized trimming
+* Output reads do not contain duplicates
+
+**Version 0.3.9**
+
+* Allowing molecular barcodes to be before the barcodes
+
+**Version 0.3.8**
+
+* Added back findIndexes
+
+**Version 0.3.7**
+
+* Removed cutadapt dependency
+
+**Version 0.3.6**
+
+* Fixed a bug in the installation
+
+**Version 0.3.5**
+
+* Added options to remove PolyC fix bugs in adaptors removal
+
+**Version 0.3.4**
+
+* Added test for STAR and STAR binary to dependencies
+* Added TAGGD and removed findIndexes
+* Improved install script
+* Added options to remove adaptors (PolyA, PolyT and PolyG)
+* Exchanged Bowtie as primary mapper with STAR.
+
+**Version 0.3.3**
+
+* Added option to keep files with discarded reads/barcodes
+* Internal refactoring and optimization
+
+**Version 0.3.2**
+
+* Outputted reads JSON now only has the portion of the read that was used to map
+* Cutadapt is integrated but only using the quality trimming for now
+* Internal refactoring and optimizations
+
+**Version 0.3.1**
+
+* Added small unit-test for molecular barcodes
+* Added more molecular barcodes algorithms (using a naive one for now)
+* Fixed small issues in JSON parsing libraries
+
+**Version 0.3.0**
+
+* Rewrite createDatasets.py
+* Clean up repository and deprecated files
+* Change the unit-test library and structure
+* Refactor the unit-test (use pipeline API instead of command line calls)
+* Ensure unit-test remove tmp files when failing
+* Add better error handling
+* Add unit-test for Molecular Barcodes
+* Add Molecular Barcodes functionality
+* General refactor and clean up
+* Add invoke options (clean, build, install)
+* Fix an important bug in createDatasets that caused incorrect computation of reads counts
+
+**Version 0.2.5**
+
+* Improved installers
+* Small bug fixes
+* Added basic unit-test to do a run of the pipeline
+
+**Version 0.2.4**
+
+* Some optimizations and bug fixes
+
+**Version 0.2.3**
+
+* Fixed a error with new version of HTSeq-count that will discard more reads
+
+**Version 0.2.2**
+
+* Added extra parameters
+* Fixed some typos
+* Fixed a bug that caused to remove some bases from the barcode ID in the rv reads
+
+**Version 0.2.1**
+
+* code refactored and modularized
+* add argparse for parameters parsing
+* add API for Amazon EMR and terminal version
+* better error handling
+* optimized code
+* new version of FindIndexes
+* remove dependencies
+* added proper installers and documentation
diff --git a/docs/_sources/contact.rst.txt b/docs/_sources/contact.rst.txt
new file mode 100644
index 0000000..857ae93
--- /dev/null
+++ b/docs/_sources/contact.rst.txt
@@ -0,0 +1,4 @@
+Contact
+-------
+
+Author: Jose Fernandez Navarro <jc.fernandez.navarro@gmail.com>
diff --git a/docs/_sources/example.rst.txt b/docs/_sources/example.rst.txt
new file mode 100644
index 0000000..7602038
--- /dev/null
+++ b/docs/_sources/example.rst.txt
@@ -0,0 +1,39 @@
+Examples
+--------
+
+The following is an example of an BASH file to run the ST pipeline. 
+This example is for version 1.6.0 of the ST pipeline.
+
+.. code-block:: bash
+
+	#!/bin/bash
+
+	# FASTQ reads
+	FW=/YOUR_RUN/R1.fastq.gz
+	RV=/YOUR_RUN/R2.fastq.gz
+
+	# References for mapping, annotation and nonRNA-filtering
+	MAP=/mouse/GRCm38_86v2/StarIndex
+	ANN=/mouse/GRCm38_86v2/annotation/annotation.gtf
+	CONT=/mouse/GRCm38_86v2/ncRNA/StarIndex
+
+	# Barcodes settings
+	ID=/stpipeline/ids/YOUR_IDs.txt
+
+	# Output folder and experiment name
+	# Do not use / or \ in the experiment name
+	OUTPUT=/your_experiment_folder
+	EXP=YOUR_EXP_NAME
+
+	# Running the pipeline
+	st_pipeline_run.py \
+	  --output-folder $OUTPUT \
+	  --ids $ID \
+	  --ref-map $MAP \
+	  --ref-annotation $ANN \
+	  --expName $EXP \
+	  --htseq-no-ambiguous \
+	  --verbose \
+	  --log-file $OUTPUT/${EXP}_log.txt \
+	  --contaminant-index $CONT \
+	  $FW $RV
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
new file mode 100644
index 0000000..bc3eca8
--- /dev/null
+++ b/docs/_sources/index.rst.txt
@@ -0,0 +1,26 @@
+.. ST Pipeline documentation.
+
+Welcome to ST Pipeline's documentation!
+=======================================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   intro
+   installation
+   manual
+   example
+   changes
+   license
+   contact
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/_sources/installation.rst.txt b/docs/_sources/installation.rst.txt
new file mode 100644
index 0000000..b079b95
--- /dev/null
+++ b/docs/_sources/installation.rst.txt
@@ -0,0 +1,57 @@
+Installing the Spatial Transcriptomics pipeline
+-----------------------------------------------
+
+These are the general instructions for installing the st_pipeline from scratch
+on you compute environment. All the commands can be performed as a user with no
+elevated permissions.
+
+We recommend to download and install Anaconda (https://www.anaconda.com/products/individual)
+
+We then create a virtual environment from which we will run the pipeline in.
+Type the following command:
+
+	``conda create -n pipeline python=3.6 anaconda``
+
+The name for the virtual environment that we have just created is specified by
+the -n flag. Here is is called pipeline, but this can be anything that you want
+to name it. To run the pipeline, this virtual environment must be activated. To
+activate the virtual environment, enter the following command:
+
+	``source activate pipeline``
+
+Where pipeline is the name of your virtual environment (here the virtual
+environment is called pipeline). To deactivate the virtual environment, type the
+following command:
+
+	``source deactivate``
+
+You need to obtain the pipeline from github to use it. The following steps will
+tell you how to perform this.
+
+Change to your home directory
+
+	``cd``
+
+Clone the repository from github
+
+	``git clone git://github.com/SpatialTranscriptomicsResearch/st_pipeline.git``
+
+Change into the st_pipeline directory
+
+	``cd st_pipeline``
+
+Activate the virtual environment (if not already active)
+
+	``source activate pipeline``
+
+Install the pipeline
+
+	``python setup.py build``
+
+	``python setup.py install``
+	
+Alternatively, you can simply install the pipeline using PyPy:
+
+	``pip install stpipeline``
+
+Now the pipeline is installed and ready to be run.
diff --git a/docs/_sources/intro.rst.txt b/docs/_sources/intro.rst.txt
new file mode 100644
index 0000000..d6e2c93
--- /dev/null
+++ b/docs/_sources/intro.rst.txt
@@ -0,0 +1,61 @@
+Introduction
+------------
+
+The ST Pipeline contains the tools and scripts needed to process 
+and analyze the raw files generated with the Spatial Transcriptomics 
+or Visium in FASTQ format to generate datasets for down-stream analysis. 
+The ST pipeline can also be used to process single cell RNA-seq data as 
+long as a file with barcodes identifying each cell is provided.
+The ST Pipeline can also process RNA-Seq datasets generated with 
+or without UMIs. 
+
+The ST Pipeline has been optimized for speed, robustness and 
+it is very easy to use with many parameters to adjust all the settings.
+The ST Pipeline is fully parallel and has constant memory use. 
+The ST Pipeline allows to skip any of the steps and to use the 
+genome or the transcriptome as reference. 
+
+The following files/parameters are required:
+
+- FASTQ files (Read 1 containing the spatial information and the UMI 
+  and read 2 containing the genomic sequence) 
+- A genome index generated with STAR 
+- An annotation file in GTF or GFF format (optional)
+- The file containing the barcodes and array coordinates 
+   (look at the folder "ids" and chose the correct one). 
+   Basically this file contains 3 columns (BARCODE, X and Y), 
+   so if you provide this file with barcodes identinfying cells (for example), 
+   the ST pipeline can be used for single cell data.
+   This file is optional too. 
+- A name for the dataset
+
+The ST pipeline has multiple parameters mostly related to trimming, 
+mapping and annotation but generally the default values are good enough. 
+You can see a full description of the parameters 
+typing "st_pipeline_run.py --help" after you have installed the ST pipeline.
+
+The input FASTQ files can be given in gzip/bzip format as well. 
+
+Basically what the ST pipeline does is:
+
+- Quality trimming (read 1 and read 2):
+	- Remove low quality bases
+	- Sanity check (reads same length, reads order, etc..)
+	- Check quality UMI (if provided)
+	- Remove artifacts (PolyT, PolyA, PolyG, PolyN and PolyC) of user defined length
+	- Check for AT and GC content
+	- Discard reads with a minimum number of bases of that failed any of the checks above
+- Contamimant filter e.x. rRNA genome (Optional)
+- Mapping with STAR (only read 2)
+- Demultiplexing with [Taggd](https://github.com/SpatialTranscriptomicsResearch/taggd) (only read 1)
+- Keep reads (read 2) that contain a valid barcode and are correctly mapped
+- Annotate the reads with htseq-count (optional)
+- Group annotated reads by barcode(spot position) and gene to get a read count
+- In the grouping/counting only unique molecules (UMIs) are kept. 
+
+You can see a graphical more detailed description of the workflow in the documents workflow.pdf and workflow_extended.pdf
+
+The output will be a matrix of counts (genes as columns, spots as rows),
+a BED file containing the transcripts (Read name, coordinate, gene, etc..), and a JSON
+file with useful stats.
+The ST pipeline will also output a log file with useful information.
\ No newline at end of file
diff --git a/docs/_sources/license.rst.txt b/docs/_sources/license.rst.txt
new file mode 100644
index 0000000..4efd572
--- /dev/null
+++ b/docs/_sources/license.rst.txt
@@ -0,0 +1,25 @@
+License
+-------
+
+The MIT License (MIT)
+Copyright (c) 2016 Jose Fernandez Navarro.
+All rights reserved.
+
+* Jose Fernandez Navarro <jc.fernandez.navarro@gmai.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software is furnished to do so,
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/docs/_sources/manual.rst.txt b/docs/_sources/manual.rst.txt
new file mode 100644
index 0000000..9f9cc8a
--- /dev/null
+++ b/docs/_sources/manual.rst.txt
@@ -0,0 +1,227 @@
+Manual
+------
+
+ST Pipeline is a tool to process the Spatial Transcriptomics raw data
+or single cell data.
+The data is filtered, aligned to a genome, annotated to a reference,
+demultiplexed by array coordinates and then aggregated by counts
+that are not duplicates using the Unique Molecular Indentifiers.
+The output contains the counts matrix, a stats file, a log file
+and a BED file with all the transcripts.
+
+The ST Pipeline requires two fastq files, an IDs files (BARCODE, X, Y),
+the path to a STAR genome index, the path to a annotation file in GTF
+format and a dataset name.
+
+The ST Pipeline has many parameters, you can see a description of them
+by typing : st_pipeline_run.py --help
+
+Note that the minimum read length is dependant on the type of kit used, and
+should be adjusted accordingly, i.e. a 150bp kit should have a different
+minimum read length than a 75bp kit.
+
+Soft clipping is also not recommended when using the 75bp kit, due to the
+shorter length.
+
+The UMI filter can be used for array batches 1000L6 and earlier. It is
+unable to be used for array batches 1000L7 and newer as the UMI in
+these arrays is fully randomised.
+
+Author Jose Fernandez Navarro <jc.fernandez.navaro@gmail.com>
+
+
+``st_pipeline_run.py [options] fastq_files fastq_files``
+
+**positional arguments**
+
+.. code-block:: bash
+
+  fastq_file_fw
+    Read_1 containing the spatial barcodes and UMIs for each sequence.
+
+  fastq_file_rv
+    Read_2 containing the gene sequence corresponding to the sequence in
+    Read_1.
+
+**optional arguments**
+
+.. code-block:: bash
+
+  -h, --help            show this help message and exit
+  --ids [FILE]          Path to the file containing the map of barcodes to the
+                        array coordinates
+  --ref-map [FOLDER]    Path to the folder with the STAR index for the genome
+                        that you want to use to align the reads
+  --ref-annotation [FILE]
+                        Path to the reference annotation file (GTF or GFF
+                        format is required) to be used to annotated the reads
+  --expName [STRING]    Name of the experiment/dataset (The output files will
+                        prepend this name)
+  --allowed-missed [INT]
+                        Number of allowed mismatches when demultiplexing
+                        against the barcodes with TaggD (default: 2)
+  --allowed-kmer [INT]  KMer length when demultiplexing against the barcodes
+                        with TaggD (default: 6)
+  --overhang [INT]      Extra flanking bases added when demultiplexing against
+                        the barcodes with TaggD (default: 2)
+  --min-length-qual-trimming [INT]
+                        Minimum length of the reads after trimming, shorter
+                        reads will be discarded (default: 20)
+  --mapping-rv-trimming [INT]
+                        Number of bases to trim in the reverse reads for the
+                        mapping step (5\' end) (default: 0)
+  --contaminant-index [FOLDER]
+                        Path to the folder with a STAR index with a
+                        contaminant genome. Reads will be filtered against the
+                        specified genome and mapping reads will be descarded
+  --qual-64             Use phred-64 quality instead of phred-33(default)
+  --htseq-mode [STRING]
+                        Mode of Annotation when using HTSeq. Modes =
+                        {union,intersection-nonempty(default),intersection-
+                        strict}
+  --htseq-no-ambiguous  When using htseq discard reads annotating ambiguous
+                        genes (default False)
+  --start-id [INT]      Start position of the IDs (Barcodes) in the R1
+                        (counting from 0) (default: 0)
+  --no-clean-up         Do not remove temporary/intermediary files (useful for
+                        debugging)
+  --verbose             Show extra information on the log file
+  --mapping-threads [INT]
+                        Number of threads to use in the mapping step (default:
+                        4)
+  --min-quality-trimming [INT]
+                        Minimum phred quality a base must have in the trimming
+                        step (default: 20)
+  --bin-path [FOLDER]   Path to folder where binary executables are present
+                        (system path by default)
+  --log-file [STR]      Name of the file that we want to use to store the logs
+                        (default output to screen)
+  --output-folder [FOLDER]
+                        Path of the output folder
+  --temp-folder [FOLDER]
+                        Path of the location for temporary files
+  --umi-allowed-mismatches [INT]
+                        Number of allowed mismatches (hamming distance) that
+                        UMIs of the same gene-spot must have in order to
+                        cluster together (default: 1)
+  --umi-start-position [INT]
+                        Position in R1 (base wise) of the first base of the
+                        UMI (starting by 0) (default: 18)
+  --umi-end-position [INT]
+                        Position in R1 (base wise) of the last base of the UMI
+                        (starting by 1) (default: 27)
+  --keep-discarded-files
+                        Writes down unaligned, un-annotated and un-
+                        demultiplexed reads to files
+  --remove-polyA [INT]  Remove PolyA stretches of the given length from R2
+                        (Use 0 to disable it) (default: 10)
+  --remove-polyT [INT]  Remove PolyT stretches of the given length from R2
+                        (Use 0 to disable it) (default: 10)
+  --remove-polyG [INT]  Remove PolyG stretches of the given length from R2
+                        (Use 0 to disable it) (default: 10)
+  --remove-polyC [INT]  Remove PolyC stretches of the given length from R2
+                        (Use 0 to disable it) (default: 10)
+  --remove-polyN [INT]  Remove PolyN stretches of the given length from R2
+                        (Use 0 to disable it) (default: 10)
+  --filter-AT-content [INT%]
+                        Discards reads whose number of A and T bases in total
+                        are more or equal than the number given in percentage
+                        (default: 90)
+  --filter-GC-content [INT%]
+                        Discards reads whose number of G and C bases in total
+                        are more or equal than the number given in percentage
+                        (default: 90)
+  --disable-multimap    If activated, multiple aligned reads obtained during
+                        mapping will be all discarded. Otherwise the highest
+                        scored one will be kept
+  --disable-clipping    If activated, disable soft-clipping (local alignment)
+                        in the mapping step
+  --umi-cluster-algorithm [STRING]
+                        Type of clustering algorithm to use when performing
+                        UMIs duplicates removal. Options = {naive,
+                        hierarchical(default), Affinity, Adjacent and
+                        AdjacentBi} Note that for the affinity method the umi
+                        allowed mismatches parameter will be ignored.
+  --min-intron-size [INT]
+                        Minimum allowed intron size when searching for splice
+                        variants with STAR Splices alignments are disabled by
+                        default (=1) but to turn it on set this parameter to a
+                        bigger number, for example 10 or 20. (default: 1)
+  --max-intron-size [INT]
+                        Maximum allowed intron size when searching for splice
+                        variants with STAR Splices alignments are disabled by
+                        default (=1) but to turn it on set this parameter to a
+                        big number, for example 10000 or 100000. (default: 1)
+  --umi-filter          Enables the UMI quality filter based on the template
+                        given in --umi-filter-template
+  --umi-filter-template [STRING]
+                        UMI template (IUPAC nucleotide code) for the UMI
+                        filter, default = WSNNWSNNV
+  --compute-saturation  Performs a saturation curve computation by sub-
+                        sampling the annotated reads, computing unique
+                        molecules and then a saturation curve (included in the
+                        log file)
+  --saturation-points SATURATION_POINTS [SATURATION_POINTS ...]
+                        Saturation points can be provided instead of using
+                        default values. Provide separate values like this for
+                        example: 10000 20000 50000 100000
+  --include-non-annotated
+                        Do not discard un-annotated reads (they will be
+                        labeled __no_feature)
+  --inverse-mapping-rv-trimming [INT]
+                        Number of bases to trim in the reverse reads for the
+                        mapping step on the 3\' end
+  --two-pass-mode       Activates the 2-pass mode in STAR to improve mapping
+                        accuracy
+  --strandness [STRING]
+                        What strandness mode to use when annotating with
+                        htseq-count [no, yes(default), reverse]
+  --umi-quality-bases [INT]
+                        Maximum number of low quality bases allowed in an UMI
+                        (default: 6)
+  --umi-counting-offset [INT]
+                        Expression count for each gene-spot combination is
+                        expressed as the number of unique UMIs in each
+                        strand/start position. However some reads might have
+                        slightly different start positions due to
+                        amplification artifacts. This parameters allows to
+                        define an offset window from where to count unique
+                        UMIs. You can set it to a veryhigh value +9999 to
+                        count unique UMIs for the whole gene (default: 250)
+  --demultiplexing-metric [STRING]
+                        Distance metric for TaggD demultiplexing: Subglobal,
+                        Levenshtein or Hamming (default: Subglobal)
+  --demultiplexing-multiple-hits-keep-one
+                        When multiple ambiguous hits with same score are found
+                        in the demultiplexing, keep one (random).
+  --demultiplexing-trim-sequences DEMULTIPLEXING_TRIM_SEQUENCES [DEMULTIPLEXING_TRIM_SEQUENCES ...]
+                        Trims from the barcodes in the input file when doing
+                        demultiplexing. The bases given in the list of tuples
+                        as START END START END .. where START is the integer
+                        position of the first base (0 based) and END is the
+                        integer position of the last base (1 based). Trimmng
+                        sequences can be given several times.
+  --homopolymer-mismatches [INT]
+                        Number of mismatches allowed when removing
+                        homopolymers (default: 0)
+  --star-genome-loading [STRING]
+                        Similar to the STAR option --genomeLoad. It allows to
+                        load the genome index into memory so it can easily be
+                        shared by other jobs so to save loading time. Read the
+                        STAR manual for more info on this. (default:
+                        NoSharedMemory)
+  --star-sort-mem-limit STAR_SORT_MEM_LIMIT
+                        The maximum available RAM for sorting BAM during
+                        mapping. Default is 0 which means that it will be set
+                        to the genome index size
+  --disable-trimming    Use this flag if you want to skip the trimming step
+  --disable-mapping     Use this flag if you want to skip the mapping step
+  --disable-annotation  Use this flag if you want to skip the annotation
+  --disable-barcode     Use this flag if you want to skip the barcode
+                        demultiplexing step
+  --disable-umi         Use this flag if you want to skip the UMI filtering
+                        step
+  --transcriptome       Use a transcriptome instead of a genome, the gene tag
+                        will be obtained from the transcriptome file
+  --version             show program's version number and exit
+
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
new file mode 100644
index 0000000..da3572e
--- /dev/null
+++ b/docs/_static/documentation_options.js
@@ -0,0 +1,12 @@
+var DOCUMENTATION_OPTIONS = {
+    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+    VERSION: '1.7.8',
+    LANGUAGE: 'None',
+    COLLAPSE_INDEX: false,
+    BUILDER: 'html',
+    FILE_SUFFIX: '.html',
+    LINK_SUFFIX: '.html',
+    HAS_SOURCE: true,
+    SOURCELINK_SUFFIX: '.txt',
+    NAVIGATION_WITH_KEYS: false
+};
\ No newline at end of file
diff --git a/docs/_static/jquery-3.4.1.js b/docs/_static/jquery-3.4.1.js
new file mode 100644
index 0000000..773ad95
--- /dev/null
+++ b/docs/_static/jquery-3.4.1.js
@@ -0,0 +1,10598 @@
+/*!
+ * jQuery JavaScript Library v3.4.1
+ * https://jquery.com/
+ *
+ * Includes Sizzle.js
+ * https://sizzlejs.com/
+ *
+ * Copyright JS Foundation and other contributors
+ * Released under the MIT license
+ * https://jquery.org/license
+ *
+ * Date: 2019-05-01T21:04Z
+ */
+( function( global, factory ) {
+
+	"use strict";
+
+	if ( typeof module === "object" && typeof module.exports === "object" ) {
+
+		// For CommonJS and CommonJS-like environments where a proper `window`
+		// is present, execute the factory and get jQuery.
+		// For environments that do not have a `window` with a `document`
+		// (such as Node.js), expose a factory as module.exports.
+		// This accentuates the need for the creation of a real `window`.
+		// e.g. var jQuery = require("jquery")(window);
+		// See ticket #14549 for more info.
+		module.exports = global.document ?
+			factory( global, true ) :
+			function( w ) {
+				if ( !w.document ) {
+					throw new Error( "jQuery requires a window with a document" );
+				}
+				return factory( w );
+			};
+	} else {
+		factory( global );
+	}
+
+// Pass this if window is not defined yet
+} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
+
+// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1
+// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode
+// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common
+// enough that all such attempts are guarded in a try block.
+"use strict";
+
+var arr = [];
+
+var document = window.document;
+
+var getProto = Object.getPrototypeOf;
+
+var slice = arr.slice;
+
+var concat = arr.concat;
+
+var push = arr.push;
+
+var indexOf = arr.indexOf;
+
+var class2type = {};
+
+var toString = class2type.toString;
+
+var hasOwn = class2type.hasOwnProperty;
+
+var fnToString = hasOwn.toString;
+
+var ObjectFunctionString = fnToString.call( Object );
+
+var support = {};
+
+var isFunction = function isFunction( obj ) {
+
+      // Support: Chrome <=57, Firefox <=52
+      // In some browsers, typeof returns "function" for HTML <object> elements
+      // (i.e., `typeof document.createElement( "object" ) === "function"`).
+      // We don't want to classify *any* DOM node as a function.
+      return typeof obj === "function" && typeof obj.nodeType !== "number";
+  };
+
+
+var isWindow = function isWindow( obj ) {
+		return obj != null && obj === obj.window;
+	};
+
+
+
+
+	var preservedScriptAttributes = {
+		type: true,
+		src: true,
+		nonce: true,
+		noModule: true
+	};
+
+	function DOMEval( code, node, doc ) {
+		doc = doc || document;
+
+		var i, val,
+			script = doc.createElement( "script" );
+
+		script.text = code;
+		if ( node ) {
+			for ( i in preservedScriptAttributes ) {
+
+				// Support: Firefox 64+, Edge 18+
+				// Some browsers don't support the "nonce" property on scripts.
+				// On the other hand, just using `getAttribute` is not enough as
+				// the `nonce` attribute is reset to an empty string whenever it
+				// becomes browsing-context connected.
+				// See https://github.com/whatwg/html/issues/2369
+				// See https://html.spec.whatwg.org/#nonce-attributes
+				// The `node.getAttribute` check was added for the sake of
+				// `jQuery.globalEval` so that it can fake a nonce-containing node
+				// via an object.
+				val = node[ i ] || node.getAttribute && node.getAttribute( i );
+				if ( val ) {
+					script.setAttribute( i, val );
+				}
+			}
+		}
+		doc.head.appendChild( script ).parentNode.removeChild( script );
+	}
+
+
+function toType( obj ) {
+	if ( obj == null ) {
+		return obj + "";
+	}
+
+	// Support: Android <=2.3 only (functionish RegExp)
+	return typeof obj === "object" || typeof obj === "function" ?
+		class2type[ toString.call( obj ) ] || "object" :
+		typeof obj;
+}
+/* global Symbol */
+// Defining this global in .eslintrc.json would create a danger of using the global
+// unguarded in another place, it seems safer to define global only for this module
+
+
+
+var
+	version = "3.4.1",
+
+	// Define a local copy of jQuery
+	jQuery = function( selector, context ) {
+
+		// The jQuery object is actually just the init constructor 'enhanced'
+		// Need init if jQuery is called (just allow error to be thrown if not included)
+		return new jQuery.fn.init( selector, context );
+	},
+
+	// Support: Android <=4.0 only
+	// Make sure we trim BOM and NBSP
+	rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g;
+
+jQuery.fn = jQuery.prototype = {
+
+	// The current version of jQuery being used
+	jquery: version,
+
+	constructor: jQuery,
+
+	// The default length of a jQuery object is 0
+	length: 0,
+
+	toArray: function() {
+		return slice.call( this );
+	},
+
+	// Get the Nth element in the matched element set OR
+	// Get the whole matched element set as a clean array
+	get: function( num ) {
+
+		// Return all the elements in a clean array
+		if ( num == null ) {
+			return slice.call( this );
+		}
+
+		// Return just the one element from the set
+		return num < 0 ? this[ num + this.length ] : this[ num ];
+	},
+
+	// Take an array of elements and push it onto the stack
+	// (returning the new matched element set)
+	pushStack: function( elems ) {
+
+		// Build a new jQuery matched element set
+		var ret = jQuery.merge( this.constructor(), elems );
+
+		// Add the old object onto the stack (as a reference)
+		ret.prevObject = this;
+
+		// Return the newly-formed element set
+		return ret;
+	},
+
+	// Execute a callback for every element in the matched set.
+	each: function( callback ) {
+		return jQuery.each( this, callback );
+	},
+
+	map: function( callback ) {
+		return this.pushStack( jQuery.map( this, function( elem, i ) {
+			return callback.call( elem, i, elem );
+		} ) );
+	},
+
+	slice: function() {
+		return this.pushStack( slice.apply( this, arguments ) );
+	},
+
+	first: function() {
+		return this.eq( 0 );
+	},
+
+	last: function() {
+		return this.eq( -1 );
+	},
+
+	eq: function( i ) {
+		var len = this.length,
+			j = +i + ( i < 0 ? len : 0 );
+		return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] );
+	},
+
+	end: function() {
+		return this.prevObject || this.constructor();
+	},
+
+	// For internal use only.
+	// Behaves like an Array's method, not like a jQuery method.
+	push: push,
+	sort: arr.sort,
+	splice: arr.splice
+};
+
+jQuery.extend = jQuery.fn.extend = function() {
+	var options, name, src, copy, copyIsArray, clone,
+		target = arguments[ 0 ] || {},
+		i = 1,
+		length = arguments.length,
+		deep = false;
+
+	// Handle a deep copy situation
+	if ( typeof target === "boolean" ) {
+		deep = target;
+
+		// Skip the boolean and the target
+		target = arguments[ i ] || {};
+		i++;
+	}
+
+	// Handle case when target is a string or something (possible in deep copy)
+	if ( typeof target !== "object" && !isFunction( target ) ) {
+		target = {};
+	}
+
+	// Extend jQuery itself if only one argument is passed
+	if ( i === length ) {
+		target = this;
+		i--;
+	}
+
+	for ( ; i < length; i++ ) {
+
+		// Only deal with non-null/undefined values
+		if ( ( options = arguments[ i ] ) != null ) {
+
+			// Extend the base object
+			for ( name in options ) {
+				copy = options[ name ];
+
+				// Prevent Object.prototype pollution
+				// Prevent never-ending loop
+				if ( name === "__proto__" || target === copy ) {
+					continue;
+				}
+
+				// Recurse if we're merging plain objects or arrays
+				if ( deep && copy && ( jQuery.isPlainObject( copy ) ||
+					( copyIsArray = Array.isArray( copy ) ) ) ) {
+					src = target[ name ];
+
+					// Ensure proper type for the source value
+					if ( copyIsArray && !Array.isArray( src ) ) {
+						clone = [];
+					} else if ( !copyIsArray && !jQuery.isPlainObject( src ) ) {
+						clone = {};
+					} else {
+						clone = src;
+					}
+					copyIsArray = false;
+
+					// Never move original objects, clone them
+					target[ name ] = jQuery.extend( deep, clone, copy );
+
+				// Don't bring in undefined values
+				} else if ( copy !== undefined ) {
+					target[ name ] = copy;
+				}
+			}
+		}
+	}
+
+	// Return the modified object
+	return target;
+};
+
+jQuery.extend( {
+
+	// Unique for each copy of jQuery on the page
+	expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ),
+
+	// Assume jQuery is ready without the ready module
+	isReady: true,
+
+	error: function( msg ) {
+		throw new Error( msg );
+	},
+
+	noop: function() {},
+
+	isPlainObject: function( obj ) {
+		var proto, Ctor;
+
+		// Detect obvious negatives
+		// Use toString instead of jQuery.type to catch host objects
+		if ( !obj || toString.call( obj ) !== "[object Object]" ) {
+			return false;
+		}
+
+		proto = getProto( obj );
+
+		// Objects with no prototype (e.g., `Object.create( null )`) are plain
+		if ( !proto ) {
+			return true;
+		}
+
+		// Objects with prototype are plain iff they were constructed by a global Object function
+		Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor;
+		return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString;
+	},
+
+	isEmptyObject: function( obj ) {
+		var name;
+
+		for ( name in obj ) {
+			return false;
+		}
+		return true;
+	},
+
+	// Evaluates a script in a global context
+	globalEval: function( code, options ) {
+		DOMEval( code, { nonce: options && options.nonce } );
+	},
+
+	each: function( obj, callback ) {
+		var length, i = 0;
+
+		if ( isArrayLike( obj ) ) {
+			length = obj.length;
+			for ( ; i < length; i++ ) {
+				if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
+					break;
+				}
+			}
+		} else {
+			for ( i in obj ) {
+				if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
+					break;
+				}
+			}
+		}
+
+		return obj;
+	},
+
+	// Support: Android <=4.0 only
+	trim: function( text ) {
+		return text == null ?
+			"" :
+			( text + "" ).replace( rtrim, "" );
+	},
+
+	// results is for internal usage only
+	makeArray: function( arr, results ) {
+		var ret = results || [];
+
+		if ( arr != null ) {
+			if ( isArrayLike( Object( arr ) ) ) {
+				jQuery.merge( ret,
+					typeof arr === "string" ?
+					[ arr ] : arr
+				);
+			} else {
+				push.call( ret, arr );
+			}
+		}
+
+		return ret;
+	},
+
+	inArray: function( elem, arr, i ) {
+		return arr == null ? -1 : indexOf.call( arr, elem, i );
+	},
+
+	// Support: Android <=4.0 only, PhantomJS 1 only
+	// push.apply(_, arraylike) throws on ancient WebKit
+	merge: function( first, second ) {
+		var len = +second.length,
+			j = 0,
+			i = first.length;
+
+		for ( ; j < len; j++ ) {
+			first[ i++ ] = second[ j ];
+		}
+
+		first.length = i;
+
+		return first;
+	},
+
+	grep: function( elems, callback, invert ) {
+		var callbackInverse,
+			matches = [],
+			i = 0,
+			length = elems.length,
+			callbackExpect = !invert;
+
+		// Go through the array, only saving the items
+		// that pass the validator function
+		for ( ; i < length; i++ ) {
+			callbackInverse = !callback( elems[ i ], i );
+			if ( callbackInverse !== callbackExpect ) {
+				matches.push( elems[ i ] );
+			}
+		}
+
+		return matches;
+	},
+
+	// arg is for internal usage only
+	map: function( elems, callback, arg ) {
+		var length, value,
+			i = 0,
+			ret = [];
+
+		// Go through the array, translating each of the items to their new values
+		if ( isArrayLike( elems ) ) {
+			length = elems.length;
+			for ( ; i < length; i++ ) {
+				value = callback( elems[ i ], i, arg );
+
+				if ( value != null ) {
+					ret.push( value );
+				}
+			}
+
+		// Go through every key on the object,
+		} else {
+			for ( i in elems ) {
+				value = callback( elems[ i ], i, arg );
+
+				if ( value != null ) {
+					ret.push( value );
+				}
+			}
+		}
+
+		// Flatten any nested arrays
+		return concat.apply( [], ret );
+	},
+
+	// A global GUID counter for objects
+	guid: 1,
+
+	// jQuery.support is not used in Core but other projects attach their
+	// properties to it so it needs to exist.
+	support: support
+} );
+
+if ( typeof Symbol === "function" ) {
+	jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ];
+}
+
+// Populate the class2type map
+jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ),
+function( i, name ) {
+	class2type[ "[object " + name + "]" ] = name.toLowerCase();
+} );
+
+function isArrayLike( obj ) {
+
+	// Support: real iOS 8.2 only (not reproducible in simulator)
+	// `in` check used to prevent JIT error (gh-2145)
+	// hasOwn isn't used here due to false negatives
+	// regarding Nodelist length in IE
+	var length = !!obj && "length" in obj && obj.length,
+		type = toType( obj );
+
+	if ( isFunction( obj ) || isWindow( obj ) ) {
+		return false;
+	}
+
+	return type === "array" || length === 0 ||
+		typeof length === "number" && length > 0 && ( length - 1 ) in obj;
+}
+var Sizzle =
+/*!
+ * Sizzle CSS Selector Engine v2.3.4
+ * https://sizzlejs.com/
+ *
+ * Copyright JS Foundation and other contributors
+ * Released under the MIT license
+ * https://js.foundation/
+ *
+ * Date: 2019-04-08
+ */
+(function( window ) {
+
+var i,
+	support,
+	Expr,
+	getText,
+	isXML,
+	tokenize,
+	compile,
+	select,
+	outermostContext,
+	sortInput,
+	hasDuplicate,
+
+	// Local document vars
+	setDocument,
+	document,
+	docElem,
+	documentIsHTML,
+	rbuggyQSA,
+	rbuggyMatches,
+	matches,
+	contains,
+
+	// Instance-specific data
+	expando = "sizzle" + 1 * new Date(),
+	preferredDoc = window.document,
+	dirruns = 0,
+	done = 0,
+	classCache = createCache(),
+	tokenCache = createCache(),
+	compilerCache = createCache(),
+	nonnativeSelectorCache = createCache(),
+	sortOrder = function( a, b ) {
+		if ( a === b ) {
+			hasDuplicate = true;
+		}
+		return 0;
+	},
+
+	// Instance methods
+	hasOwn = ({}).hasOwnProperty,
+	arr = [],
+	pop = arr.pop,
+	push_native = arr.push,
+	push = arr.push,
+	slice = arr.slice,
+	// Use a stripped-down indexOf as it's faster than native
+	// https://jsperf.com/thor-indexof-vs-for/5
+	indexOf = function( list, elem ) {
+		var i = 0,
+			len = list.length;
+		for ( ; i < len; i++ ) {
+			if ( list[i] === elem ) {
+				return i;
+			}
+		}
+		return -1;
+	},
+
+	booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped",
+
+	// Regular expressions
+
+	// http://www.w3.org/TR/css3-selectors/#whitespace
+	whitespace = "[\\x20\\t\\r\\n\\f]",
+
+	// http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
+	identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+",
+
+	// Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors
+	attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace +
+		// Operator (capture 2)
+		"*([*^$|!~]?=)" + whitespace +
+		// "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]"
+		"*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace +
+		"*\\]",
+
+	pseudos = ":(" + identifier + ")(?:\\((" +
+		// To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:
+		// 1. quoted (capture 3; capture 4 or capture 5)
+		"('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" +
+		// 2. simple (capture 6)
+		"((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" +
+		// 3. anything else (capture 2)
+		".*" +
+		")\\)|)",
+
+	// Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
+	rwhitespace = new RegExp( whitespace + "+", "g" ),
+	rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
+
+	rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
+	rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ),
+	rdescend = new RegExp( whitespace + "|>" ),
+
+	rpseudo = new RegExp( pseudos ),
+	ridentifier = new RegExp( "^" + identifier + "$" ),
+
+	matchExpr = {
+		"ID": new RegExp( "^#(" + identifier + ")" ),
+		"CLASS": new RegExp( "^\\.(" + identifier + ")" ),
+		"TAG": new RegExp( "^(" + identifier + "|[*])" ),
+		"ATTR": new RegExp( "^" + attributes ),
+		"PSEUDO": new RegExp( "^" + pseudos ),
+		"CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace +
+			"*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace +
+			"*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
+		"bool": new RegExp( "^(?:" + booleans + ")$", "i" ),
+		// For use in libraries implementing .is()
+		// We use this for POS matching in `select`
+		"needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" +
+			whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" )
+	},
+
+	rhtml = /HTML$/i,
+	rinputs = /^(?:input|select|textarea|button)$/i,
+	rheader = /^h\d$/i,
+
+	rnative = /^[^{]+\{\s*\[native \w/,
+
+	// Easily-parseable/retrievable ID or TAG or CLASS selectors
+	rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
+
+	rsibling = /[+~]/,
+
+	// CSS escapes
+	// http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
+	runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ),
+	funescape = function( _, escaped, escapedWhitespace ) {
+		var high = "0x" + escaped - 0x10000;
+		// NaN means non-codepoint
+		// Support: Firefox<24
+		// Workaround erroneous numeric interpretation of +"0x"
+		return high !== high || escapedWhitespace ?
+			escaped :
+			high < 0 ?
+				// BMP codepoint
+				String.fromCharCode( high + 0x10000 ) :
+				// Supplemental Plane codepoint (surrogate pair)
+				String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
+	},
+
+	// CSS string/identifier serialization
+	// https://drafts.csswg.org/cssom/#common-serializing-idioms
+	rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g,
+	fcssescape = function( ch, asCodePoint ) {
+		if ( asCodePoint ) {
+
+			// U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER
+			if ( ch === "\0" ) {
+				return "\uFFFD";
+			}
+
+			// Control characters and (dependent upon position) numbers get escaped as code points
+			return ch.slice( 0, -1 ) + "\\" + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " ";
+		}
+
+		// Other potentially-special ASCII characters get backslash-escaped
+		return "\\" + ch;
+	},
+
+	// Used for iframes
+	// See setDocument()
+	// Removing the function wrapper causes a "Permission Denied"
+	// error in IE
+	unloadHandler = function() {
+		setDocument();
+	},
+
+	inDisabledFieldset = addCombinator(
+		function( elem ) {
+			return elem.disabled === true && elem.nodeName.toLowerCase() === "fieldset";
+		},
+		{ dir: "parentNode", next: "legend" }
+	);
+
+// Optimize for push.apply( _, NodeList )
+try {
+	push.apply(
+		(arr = slice.call( preferredDoc.childNodes )),
+		preferredDoc.childNodes
+	);
+	// Support: Android<4.0
+	// Detect silently failing push.apply
+	arr[ preferredDoc.childNodes.length ].nodeType;
+} catch ( e ) {
+	push = { apply: arr.length ?
+
+		// Leverage slice if possible
+		function( target, els ) {
+			push_native.apply( target, slice.call(els) );
+		} :
+
+		// Support: IE<9
+		// Otherwise append directly
+		function( target, els ) {
+			var j = target.length,
+				i = 0;
+			// Can't trust NodeList.length
+			while ( (target[j++] = els[i++]) ) {}
+			target.length = j - 1;
+		}
+	};
+}
+
+function Sizzle( selector, context, results, seed ) {
+	var m, i, elem, nid, match, groups, newSelector,
+		newContext = context && context.ownerDocument,
+
+		// nodeType defaults to 9, since context defaults to document
+		nodeType = context ? context.nodeType : 9;
+
+	results = results || [];
+
+	// Return early from calls with invalid selector or context
+	if ( typeof selector !== "string" || !selector ||
+		nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) {
+
+		return results;
+	}
+
+	// Try to shortcut find operations (as opposed to filters) in HTML documents
+	if ( !seed ) {
+
+		if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
+			setDocument( context );
+		}
+		context = context || document;
+
+		if ( documentIsHTML ) {
+
+			// If the selector is sufficiently simple, try using a "get*By*" DOM method
+			// (excepting DocumentFragment context, where the methods don't exist)
+			if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) {
+
+				// ID selector
+				if ( (m = match[1]) ) {
+
+					// Document context
+					if ( nodeType === 9 ) {
+						if ( (elem = context.getElementById( m )) ) {
+
+							// Support: IE, Opera, Webkit
+							// TODO: identify versions
+							// getElementById can match elements by name instead of ID
+							if ( elem.id === m ) {
+								results.push( elem );
+								return results;
+							}
+						} else {
+							return results;
+						}
+
+					// Element context
+					} else {
+
+						// Support: IE, Opera, Webkit
+						// TODO: identify versions
+						// getElementById can match elements by name instead of ID
+						if ( newContext && (elem = newContext.getElementById( m )) &&
+							contains( context, elem ) &&
+							elem.id === m ) {
+
+							results.push( elem );
+							return results;
+						}
+					}
+
+				// Type selector
+				} else if ( match[2] ) {
+					push.apply( results, context.getElementsByTagName( selector ) );
+					return results;
+
+				// Class selector
+				} else if ( (m = match[3]) && support.getElementsByClassName &&
+					context.getElementsByClassName ) {
+
+					push.apply( results, context.getElementsByClassName( m ) );
+					return results;
+				}
+			}
+
+			// Take advantage of querySelectorAll
+			if ( support.qsa &&
+				!nonnativeSelectorCache[ selector + " " ] &&
+				(!rbuggyQSA || !rbuggyQSA.test( selector )) &&
+
+				// Support: IE 8 only
+				// Exclude object elements
+				(nodeType !== 1 || context.nodeName.toLowerCase() !== "object") ) {
+
+				newSelector = selector;
+				newContext = context;
+
+				// qSA considers elements outside a scoping root when evaluating child or
+				// descendant combinators, which is not what we want.
+				// In such cases, we work around the behavior by prefixing every selector in the
+				// list with an ID selector referencing the scope context.
+				// Thanks to Andrew Dupont for this technique.
+				if ( nodeType === 1 && rdescend.test( selector ) ) {
+
+					// Capture the context ID, setting it first if necessary
+					if ( (nid = context.getAttribute( "id" )) ) {
+						nid = nid.replace( rcssescape, fcssescape );
+					} else {
+						context.setAttribute( "id", (nid = expando) );
+					}
+
+					// Prefix every selector in the list
+					groups = tokenize( selector );
+					i = groups.length;
+					while ( i-- ) {
+						groups[i] = "#" + nid + " " + toSelector( groups[i] );
+					}
+					newSelector = groups.join( "," );
+
+					// Expand context for sibling selectors
+					newContext = rsibling.test( selector ) && testContext( context.parentNode ) ||
+						context;
+				}
+
+				try {
+					push.apply( results,
+						newContext.querySelectorAll( newSelector )
+					);
+					return results;
+				} catch ( qsaError ) {
+					nonnativeSelectorCache( selector, true );
+				} finally {
+					if ( nid === expando ) {
+						context.removeAttribute( "id" );
+					}
+				}
+			}
+		}
+	}
+
+	// All others
+	return select( selector.replace( rtrim, "$1" ), context, results, seed );
+}
+
+/**
+ * Create key-value caches of limited size
+ * @returns {function(string, object)} Returns the Object data after storing it on itself with
+ *	property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
+ *	deleting the oldest entry
+ */
+function createCache() {
+	var keys = [];
+
+	function cache( key, value ) {
+		// Use (key + " ") to avoid collision with native prototype properties (see Issue #157)
+		if ( keys.push( key + " " ) > Expr.cacheLength ) {
+			// Only keep the most recent entries
+			delete cache[ keys.shift() ];
+		}
+		return (cache[ key + " " ] = value);
+	}
+	return cache;
+}
+
+/**
+ * Mark a function for special use by Sizzle
+ * @param {Function} fn The function to mark
+ */
+function markFunction( fn ) {
+	fn[ expando ] = true;
+	return fn;
+}
+
+/**
+ * Support testing using an element
+ * @param {Function} fn Passed the created element and returns a boolean result
+ */
+function assert( fn ) {
+	var el = document.createElement("fieldset");
+
+	try {
+		return !!fn( el );
+	} catch (e) {
+		return false;
+	} finally {
+		// Remove from its parent by default
+		if ( el.parentNode ) {
+			el.parentNode.removeChild( el );
+		}
+		// release memory in IE
+		el = null;
+	}
+}
+
+/**
+ * Adds the same handler for all of the specified attrs
+ * @param {String} attrs Pipe-separated list of attributes
+ * @param {Function} handler The method that will be applied
+ */
+function addHandle( attrs, handler ) {
+	var arr = attrs.split("|"),
+		i = arr.length;
+
+	while ( i-- ) {
+		Expr.attrHandle[ arr[i] ] = handler;
+	}
+}
+
+/**
+ * Checks document order of two siblings
+ * @param {Element} a
+ * @param {Element} b
+ * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b
+ */
+function siblingCheck( a, b ) {
+	var cur = b && a,
+		diff = cur && a.nodeType === 1 && b.nodeType === 1 &&
+			a.sourceIndex - b.sourceIndex;
+
+	// Use IE sourceIndex if available on both nodes
+	if ( diff ) {
+		return diff;
+	}
+
+	// Check if b follows a
+	if ( cur ) {
+		while ( (cur = cur.nextSibling) ) {
+			if ( cur === b ) {
+				return -1;
+			}
+		}
+	}
+
+	return a ? 1 : -1;
+}
+
+/**
+ * Returns a function to use in pseudos for input types
+ * @param {String} type
+ */
+function createInputPseudo( type ) {
+	return function( elem ) {
+		var name = elem.nodeName.toLowerCase();
+		return name === "input" && elem.type === type;
+	};
+}
+
+/**
+ * Returns a function to use in pseudos for buttons
+ * @param {String} type
+ */
+function createButtonPseudo( type ) {
+	return function( elem ) {
+		var name = elem.nodeName.toLowerCase();
+		return (name === "input" || name === "button") && elem.type === type;
+	};
+}
+
+/**
+ * Returns a function to use in pseudos for :enabled/:disabled
+ * @param {Boolean} disabled true for :disabled; false for :enabled
+ */
+function createDisabledPseudo( disabled ) {
+
+	// Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable
+	return function( elem ) {
+
+		// Only certain elements can match :enabled or :disabled
+		// https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled
+		// https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled
+		if ( "form" in elem ) {
+
+			// Check for inherited disabledness on relevant non-disabled elements:
+			// * listed form-associated elements in a disabled fieldset
+			//   https://html.spec.whatwg.org/multipage/forms.html#category-listed
+			//   https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled
+			// * option elements in a disabled optgroup
+			//   https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled
+			// All such elements have a "form" property.
+			if ( elem.parentNode && elem.disabled === false ) {
+
+				// Option elements defer to a parent optgroup if present
+				if ( "label" in elem ) {
+					if ( "label" in elem.parentNode ) {
+						return elem.parentNode.disabled === disabled;
+					} else {
+						return elem.disabled === disabled;
+					}
+				}
+
+				// Support: IE 6 - 11
+				// Use the isDisabled shortcut property to check for disabled fieldset ancestors
+				return elem.isDisabled === disabled ||
+
+					// Where there is no isDisabled, check manually
+					/* jshint -W018 */
+					elem.isDisabled !== !disabled &&
+						inDisabledFieldset( elem ) === disabled;
+			}
+
+			return elem.disabled === disabled;
+
+		// Try to winnow out elements that can't be disabled before trusting the disabled property.
+		// Some victims get caught in our net (label, legend, menu, track), but it shouldn't
+		// even exist on them, let alone have a boolean value.
+		} else if ( "label" in elem ) {
+			return elem.disabled === disabled;
+		}
+
+		// Remaining elements are neither :enabled nor :disabled
+		return false;
+	};
+}
+
+/**
+ * Returns a function to use in pseudos for positionals
+ * @param {Function} fn
+ */
+function createPositionalPseudo( fn ) {
+	return markFunction(function( argument ) {
+		argument = +argument;
+		return markFunction(function( seed, matches ) {
+			var j,
+				matchIndexes = fn( [], seed.length, argument ),
+				i = matchIndexes.length;
+
+			// Match elements found at the specified indexes
+			while ( i-- ) {
+				if ( seed[ (j = matchIndexes[i]) ] ) {
+					seed[j] = !(matches[j] = seed[j]);
+				}
+			}
+		});
+	});
+}
+
+/**
+ * Checks a node for validity as a Sizzle context
+ * @param {Element|Object=} context
+ * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value
+ */
+function testContext( context ) {
+	return context && typeof context.getElementsByTagName !== "undefined" && context;
+}
+
+// Expose support vars for convenience
+support = Sizzle.support = {};
+
+/**
+ * Detects XML nodes
+ * @param {Element|Object} elem An element or a document
+ * @returns {Boolean} True iff elem is a non-HTML XML node
+ */
+isXML = Sizzle.isXML = function( elem ) {
+	var namespace = elem.namespaceURI,
+		docElem = (elem.ownerDocument || elem).documentElement;
+
+	// Support: IE <=8
+	// Assume HTML when documentElement doesn't yet exist, such as inside loading iframes
+	// https://bugs.jquery.com/ticket/4833
+	return !rhtml.test( namespace || docElem && docElem.nodeName || "HTML" );
+};
+
+/**
+ * Sets document-related variables once based on the current document
+ * @param {Element|Object} [doc] An element or document object to use to set the document
+ * @returns {Object} Returns the current document
+ */
+setDocument = Sizzle.setDocument = function( node ) {
+	var hasCompare, subWindow,
+		doc = node ? node.ownerDocument || node : preferredDoc;
+
+	// Return early if doc is invalid or already selected
+	if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {
+		return document;
+	}
+
+	// Update global variables
+	document = doc;
+	docElem = document.documentElement;
+	documentIsHTML = !isXML( document );
+
+	// Support: IE 9-11, Edge
+	// Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936)
+	if ( preferredDoc !== document &&
+		(subWindow = document.defaultView) && subWindow.top !== subWindow ) {
+
+		// Support: IE 11, Edge
+		if ( subWindow.addEventListener ) {
+			subWindow.addEventListener( "unload", unloadHandler, false );
+
+		// Support: IE 9 - 10 only
+		} else if ( subWindow.attachEvent ) {
+			subWindow.attachEvent( "onunload", unloadHandler );
+		}
+	}
+
+	/* Attributes
+	---------------------------------------------------------------------- */
+
+	// Support: IE<8
+	// Verify that getAttribute really returns attributes and not properties
+	// (excepting IE8 booleans)
+	support.attributes = assert(function( el ) {
+		el.className = "i";
+		return !el.getAttribute("className");
+	});
+
+	/* getElement(s)By*
+	---------------------------------------------------------------------- */
+
+	// Check if getElementsByTagName("*") returns only elements
+	support.getElementsByTagName = assert(function( el ) {
+		el.appendChild( document.createComment("") );
+		return !el.getElementsByTagName("*").length;
+	});
+
+	// Support: IE<9
+	support.getElementsByClassName = rnative.test( document.getElementsByClassName );
+
+	// Support: IE<10
+	// Check if getElementById returns elements by name
+	// The broken getElementById methods don't pick up programmatically-set names,
+	// so use a roundabout getElementsByName test
+	support.getById = assert(function( el ) {
+		docElem.appendChild( el ).id = expando;
+		return !document.getElementsByName || !document.getElementsByName( expando ).length;
+	});
+
+	// ID filter and find
+	if ( support.getById ) {
+		Expr.filter["ID"] = function( id ) {
+			var attrId = id.replace( runescape, funescape );
+			return function( elem ) {
+				return elem.getAttribute("id") === attrId;
+			};
+		};
+		Expr.find["ID"] = function( id, context ) {
+			if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
+				var elem = context.getElementById( id );
+				return elem ? [ elem ] : [];
+			}
+		};
+	} else {
+		Expr.filter["ID"] =  function( id ) {
+			var attrId = id.replace( runescape, funescape );
+			return function( elem ) {
+				var node = typeof elem.getAttributeNode !== "undefined" &&
+					elem.getAttributeNode("id");
+				return node && node.value === attrId;
+			};
+		};
+
+		// Support: IE 6 - 7 only
+		// getElementById is not reliable as a find shortcut
+		Expr.find["ID"] = function( id, context ) {
+			if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
+				var node, i, elems,
+					elem = context.getElementById( id );
+
+				if ( elem ) {
+
+					// Verify the id attribute
+					node = elem.getAttributeNode("id");
+					if ( node && node.value === id ) {
+						return [ elem ];
+					}
+
+					// Fall back on getElementsByName
+					elems = context.getElementsByName( id );
+					i = 0;
+					while ( (elem = elems[i++]) ) {
+						node = elem.getAttributeNode("id");
+						if ( node && node.value === id ) {
+							return [ elem ];
+						}
+					}
+				}
+
+				return [];
+			}
+		};
+	}
+
+	// Tag
+	Expr.find["TAG"] = support.getElementsByTagName ?
+		function( tag, context ) {
+			if ( typeof context.getElementsByTagName !== "undefined" ) {
+				return context.getElementsByTagName( tag );
+
+			// DocumentFragment nodes don't have gEBTN
+			} else if ( support.qsa ) {
+				return context.querySelectorAll( tag );
+			}
+		} :
+
+		function( tag, context ) {
+			var elem,
+				tmp = [],
+				i = 0,
+				// By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too
+				results = context.getElementsByTagName( tag );
+
+			// Filter out possible comments
+			if ( tag === "*" ) {
+				while ( (elem = results[i++]) ) {
+					if ( elem.nodeType === 1 ) {
+						tmp.push( elem );
+					}
+				}
+
+				return tmp;
+			}
+			return results;
+		};
+
+	// Class
+	Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) {
+		if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) {
+			return context.getElementsByClassName( className );
+		}
+	};
+
+	/* QSA/matchesSelector
+	---------------------------------------------------------------------- */
+
+	// QSA and matchesSelector support
+
+	// matchesSelector(:active) reports false when true (IE9/Opera 11.5)
+	rbuggyMatches = [];
+
+	// qSa(:focus) reports false when true (Chrome 21)
+	// We allow this because of a bug in IE8/9 that throws an error
+	// whenever `document.activeElement` is accessed on an iframe
+	// So, we allow :focus to pass through QSA all the time to avoid the IE error
+	// See https://bugs.jquery.com/ticket/13378
+	rbuggyQSA = [];
+
+	if ( (support.qsa = rnative.test( document.querySelectorAll )) ) {
+		// Build QSA regex
+		// Regex strategy adopted from Diego Perini
+		assert(function( el ) {
+			// Select is set to empty string on purpose
+			// This is to test IE's treatment of not explicitly
+			// setting a boolean content attribute,
+			// since its presence should be enough
+			// https://bugs.jquery.com/ticket/12359
+			docElem.appendChild( el ).innerHTML = "<a id='" + expando + "'></a>" +
+				"<select id='" + expando + "-\r\\' msallowcapture=''>" +
+				"<option selected=''></option></select>";
+
+			// Support: IE8, Opera 11-12.16
+			// Nothing should be selected when empty strings follow ^= or $= or *=
+			// The test attribute must be unknown in Opera but "safe" for WinRT
+			// https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
+			if ( el.querySelectorAll("[msallowcapture^='']").length ) {
+				rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
+			}
+
+			// Support: IE8
+			// Boolean attributes and "value" are not treated correctly
+			if ( !el.querySelectorAll("[selected]").length ) {
+				rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" );
+			}
+
+			// Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+
+			if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) {
+				rbuggyQSA.push("~=");
+			}
+
+			// Webkit/Opera - :checked should return selected option elements
+			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+			// IE8 throws error here and will not see later tests
+			if ( !el.querySelectorAll(":checked").length ) {
+				rbuggyQSA.push(":checked");
+			}
+
+			// Support: Safari 8+, iOS 8+
+			// https://bugs.webkit.org/show_bug.cgi?id=136851
+			// In-page `selector#id sibling-combinator selector` fails
+			if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) {
+				rbuggyQSA.push(".#.+[+~]");
+			}
+		});
+
+		assert(function( el ) {
+			el.innerHTML = "<a href='' disabled='disabled'></a>" +
+				"<select disabled='disabled'><option/></select>";
+
+			// Support: Windows 8 Native Apps
+			// The type and name attributes are restricted during .innerHTML assignment
+			var input = document.createElement("input");
+			input.setAttribute( "type", "hidden" );
+			el.appendChild( input ).setAttribute( "name", "D" );
+
+			// Support: IE8
+			// Enforce case-sensitivity of name attribute
+			if ( el.querySelectorAll("[name=d]").length ) {
+				rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" );
+			}
+
+			// FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
+			// IE8 throws error here and will not see later tests
+			if ( el.querySelectorAll(":enabled").length !== 2 ) {
+				rbuggyQSA.push( ":enabled", ":disabled" );
+			}
+
+			// Support: IE9-11+
+			// IE's :disabled selector does not pick up the children of disabled fieldsets
+			docElem.appendChild( el ).disabled = true;
+			if ( el.querySelectorAll(":disabled").length !== 2 ) {
+				rbuggyQSA.push( ":enabled", ":disabled" );
+			}
+
+			// Opera 10-11 does not throw on post-comma invalid pseudos
+			el.querySelectorAll("*,:x");
+			rbuggyQSA.push(",.*:");
+		});
+	}
+
+	if ( (support.matchesSelector = rnative.test( (matches = docElem.matches ||
+		docElem.webkitMatchesSelector ||
+		docElem.mozMatchesSelector ||
+		docElem.oMatchesSelector ||
+		docElem.msMatchesSelector) )) ) {
+
+		assert(function( el ) {
+			// Check to see if it's possible to do matchesSelector
+			// on a disconnected node (IE 9)
+			support.disconnectedMatch = matches.call( el, "*" );
+
+			// This should fail with an exception
+			// Gecko does not error, returns false instead
+			matches.call( el, "[s!='']:x" );
+			rbuggyMatches.push( "!=", pseudos );
+		});
+	}
+
+	rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join("|") );
+	rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join("|") );
+
+	/* Contains
+	---------------------------------------------------------------------- */
+	hasCompare = rnative.test( docElem.compareDocumentPosition );
+
+	// Element contains another
+	// Purposefully self-exclusive
+	// As in, an element does not contain itself
+	contains = hasCompare || rnative.test( docElem.contains ) ?
+		function( a, b ) {
+			var adown = a.nodeType === 9 ? a.documentElement : a,
+				bup = b && b.parentNode;
+			return a === bup || !!( bup && bup.nodeType === 1 && (
+				adown.contains ?
+					adown.contains( bup ) :
+					a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16
+			));
+		} :
+		function( a, b ) {
+			if ( b ) {
+				while ( (b = b.parentNode) ) {
+					if ( b === a ) {
+						return true;
+					}
+				}
+			}
+			return false;
+		};
+
+	/* Sorting
+	---------------------------------------------------------------------- */
+
+	// Document order sorting
+	sortOrder = hasCompare ?
+	function( a, b ) {
+
+		// Flag for duplicate removal
+		if ( a === b ) {
+			hasDuplicate = true;
+			return 0;
+		}
+
+		// Sort on method existence if only one input has compareDocumentPosition
+		var compare = !a.compareDocumentPosition - !b.compareDocumentPosition;
+		if ( compare ) {
+			return compare;
+		}
+
+		// Calculate position if both inputs belong to the same document
+		compare = ( a.ownerDocument || a ) === ( b.ownerDocument || b ) ?
+			a.compareDocumentPosition( b ) :
+
+			// Otherwise we know they are disconnected
+			1;
+
+		// Disconnected nodes
+		if ( compare & 1 ||
+			(!support.sortDetached && b.compareDocumentPosition( a ) === compare) ) {
+
+			// Choose the first element that is related to our preferred document
+			if ( a === document || a.ownerDocument === preferredDoc && contains(preferredDoc, a) ) {
+				return -1;
+			}
+			if ( b === document || b.ownerDocument === preferredDoc && contains(preferredDoc, b) ) {
+				return 1;
+			}
+
+			// Maintain original order
+			return sortInput ?
+				( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
+				0;
+		}
+
+		return compare & 4 ? -1 : 1;
+	} :
+	function( a, b ) {
+		// Exit early if the nodes are identical
+		if ( a === b ) {
+			hasDuplicate = true;
+			return 0;
+		}
+
+		var cur,
+			i = 0,
+			aup = a.parentNode,
+			bup = b.parentNode,
+			ap = [ a ],
+			bp = [ b ];
+
+		// Parentless nodes are either documents or disconnected
+		if ( !aup || !bup ) {
+			return a === document ? -1 :
+				b === document ? 1 :
+				aup ? -1 :
+				bup ? 1 :
+				sortInput ?
+				( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
+				0;
+
+		// If the nodes are siblings, we can do a quick check
+		} else if ( aup === bup ) {
+			return siblingCheck( a, b );
+		}
+
+		// Otherwise we need full lists of their ancestors for comparison
+		cur = a;
+		while ( (cur = cur.parentNode) ) {
+			ap.unshift( cur );
+		}
+		cur = b;
+		while ( (cur = cur.parentNode) ) {
+			bp.unshift( cur );
+		}
+
+		// Walk down the tree looking for a discrepancy
+		while ( ap[i] === bp[i] ) {
+			i++;
+		}
+
+		return i ?
+			// Do a sibling check if the nodes have a common ancestor
+			siblingCheck( ap[i], bp[i] ) :
+
+			// Otherwise nodes in our document sort first
+			ap[i] === preferredDoc ? -1 :
+			bp[i] === preferredDoc ? 1 :
+			0;
+	};
+
+	return document;
+};
+
+Sizzle.matches = function( expr, elements ) {
+	return Sizzle( expr, null, null, elements );
+};
+
+Sizzle.matchesSelector = function( elem, expr ) {
+	// Set document vars if needed
+	if ( ( elem.ownerDocument || elem ) !== document ) {
+		setDocument( elem );
+	}
+
+	if ( support.matchesSelector && documentIsHTML &&
+		!nonnativeSelectorCache[ expr + " " ] &&
+		( !rbuggyMatches || !rbuggyMatches.test( expr ) ) &&
+		( !rbuggyQSA     || !rbuggyQSA.test( expr ) ) ) {
+
+		try {
+			var ret = matches.call( elem, expr );
+
+			// IE 9's matchesSelector returns false on disconnected nodes
+			if ( ret || support.disconnectedMatch ||
+					// As well, disconnected nodes are said to be in a document
+					// fragment in IE 9
+					elem.document && elem.document.nodeType !== 11 ) {
+				return ret;
+			}
+		} catch (e) {
+			nonnativeSelectorCache( expr, true );
+		}
+	}
+
+	return Sizzle( expr, document, null, [ elem ] ).length > 0;
+};
+
+Sizzle.contains = function( context, elem ) {
+	// Set document vars if needed
+	if ( ( context.ownerDocument || context ) !== document ) {
+		setDocument( context );
+	}
+	return contains( context, elem );
+};
+
+Sizzle.attr = function( elem, name ) {
+	// Set document vars if needed
+	if ( ( elem.ownerDocument || elem ) !== document ) {
+		setDocument( elem );
+	}
+
+	var fn = Expr.attrHandle[ name.toLowerCase() ],
+		// Don't get fooled by Object.prototype properties (jQuery #13807)
+		val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ?
+			fn( elem, name, !documentIsHTML ) :
+			undefined;
+
+	return val !== undefined ?
+		val :
+		support.attributes || !documentIsHTML ?
+			elem.getAttribute( name ) :
+			(val = elem.getAttributeNode(name)) && val.specified ?
+				val.value :
+				null;
+};
+
+Sizzle.escape = function( sel ) {
+	return (sel + "").replace( rcssescape, fcssescape );
+};
+
+Sizzle.error = function( msg ) {
+	throw new Error( "Syntax error, unrecognized expression: " + msg );
+};
+
+/**
+ * Document sorting and removing duplicates
+ * @param {ArrayLike} results
+ */
+Sizzle.uniqueSort = function( results ) {
+	var elem,
+		duplicates = [],
+		j = 0,
+		i = 0;
+
+	// Unless we *know* we can detect duplicates, assume their presence
+	hasDuplicate = !support.detectDuplicates;
+	sortInput = !support.sortStable && results.slice( 0 );
+	results.sort( sortOrder );
+
+	if ( hasDuplicate ) {
+		while ( (elem = results[i++]) ) {
+			if ( elem === results[ i ] ) {
+				j = duplicates.push( i );
+			}
+		}
+		while ( j-- ) {
+			results.splice( duplicates[ j ], 1 );
+		}
+	}
+
+	// Clear input after sorting to release objects
+	// See https://github.com/jquery/sizzle/pull/225
+	sortInput = null;
+
+	return results;
+};
+
+/**
+ * Utility function for retrieving the text value of an array of DOM nodes
+ * @param {Array|Element} elem
+ */
+getText = Sizzle.getText = function( elem ) {
+	var node,
+		ret = "",
+		i = 0,
+		nodeType = elem.nodeType;
+
+	if ( !nodeType ) {
+		// If no nodeType, this is expected to be an array
+		while ( (node = elem[i++]) ) {
+			// Do not traverse comment nodes
+			ret += getText( node );
+		}
+	} else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
+		// Use textContent for elements
+		// innerText usage removed for consistency of new lines (jQuery #11153)
+		if ( typeof elem.textContent === "string" ) {
+			return elem.textContent;
+		} else {
+			// Traverse its children
+			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+				ret += getText( elem );
+			}
+		}
+	} else if ( nodeType === 3 || nodeType === 4 ) {
+		return elem.nodeValue;
+	}
+	// Do not include comment or processing instruction nodes
+
+	return ret;
+};
+
+Expr = Sizzle.selectors = {
+
+	// Can be adjusted by the user
+	cacheLength: 50,
+
+	createPseudo: markFunction,
+
+	match: matchExpr,
+
+	attrHandle: {},
+
+	find: {},
+
+	relative: {
+		">": { dir: "parentNode", first: true },
+		" ": { dir: "parentNode" },
+		"+": { dir: "previousSibling", first: true },
+		"~": { dir: "previousSibling" }
+	},
+
+	preFilter: {
+		"ATTR": function( match ) {
+			match[1] = match[1].replace( runescape, funescape );
+
+			// Move the given value to match[3] whether quoted or unquoted
+			match[3] = ( match[3] || match[4] || match[5] || "" ).replace( runescape, funescape );
+
+			if ( match[2] === "~=" ) {
+				match[3] = " " + match[3] + " ";
+			}
+
+			return match.slice( 0, 4 );
+		},
+
+		"CHILD": function( match ) {
+			/* matches from matchExpr["CHILD"]
+				1 type (only|nth|...)
+				2 what (child|of-type)
+				3 argument (even|odd|\d*|\d*n([+-]\d+)?|...)
+				4 xn-component of xn+y argument ([+-]?\d*n|)
+				5 sign of xn-component
+				6 x of xn-component
+				7 sign of y-component
+				8 y of y-component
+			*/
+			match[1] = match[1].toLowerCase();
+
+			if ( match[1].slice( 0, 3 ) === "nth" ) {
+				// nth-* requires argument
+				if ( !match[3] ) {
+					Sizzle.error( match[0] );
+				}
+
+				// numeric x and y parameters for Expr.filter.CHILD
+				// remember that false/true cast respectively to 0/1
+				match[4] = +( match[4] ? match[5] + (match[6] || 1) : 2 * ( match[3] === "even" || match[3] === "odd" ) );
+				match[5] = +( ( match[7] + match[8] ) || match[3] === "odd" );
+
+			// other types prohibit arguments
+			} else if ( match[3] ) {
+				Sizzle.error( match[0] );
+			}
+
+			return match;
+		},
+
+		"PSEUDO": function( match ) {
+			var excess,
+				unquoted = !match[6] && match[2];
+
+			if ( matchExpr["CHILD"].test( match[0] ) ) {
+				return null;
+			}
+
+			// Accept quoted arguments as-is
+			if ( match[3] ) {
+				match[2] = match[4] || match[5] || "";
+
+			// Strip excess characters from unquoted arguments
+			} else if ( unquoted && rpseudo.test( unquoted ) &&
+				// Get excess from tokenize (recursively)
+				(excess = tokenize( unquoted, true )) &&
+				// advance to the next closing parenthesis
+				(excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length) ) {
+
+				// excess is a negative index
+				match[0] = match[0].slice( 0, excess );
+				match[2] = unquoted.slice( 0, excess );
+			}
+
+			// Return only captures needed by the pseudo filter method (type and argument)
+			return match.slice( 0, 3 );
+		}
+	},
+
+	filter: {
+
+		"TAG": function( nodeNameSelector ) {
+			var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase();
+			return nodeNameSelector === "*" ?
+				function() { return true; } :
+				function( elem ) {
+					return elem.nodeName && elem.nodeName.toLowerCase() === nodeName;
+				};
+		},
+
+		"CLASS": function( className ) {
+			var pattern = classCache[ className + " " ];
+
+			return pattern ||
+				(pattern = new RegExp( "(^|" + whitespace + ")" + className + "(" + whitespace + "|$)" )) &&
+				classCache( className, function( elem ) {
+					return pattern.test( typeof elem.className === "string" && elem.className || typeof elem.getAttribute !== "undefined" && elem.getAttribute("class") || "" );
+				});
+		},
+
+		"ATTR": function( name, operator, check ) {
+			return function( elem ) {
+				var result = Sizzle.attr( elem, name );
+
+				if ( result == null ) {
+					return operator === "!=";
+				}
+				if ( !operator ) {
+					return true;
+				}
+
+				result += "";
+
+				return operator === "=" ? result === check :
+					operator === "!=" ? result !== check :
+					operator === "^=" ? check && result.indexOf( check ) === 0 :
+					operator === "*=" ? check && result.indexOf( check ) > -1 :
+					operator === "$=" ? check && result.slice( -check.length ) === check :
+					operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 :
+					operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" :
+					false;
+			};
+		},
+
+		"CHILD": function( type, what, argument, first, last ) {
+			var simple = type.slice( 0, 3 ) !== "nth",
+				forward = type.slice( -4 ) !== "last",
+				ofType = what === "of-type";
+
+			return first === 1 && last === 0 ?
+
+				// Shortcut for :nth-*(n)
+				function( elem ) {
+					return !!elem.parentNode;
+				} :
+
+				function( elem, context, xml ) {
+					var cache, uniqueCache, outerCache, node, nodeIndex, start,
+						dir = simple !== forward ? "nextSibling" : "previousSibling",
+						parent = elem.parentNode,
+						name = ofType && elem.nodeName.toLowerCase(),
+						useCache = !xml && !ofType,
+						diff = false;
+
+					if ( parent ) {
+
+						// :(first|last|only)-(child|of-type)
+						if ( simple ) {
+							while ( dir ) {
+								node = elem;
+								while ( (node = node[ dir ]) ) {
+									if ( ofType ?
+										node.nodeName.toLowerCase() === name :
+										node.nodeType === 1 ) {
+
+										return false;
+									}
+								}
+								// Reverse direction for :only-* (if we haven't yet done so)
+								start = dir = type === "only" && !start && "nextSibling";
+							}
+							return true;
+						}
+
+						start = [ forward ? parent.firstChild : parent.lastChild ];
+
+						// non-xml :nth-child(...) stores cache data on `parent`
+						if ( forward && useCache ) {
+
+							// Seek `elem` from a previously-cached index
+
+							// ...in a gzip-friendly way
+							node = parent;
+							outerCache = node[ expando ] || (node[ expando ] = {});
+
+							// Support: IE <9 only
+							// Defend against cloned attroperties (jQuery gh-1709)
+							uniqueCache = outerCache[ node.uniqueID ] ||
+								(outerCache[ node.uniqueID ] = {});
+
+							cache = uniqueCache[ type ] || [];
+							nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];
+							diff = nodeIndex && cache[ 2 ];
+							node = nodeIndex && parent.childNodes[ nodeIndex ];
+
+							while ( (node = ++nodeIndex && node && node[ dir ] ||
+
+								// Fallback to seeking `elem` from the start
+								(diff = nodeIndex = 0) || start.pop()) ) {
+
+								// When found, cache indexes on `parent` and break
+								if ( node.nodeType === 1 && ++diff && node === elem ) {
+									uniqueCache[ type ] = [ dirruns, nodeIndex, diff ];
+									break;
+								}
+							}
+
+						} else {
+							// Use previously-cached element index if available
+							if ( useCache ) {
+								// ...in a gzip-friendly way
+								node = elem;
+								outerCache = node[ expando ] || (node[ expando ] = {});
+
+								// Support: IE <9 only
+								// Defend against cloned attroperties (jQuery gh-1709)
+								uniqueCache = outerCache[ node.uniqueID ] ||
+									(outerCache[ node.uniqueID ] = {});
+
+								cache = uniqueCache[ type ] || [];
+								nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];
+								diff = nodeIndex;
+							}
+
+							// xml :nth-child(...)
+							// or :nth-last-child(...) or :nth(-last)?-of-type(...)
+							if ( diff === false ) {
+								// Use the same loop as above to seek `elem` from the start
+								while ( (node = ++nodeIndex && node && node[ dir ] ||
+									(diff = nodeIndex = 0) || start.pop()) ) {
+
+									if ( ( ofType ?
+										node.nodeName.toLowerCase() === name :
+										node.nodeType === 1 ) &&
+										++diff ) {
+
+										// Cache the index of each encountered element
+										if ( useCache ) {
+											outerCache = node[ expando ] || (node[ expando ] = {});
+
+											// Support: IE <9 only
+											// Defend against cloned attroperties (jQuery gh-1709)
+											uniqueCache = outerCache[ node.uniqueID ] ||
+												(outerCache[ node.uniqueID ] = {});
+
+											uniqueCache[ type ] = [ dirruns, diff ];
+										}
+
+										if ( node === elem ) {
+											break;
+										}
+									}
+								}
+							}
+						}
+
+						// Incorporate the offset, then check against cycle size
+						diff -= last;
+						return diff === first || ( diff % first === 0 && diff / first >= 0 );
+					}
+				};
+		},
+
+		"PSEUDO": function( pseudo, argument ) {
+			// pseudo-class names are case-insensitive
+			// http://www.w3.org/TR/selectors/#pseudo-classes
+			// Prioritize by case sensitivity in case custom pseudos are added with uppercase letters
+			// Remember that setFilters inherits from pseudos
+			var args,
+				fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||
+					Sizzle.error( "unsupported pseudo: " + pseudo );
+
+			// The user may use createPseudo to indicate that
+			// arguments are needed to create the filter function
+			// just as Sizzle does
+			if ( fn[ expando ] ) {
+				return fn( argument );
+			}
+
+			// But maintain support for old signatures
+			if ( fn.length > 1 ) {
+				args = [ pseudo, pseudo, "", argument ];
+				return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?
+					markFunction(function( seed, matches ) {
+						var idx,
+							matched = fn( seed, argument ),
+							i = matched.length;
+						while ( i-- ) {
+							idx = indexOf( seed, matched[i] );
+							seed[ idx ] = !( matches[ idx ] = matched[i] );
+						}
+					}) :
+					function( elem ) {
+						return fn( elem, 0, args );
+					};
+			}
+
+			return fn;
+		}
+	},
+
+	pseudos: {
+		// Potentially complex pseudos
+		"not": markFunction(function( selector ) {
+			// Trim the selector passed to compile
+			// to avoid treating leading and trailing
+			// spaces as combinators
+			var input = [],
+				results = [],
+				matcher = compile( selector.replace( rtrim, "$1" ) );
+
+			return matcher[ expando ] ?
+				markFunction(function( seed, matches, context, xml ) {
+					var elem,
+						unmatched = matcher( seed, null, xml, [] ),
+						i = seed.length;
+
+					// Match elements unmatched by `matcher`
+					while ( i-- ) {
+						if ( (elem = unmatched[i]) ) {
+							seed[i] = !(matches[i] = elem);
+						}
+					}
+				}) :
+				function( elem, context, xml ) {
+					input[0] = elem;
+					matcher( input, null, xml, results );
+					// Don't keep the element (issue #299)
+					input[0] = null;
+					return !results.pop();
+				};
+		}),
+
+		"has": markFunction(function( selector ) {
+			return function( elem ) {
+				return Sizzle( selector, elem ).length > 0;
+			};
+		}),
+
+		"contains": markFunction(function( text ) {
+			text = text.replace( runescape, funescape );
+			return function( elem ) {
+				return ( elem.textContent || getText( elem ) ).indexOf( text ) > -1;
+			};
+		}),
+
+		// "Whether an element is represented by a :lang() selector
+		// is based solely on the element's language value
+		// being equal to the identifier C,
+		// or beginning with the identifier C immediately followed by "-".
+		// The matching of C against the element's language value is performed case-insensitively.
+		// The identifier C does not have to be a valid language name."
+		// http://www.w3.org/TR/selectors/#lang-pseudo
+		"lang": markFunction( function( lang ) {
+			// lang value must be a valid identifier
+			if ( !ridentifier.test(lang || "") ) {
+				Sizzle.error( "unsupported lang: " + lang );
+			}
+			lang = lang.replace( runescape, funescape ).toLowerCase();
+			return function( elem ) {
+				var elemLang;
+				do {
+					if ( (elemLang = documentIsHTML ?
+						elem.lang :
+						elem.getAttribute("xml:lang") || elem.getAttribute("lang")) ) {
+
+						elemLang = elemLang.toLowerCase();
+						return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0;
+					}
+				} while ( (elem = elem.parentNode) && elem.nodeType === 1 );
+				return false;
+			};
+		}),
+
+		// Miscellaneous
+		"target": function( elem ) {
+			var hash = window.location && window.location.hash;
+			return hash && hash.slice( 1 ) === elem.id;
+		},
+
+		"root": function( elem ) {
+			return elem === docElem;
+		},
+
+		"focus": function( elem ) {
+			return elem === document.activeElement && (!document.hasFocus || document.hasFocus()) && !!(elem.type || elem.href || ~elem.tabIndex);
+		},
+
+		// Boolean properties
+		"enabled": createDisabledPseudo( false ),
+		"disabled": createDisabledPseudo( true ),
+
+		"checked": function( elem ) {
+			// In CSS3, :checked should return both checked and selected elements
+			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
+			var nodeName = elem.nodeName.toLowerCase();
+			return (nodeName === "input" && !!elem.checked) || (nodeName === "option" && !!elem.selected);
+		},
+
+		"selected": function( elem ) {
+			// Accessing this property makes selected-by-default
+			// options in Safari work properly
+			if ( elem.parentNode ) {
+				elem.parentNode.selectedIndex;
+			}
+
+			return elem.selected === true;
+		},
+
+		// Contents
+		"empty": function( elem ) {
+			// http://www.w3.org/TR/selectors/#empty-pseudo
+			// :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5),
+			//   but not by others (comment: 8; processing instruction: 7; etc.)
+			// nodeType < 6 works because attributes (2) do not appear as children
+			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
+				if ( elem.nodeType < 6 ) {
+					return false;
+				}
+			}
+			return true;
+		},
+
+		"parent": function( elem ) {
+			return !Expr.pseudos["empty"]( elem );
+		},
+
+		// Element/input types
+		"header": function( elem ) {
+			return rheader.test( elem.nodeName );
+		},
+
+		"input": function( elem ) {
+			return rinputs.test( elem.nodeName );
+		},
+
+		"button": function( elem ) {
+			var name = elem.nodeName.toLowerCase();
+			return name === "input" && elem.type === "button" || name === "button";
+		},
+
+		"text": function( elem ) {
+			var attr;
+			return elem.nodeName.toLowerCase() === "input" &&
+				elem.type === "text" &&
+
+				// Support: IE<8
+				// New HTML5 attribute values (e.g., "search") appear with elem.type === "text"
+				( (attr = elem.getAttribute("type")) == null || attr.toLowerCase() === "text" );
+		},
+
+		// Position-in-collection
+		"first": createPositionalPseudo(function() {
+			return [ 0 ];
+		}),
+
+		"last": createPositionalPseudo(function( matchIndexes, length ) {
+			return [ length - 1 ];
+		}),
+
+		"eq": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			return [ argument < 0 ? argument + length : argument ];
+		}),
+
+		"even": createPositionalPseudo(function( matchIndexes, length ) {
+			var i = 0;
+			for ( ; i < length; i += 2 ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		}),
+
+		"odd": createPositionalPseudo(function( matchIndexes, length ) {
+			var i = 1;
+			for ( ; i < length; i += 2 ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		}),
+
+		"lt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			var i = argument < 0 ?
+				argument + length :
+				argument > length ?
+					length :
+					argument;
+			for ( ; --i >= 0; ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		}),
+
+		"gt": createPositionalPseudo(function( matchIndexes, length, argument ) {
+			var i = argument < 0 ? argument + length : argument;
+			for ( ; ++i < length; ) {
+				matchIndexes.push( i );
+			}
+			return matchIndexes;
+		})
+	}
+};
+
+Expr.pseudos["nth"] = Expr.pseudos["eq"];
+
+// Add button/input type pseudos
+for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) {
+	Expr.pseudos[ i ] = createInputPseudo( i );
+}
+for ( i in { submit: true, reset: true } ) {
+	Expr.pseudos[ i ] = createButtonPseudo( i );
+}
+
+// Easy API for creating new setFilters
+function setFilters() {}
+setFilters.prototype = Expr.filters = Expr.pseudos;
+Expr.setFilters = new setFilters();
+
+tokenize = Sizzle.tokenize = function( selector, parseOnly ) {
+	var matched, match, tokens, type,
+		soFar, groups, preFilters,
+		cached = tokenCache[ selector + " " ];
+
+	if ( cached ) {
+		return parseOnly ? 0 : cached.slice( 0 );
+	}
+
+	soFar = selector;
+	groups = [];
+	preFilters = Expr.preFilter;
+
+	while ( soFar ) {
+
+		// Comma and first run
+		if ( !matched || (match = rcomma.exec( soFar )) ) {
+			if ( match ) {
+				// Don't consume trailing commas as valid
+				soFar = soFar.slice( match[0].length ) || soFar;
+			}
+			groups.push( (tokens = []) );
+		}
+
+		matched = false;
+
+		// Combinators
+		if ( (match = rcombinators.exec( soFar )) ) {
+			matched = match.shift();
+			tokens.push({
+				value: matched,
+				// Cast descendant combinators to space
+				type: match[0].replace( rtrim, " " )
+			});
+			soFar = soFar.slice( matched.length );
+		}
+
+		// Filters
+		for ( type in Expr.filter ) {
+			if ( (match = matchExpr[ type ].exec( soFar )) && (!preFilters[ type ] ||
+				(match = preFilters[ type ]( match ))) ) {
+				matched = match.shift();
+				tokens.push({
+					value: matched,
+					type: type,
+					matches: match
+				});
+				soFar = soFar.slice( matched.length );
+			}
+		}
+
+		if ( !matched ) {
+			break;
+		}
+	}
+
+	// Return the length of the invalid excess
+	// if we're just parsing
+	// Otherwise, throw an error or return tokens
+	return parseOnly ?
+		soFar.length :
+		soFar ?
+			Sizzle.error( selector ) :
+			// Cache the tokens
+			tokenCache( selector, groups ).slice( 0 );
+};
+
+function toSelector( tokens ) {
+	var i = 0,
+		len = tokens.length,
+		selector = "";
+	for ( ; i < len; i++ ) {
+		selector += tokens[i].value;
+	}
+	return selector;
+}
+
+function addCombinator( matcher, combinator, base ) {
+	var dir = combinator.dir,
+		skip = combinator.next,
+		key = skip || dir,
+		checkNonElements = base && key === "parentNode",
+		doneName = done++;
+
+	return combinator.first ?
+		// Check against closest ancestor/preceding element
+		function( elem, context, xml ) {
+			while ( (elem = elem[ dir ]) ) {
+				if ( elem.nodeType === 1 || checkNonElements ) {
+					return matcher( elem, context, xml );
+				}
+			}
+			return false;
+		} :
+
+		// Check against all ancestor/preceding elements
+		function( elem, context, xml ) {
+			var oldCache, uniqueCache, outerCache,
+				newCache = [ dirruns, doneName ];
+
+			// We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching
+			if ( xml ) {
+				while ( (elem = elem[ dir ]) ) {
+					if ( elem.nodeType === 1 || checkNonElements ) {
+						if ( matcher( elem, context, xml ) ) {
+							return true;
+						}
+					}
+				}
+			} else {
+				while ( (elem = elem[ dir ]) ) {
+					if ( elem.nodeType === 1 || checkNonElements ) {
+						outerCache = elem[ expando ] || (elem[ expando ] = {});
+
+						// Support: IE <9 only
+						// Defend against cloned attroperties (jQuery gh-1709)
+						uniqueCache = outerCache[ elem.uniqueID ] || (outerCache[ elem.uniqueID ] = {});
+
+						if ( skip && skip === elem.nodeName.toLowerCase() ) {
+							elem = elem[ dir ] || elem;
+						} else if ( (oldCache = uniqueCache[ key ]) &&
+							oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) {
+
+							// Assign to newCache so results back-propagate to previous elements
+							return (newCache[ 2 ] = oldCache[ 2 ]);
+						} else {
+							// Reuse newcache so results back-propagate to previous elements
+							uniqueCache[ key ] = newCache;
+
+							// A match means we're done; a fail means we have to keep checking
+							if ( (newCache[ 2 ] = matcher( elem, context, xml )) ) {
+								return true;
+							}
+						}
+					}
+				}
+			}
+			return false;
+		};
+}
+
+function elementMatcher( matchers ) {
+	return matchers.length > 1 ?
+		function( elem, context, xml ) {
+			var i = matchers.length;
+			while ( i-- ) {
+				if ( !matchers[i]( elem, context, xml ) ) {
+					return false;
+				}
+			}
+			return true;
+		} :
+		matchers[0];
+}
+
+function multipleContexts( selector, contexts, results ) {
+	var i = 0,
+		len = contexts.length;
+	for ( ; i < len; i++ ) {
+		Sizzle( selector, contexts[i], results );
+	}
+	return results;
+}
+
+function condense( unmatched, map, filter, context, xml ) {
+	var elem,
+		newUnmatched = [],
+		i = 0,
+		len = unmatched.length,
+		mapped = map != null;
+
+	for ( ; i < len; i++ ) {
+		if ( (elem = unmatched[i]) ) {
+			if ( !filter || filter( elem, context, xml ) ) {
+				newUnmatched.push( elem );
+				if ( mapped ) {
+					map.push( i );
+				}
+			}
+		}
+	}
+
+	return newUnmatched;
+}
+
+function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
+	if ( postFilter && !postFilter[ expando ] ) {
+		postFilter = setMatcher( postFilter );
+	}
+	if ( postFinder && !postFinder[ expando ] ) {
+		postFinder = setMatcher( postFinder, postSelector );
+	}
+	return markFunction(function( seed, results, context, xml ) {
+		var temp, i, elem,
+			preMap = [],
+			postMap = [],
+			preexisting = results.length,
+
+			// Get initial elements from seed or context
+			elems = seed || multipleContexts( selector || "*", context.nodeType ? [ context ] : context, [] ),
+
+			// Prefilter to get matcher input, preserving a map for seed-results synchronization
+			matcherIn = preFilter && ( seed || !selector ) ?
+				condense( elems, preMap, preFilter, context, xml ) :
+				elems,
+
+			matcherOut = matcher ?
+				// If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,
+				postFinder || ( seed ? preFilter : preexisting || postFilter ) ?
+
+					// ...intermediate processing is necessary
+					[] :
+
+					// ...otherwise use results directly
+					results :
+				matcherIn;
+
+		// Find primary matches
+		if ( matcher ) {
+			matcher( matcherIn, matcherOut, context, xml );
+		}
+
+		// Apply postFilter
+		if ( postFilter ) {
+			temp = condense( matcherOut, postMap );
+			postFilter( temp, [], context, xml );
+
+			// Un-match failing elements by moving them back to matcherIn
+			i = temp.length;
+			while ( i-- ) {
+				if ( (elem = temp[i]) ) {
+					matcherOut[ postMap[i] ] = !(matcherIn[ postMap[i] ] = elem);
+				}
+			}
+		}
+
+		if ( seed ) {
+			if ( postFinder || preFilter ) {
+				if ( postFinder ) {
+					// Get the final matcherOut by condensing this intermediate into postFinder contexts
+					temp = [];
+					i = matcherOut.length;
+					while ( i-- ) {
+						if ( (elem = matcherOut[i]) ) {
+							// Restore matcherIn since elem is not yet a final match
+							temp.push( (matcherIn[i] = elem) );
+						}
+					}
+					postFinder( null, (matcherOut = []), temp, xml );
+				}
+
+				// Move matched elements from seed to results to keep them synchronized
+				i = matcherOut.length;
+				while ( i-- ) {
+					if ( (elem = matcherOut[i]) &&
+						(temp = postFinder ? indexOf( seed, elem ) : preMap[i]) > -1 ) {
+
+						seed[temp] = !(results[temp] = elem);
+					}
+				}
+			}
+
+		// Add elements to results, through postFinder if defined
+		} else {
+			matcherOut = condense(
+				matcherOut === results ?
+					matcherOut.splice( preexisting, matcherOut.length ) :
+					matcherOut
+			);
+			if ( postFinder ) {
+				postFinder( null, results, matcherOut, xml );
+			} else {
+				push.apply( results, matcherOut );
+			}
+		}
+	});
+}
+
+function matcherFromTokens( tokens ) {
+	var checkContext, matcher, j,
+		len = tokens.length,
+		leadingRelative = Expr.relative[ tokens[0].type ],
+		implicitRelative = leadingRelative || Expr.relative[" "],
+		i = leadingRelative ? 1 : 0,
+
+		// The foundational matcher ensures that elements are reachable from top-level context(s)
+		matchContext = addCombinator( function( elem ) {
+			return elem === checkContext;
+		}, implicitRelative, true ),
+		matchAnyContext = addCombinator( function( elem ) {
+			return indexOf( checkContext, elem ) > -1;
+		}, implicitRelative, true ),
+		matchers = [ function( elem, context, xml ) {
+			var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
+				(checkContext = context).nodeType ?
+					matchContext( elem, context, xml ) :
+					matchAnyContext( elem, context, xml ) );
+			// Avoid hanging onto element (issue #299)
+			checkContext = null;
+			return ret;
+		} ];
+
+	for ( ; i < len; i++ ) {
+		if ( (matcher = Expr.relative[ tokens[i].type ]) ) {
+			matchers = [ addCombinator(elementMatcher( matchers ), matcher) ];
+		} else {
+			matcher = Expr.filter[ tokens[i].type ].apply( null, tokens[i].matches );
+
+			// Return special upon seeing a positional matcher
+			if ( matcher[ expando ] ) {
+				// Find the next relative operator (if any) for proper handling
+				j = ++i;
+				for ( ; j < len; j++ ) {
+					if ( Expr.relative[ tokens[j].type ] ) {
+						break;
+					}
+				}
+				return setMatcher(
+					i > 1 && elementMatcher( matchers ),
+					i > 1 && toSelector(
+						// If the preceding token was a descendant combinator, insert an implicit any-element `*`
+						tokens.slice( 0, i - 1 ).concat({ value: tokens[ i - 2 ].type === " " ? "*" : "" })
+					).replace( rtrim, "$1" ),
+					matcher,
+					i < j && matcherFromTokens( tokens.slice( i, j ) ),
+					j < len && matcherFromTokens( (tokens = tokens.slice( j )) ),
+					j < len && toSelector( tokens )
+				);
+			}
+			matchers.push( matcher );
+		}
+	}
+
+	return elementMatcher( matchers );
+}
+
+function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
+	var bySet = setMatchers.length > 0,
+		byElement = elementMatchers.length > 0,
+		superMatcher = function( seed, context, xml, results, outermost ) {
+			var elem, j, matcher,
+				matchedCount = 0,
+				i = "0",
+				unmatched = seed && [],
+				setMatched = [],
+				contextBackup = outermostContext,
+				// We must always have either seed elements or outermost context
+				elems = seed || byElement && Expr.find["TAG"]( "*", outermost ),
+				// Use integer dirruns iff this is the outermost matcher
+				dirrunsUnique = (dirruns += contextBackup == null ? 1 : Math.random() || 0.1),
+				len = elems.length;
+
+			if ( outermost ) {
+				outermostContext = context === document || context || outermost;
+			}
+
+			// Add elements passing elementMatchers directly to results
+			// Support: IE<9, Safari
+			// Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id
+			for ( ; i !== len && (elem = elems[i]) != null; i++ ) {
+				if ( byElement && elem ) {
+					j = 0;
+					if ( !context && elem.ownerDocument !== document ) {
+						setDocument( elem );
+						xml = !documentIsHTML;
+					}
+					while ( (matcher = elementMatchers[j++]) ) {
+						if ( matcher( elem, context || document, xml) ) {
+							results.push( elem );
+							break;
+						}
+					}
+					if ( outermost ) {
+						dirruns = dirrunsUnique;
+					}
+				}
+
+				// Track unmatched elements for set filters
+				if ( bySet ) {
+					// They will have gone through all possible matchers
+					if ( (elem = !matcher && elem) ) {
+						matchedCount--;
+					}
+
+					// Lengthen the array for every element, matched or not
+					if ( seed ) {
+						unmatched.push( elem );
+					}
+				}
+			}
+
+			// `i` is now the count of elements visited above, and adding it to `matchedCount`
+			// makes the latter nonnegative.
+			matchedCount += i;
+
+			// Apply set filters to unmatched elements
+			// NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount`
+			// equals `i`), unless we didn't visit _any_ elements in the above loop because we have
+			// no element matchers and no seed.
+			// Incrementing an initially-string "0" `i` allows `i` to remain a string only in that
+			// case, which will result in a "00" `matchedCount` that differs from `i` but is also
+			// numerically zero.
+			if ( bySet && i !== matchedCount ) {
+				j = 0;
+				while ( (matcher = setMatchers[j++]) ) {
+					matcher( unmatched, setMatched, context, xml );
+				}
+
+				if ( seed ) {
+					// Reintegrate element matches to eliminate the need for sorting
+					if ( matchedCount > 0 ) {
+						while ( i-- ) {
+							if ( !(unmatched[i] || setMatched[i]) ) {
+								setMatched[i] = pop.call( results );
+							}
+						}
+					}
+
+					// Discard index placeholder values to get only actual matches
+					setMatched = condense( setMatched );
+				}
+
+				// Add matches to results
+				push.apply( results, setMatched );
+
+				// Seedless set matches succeeding multiple successful matchers stipulate sorting
+				if ( outermost && !seed && setMatched.length > 0 &&
+					( matchedCount + setMatchers.length ) > 1 ) {
+
+					Sizzle.uniqueSort( results );
+				}
+			}
+
+			// Override manipulation of globals by nested matchers
+			if ( outermost ) {
+				dirruns = dirrunsUnique;
+				outermostContext = contextBackup;
+			}
+
+			return unmatched;
+		};
+
+	return bySet ?
+		markFunction( superMatcher ) :
+		superMatcher;
+}
+
+compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) {
+	var i,
+		setMatchers = [],
+		elementMatchers = [],
+		cached = compilerCache[ selector + " " ];
+
+	if ( !cached ) {
+		// Generate a function of recursive functions that can be used to check each element
+		if ( !match ) {
+			match = tokenize( selector );
+		}
+		i = match.length;
+		while ( i-- ) {
+			cached = matcherFromTokens( match[i] );
+			if ( cached[ expando ] ) {
+				setMatchers.push( cached );
+			} else {
+				elementMatchers.push( cached );
+			}
+		}
+
+		// Cache the compiled function
+		cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );
+
+		// Save selector and tokenization
+		cached.selector = selector;
+	}
+	return cached;
+};
+
+/**
+ * A low-level selection function that works with Sizzle's compiled
+ *  selector functions
+ * @param {String|Function} selector A selector or a pre-compiled
+ *  selector function built with Sizzle.compile
+ * @param {Element} context
+ * @param {Array} [results]
+ * @param {Array} [seed] A set of elements to match against
+ */
+select = Sizzle.select = function( selector, context, results, seed ) {
+	var i, tokens, token, type, find,
+		compiled = typeof selector === "function" && selector,
+		match = !seed && tokenize( (selector = compiled.selector || selector) );
+
+	results = results || [];
+
+	// Try to minimize operations if there is only one selector in the list and no seed
+	// (the latter of which guarantees us context)
+	if ( match.length === 1 ) {
+
+		// Reduce context if the leading compound selector is an ID
+		tokens = match[0] = match[0].slice( 0 );
+		if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
+				context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[1].type ] ) {
+
+			context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0];
+			if ( !context ) {
+				return results;
+
+			// Precompiled matchers will still verify ancestry, so step up a level
+			} else if ( compiled ) {
+				context = context.parentNode;
+			}
+
+			selector = selector.slice( tokens.shift().value.length );
+		}
+
+		// Fetch a seed set for right-to-left matching
+		i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length;
+		while ( i-- ) {
+			token = tokens[i];
+
+			// Abort if we hit a combinator
+			if ( Expr.relative[ (type = token.type) ] ) {
+				break;
+			}
+			if ( (find = Expr.find[ type ]) ) {
+				// Search, expanding context for leading sibling combinators
+				if ( (seed = find(
+					token.matches[0].replace( runescape, funescape ),
+					rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context
+				)) ) {
+
+					// If seed is empty or no tokens remain, we can return early
+					tokens.splice( i, 1 );
+					selector = seed.length && toSelector( tokens );
+					if ( !selector ) {
+						push.apply( results, seed );
+						return results;
+					}
+
+					break;
+				}
+			}
+		}
+	}
+
+	// Compile and execute a filtering function if one is not provided
+	// Provide `match` to avoid retokenization if we modified the selector above
+	( compiled || compile( selector, match ) )(
+		seed,
+		context,
+		!documentIsHTML,
+		results,
+		!context || rsibling.test( selector ) && testContext( context.parentNode ) || context
+	);
+	return results;
+};
+
+// One-time assignments
+
+// Sort stability
+support.sortStable = expando.split("").sort( sortOrder ).join("") === expando;
+
+// Support: Chrome 14-35+
+// Always assume duplicates if they aren't passed to the comparison function
+support.detectDuplicates = !!hasDuplicate;
+
+// Initialize against the default document
+setDocument();
+
+// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)
+// Detached nodes confoundingly follow *each other*
+support.sortDetached = assert(function( el ) {
+	// Should return 1, but returns 4 (following)
+	return el.compareDocumentPosition( document.createElement("fieldset") ) & 1;
+});
+
+// Support: IE<8
+// Prevent attribute/property "interpolation"
+// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
+if ( !assert(function( el ) {
+	el.innerHTML = "<a href='#'></a>";
+	return el.firstChild.getAttribute("href") === "#" ;
+}) ) {
+	addHandle( "type|href|height|width", function( elem, name, isXML ) {
+		if ( !isXML ) {
+			return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 );
+		}
+	});
+}
+
+// Support: IE<9
+// Use defaultValue in place of getAttribute("value")
+if ( !support.attributes || !assert(function( el ) {
+	el.innerHTML = "<input/>";
+	el.firstChild.setAttribute( "value", "" );
+	return el.firstChild.getAttribute( "value" ) === "";
+}) ) {
+	addHandle( "value", function( elem, name, isXML ) {
+		if ( !isXML && elem.nodeName.toLowerCase() === "input" ) {
+			return elem.defaultValue;
+		}
+	});
+}
+
+// Support: IE<9
+// Use getAttributeNode to fetch booleans when getAttribute lies
+if ( !assert(function( el ) {
+	return el.getAttribute("disabled") == null;
+}) ) {
+	addHandle( booleans, function( elem, name, isXML ) {
+		var val;
+		if ( !isXML ) {
+			return elem[ name ] === true ? name.toLowerCase() :
+					(val = elem.getAttributeNode( name )) && val.specified ?
+					val.value :
+				null;
+		}
+	});
+}
+
+return Sizzle;
+
+})( window );
+
+
+
+jQuery.find = Sizzle;
+jQuery.expr = Sizzle.selectors;
+
+// Deprecated
+jQuery.expr[ ":" ] = jQuery.expr.pseudos;
+jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort;
+jQuery.text = Sizzle.getText;
+jQuery.isXMLDoc = Sizzle.isXML;
+jQuery.contains = Sizzle.contains;
+jQuery.escapeSelector = Sizzle.escape;
+
+
+
+
+var dir = function( elem, dir, until ) {
+	var matched = [],
+		truncate = until !== undefined;
+
+	while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) {
+		if ( elem.nodeType === 1 ) {
+			if ( truncate && jQuery( elem ).is( until ) ) {
+				break;
+			}
+			matched.push( elem );
+		}
+	}
+	return matched;
+};
+
+
+var siblings = function( n, elem ) {
+	var matched = [];
+
+	for ( ; n; n = n.nextSibling ) {
+		if ( n.nodeType === 1 && n !== elem ) {
+			matched.push( n );
+		}
+	}
+
+	return matched;
+};
+
+
+var rneedsContext = jQuery.expr.match.needsContext;
+
+
+
+function nodeName( elem, name ) {
+
+  return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
+
+};
+var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i );
+
+
+
+// Implement the identical functionality for filter and not
+function winnow( elements, qualifier, not ) {
+	if ( isFunction( qualifier ) ) {
+		return jQuery.grep( elements, function( elem, i ) {
+			return !!qualifier.call( elem, i, elem ) !== not;
+		} );
+	}
+
+	// Single element
+	if ( qualifier.nodeType ) {
+		return jQuery.grep( elements, function( elem ) {
+			return ( elem === qualifier ) !== not;
+		} );
+	}
+
+	// Arraylike of elements (jQuery, arguments, Array)
+	if ( typeof qualifier !== "string" ) {
+		return jQuery.grep( elements, function( elem ) {
+			return ( indexOf.call( qualifier, elem ) > -1 ) !== not;
+		} );
+	}
+
+	// Filtered directly for both simple and complex selectors
+	return jQuery.filter( qualifier, elements, not );
+}
+
+jQuery.filter = function( expr, elems, not ) {
+	var elem = elems[ 0 ];
+
+	if ( not ) {
+		expr = ":not(" + expr + ")";
+	}
+
+	if ( elems.length === 1 && elem.nodeType === 1 ) {
+		return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [];
+	}
+
+	return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {
+		return elem.nodeType === 1;
+	} ) );
+};
+
+jQuery.fn.extend( {
+	find: function( selector ) {
+		var i, ret,
+			len = this.length,
+			self = this;
+
+		if ( typeof selector !== "string" ) {
+			return this.pushStack( jQuery( selector ).filter( function() {
+				for ( i = 0; i < len; i++ ) {
+					if ( jQuery.contains( self[ i ], this ) ) {
+						return true;
+					}
+				}
+			} ) );
+		}
+
+		ret = this.pushStack( [] );
+
+		for ( i = 0; i < len; i++ ) {
+			jQuery.find( selector, self[ i ], ret );
+		}
+
+		return len > 1 ? jQuery.uniqueSort( ret ) : ret;
+	},
+	filter: function( selector ) {
+		return this.pushStack( winnow( this, selector || [], false ) );
+	},
+	not: function( selector ) {
+		return this.pushStack( winnow( this, selector || [], true ) );
+	},
+	is: function( selector ) {
+		return !!winnow(
+			this,
+
+			// If this is a positional/relative selector, check membership in the returned set
+			// so $("p:first").is("p:last") won't return true for a doc with two "p".
+			typeof selector === "string" && rneedsContext.test( selector ) ?
+				jQuery( selector ) :
+				selector || [],
+			false
+		).length;
+	}
+} );
+
+
+// Initialize a jQuery object
+
+
+// A central reference to the root jQuery(document)
+var rootjQuery,
+
+	// A simple way to check for HTML strings
+	// Prioritize #id over <tag> to avoid XSS via location.hash (#9521)
+	// Strict HTML recognition (#11290: must start with <)
+	// Shortcut simple #id case for speed
+	rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/,
+
+	init = jQuery.fn.init = function( selector, context, root ) {
+		var match, elem;
+
+		// HANDLE: $(""), $(null), $(undefined), $(false)
+		if ( !selector ) {
+			return this;
+		}
+
+		// Method init() accepts an alternate rootjQuery
+		// so migrate can support jQuery.sub (gh-2101)
+		root = root || rootjQuery;
+
+		// Handle HTML strings
+		if ( typeof selector === "string" ) {
+			if ( selector[ 0 ] === "<" &&
+				selector[ selector.length - 1 ] === ">" &&
+				selector.length >= 3 ) {
+
+				// Assume that strings that start and end with <> are HTML and skip the regex check
+				match = [ null, selector, null ];
+
+			} else {
+				match = rquickExpr.exec( selector );
+			}
+
+			// Match html or make sure no context is specified for #id
+			if ( match && ( match[ 1 ] || !context ) ) {
+
+				// HANDLE: $(html) -> $(array)
+				if ( match[ 1 ] ) {
+					context = context instanceof jQuery ? context[ 0 ] : context;
+
+					// Option to run scripts is true for back-compat
+					// Intentionally let the error be thrown if parseHTML is not present
+					jQuery.merge( this, jQuery.parseHTML(
+						match[ 1 ],
+						context && context.nodeType ? context.ownerDocument || context : document,
+						true
+					) );
+
+					// HANDLE: $(html, props)
+					if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) {
+						for ( match in context ) {
+
+							// Properties of context are called as methods if possible
+							if ( isFunction( this[ match ] ) ) {
+								this[ match ]( context[ match ] );
+
+							// ...and otherwise set as attributes
+							} else {
+								this.attr( match, context[ match ] );
+							}
+						}
+					}
+
+					return this;
+
+				// HANDLE: $(#id)
+				} else {
+					elem = document.getElementById( match[ 2 ] );
+
+					if ( elem ) {
+
+						// Inject the element directly into the jQuery object
+						this[ 0 ] = elem;
+						this.length = 1;
+					}
+					return this;
+				}
+
+			// HANDLE: $(expr, $(...))
+			} else if ( !context || context.jquery ) {
+				return ( context || root ).find( selector );
+
+			// HANDLE: $(expr, context)
+			// (which is just equivalent to: $(context).find(expr)
+			} else {
+				return this.constructor( context ).find( selector );
+			}
+
+		// HANDLE: $(DOMElement)
+		} else if ( selector.nodeType ) {
+			this[ 0 ] = selector;
+			this.length = 1;
+			return this;
+
+		// HANDLE: $(function)
+		// Shortcut for document ready
+		} else if ( isFunction( selector ) ) {
+			return root.ready !== undefined ?
+				root.ready( selector ) :
+
+				// Execute immediately if ready is not present
+				selector( jQuery );
+		}
+
+		return jQuery.makeArray( selector, this );
+	};
+
+// Give the init function the jQuery prototype for later instantiation
+init.prototype = jQuery.fn;
+
+// Initialize central reference
+rootjQuery = jQuery( document );
+
+
+var rparentsprev = /^(?:parents|prev(?:Until|All))/,
+
+	// Methods guaranteed to produce a unique set when starting from a unique set
+	guaranteedUnique = {
+		children: true,
+		contents: true,
+		next: true,
+		prev: true
+	};
+
+jQuery.fn.extend( {
+	has: function( target ) {
+		var targets = jQuery( target, this ),
+			l = targets.length;
+
+		return this.filter( function() {
+			var i = 0;
+			for ( ; i < l; i++ ) {
+				if ( jQuery.contains( this, targets[ i ] ) ) {
+					return true;
+				}
+			}
+		} );
+	},
+
+	closest: function( selectors, context ) {
+		var cur,
+			i = 0,
+			l = this.length,
+			matched = [],
+			targets = typeof selectors !== "string" && jQuery( selectors );
+
+		// Positional selectors never match, since there's no _selection_ context
+		if ( !rneedsContext.test( selectors ) ) {
+			for ( ; i < l; i++ ) {
+				for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) {
+
+					// Always skip document fragments
+					if ( cur.nodeType < 11 && ( targets ?
+						targets.index( cur ) > -1 :
+
+						// Don't pass non-elements to Sizzle
+						cur.nodeType === 1 &&
+							jQuery.find.matchesSelector( cur, selectors ) ) ) {
+
+						matched.push( cur );
+						break;
+					}
+				}
+			}
+		}
+
+		return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched );
+	},
+
+	// Determine the position of an element within the set
+	index: function( elem ) {
+
+		// No argument, return index in parent
+		if ( !elem ) {
+			return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1;
+		}
+
+		// Index in selector
+		if ( typeof elem === "string" ) {
+			return indexOf.call( jQuery( elem ), this[ 0 ] );
+		}
+
+		// Locate the position of the desired element
+		return indexOf.call( this,
+
+			// If it receives a jQuery object, the first element is used
+			elem.jquery ? elem[ 0 ] : elem
+		);
+	},
+
+	add: function( selector, context ) {
+		return this.pushStack(
+			jQuery.uniqueSort(
+				jQuery.merge( this.get(), jQuery( selector, context ) )
+			)
+		);
+	},
+
+	addBack: function( selector ) {
+		return this.add( selector == null ?
+			this.prevObject : this.prevObject.filter( selector )
+		);
+	}
+} );
+
+function sibling( cur, dir ) {
+	while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {}
+	return cur;
+}
+
+jQuery.each( {
+	parent: function( elem ) {
+		var parent = elem.parentNode;
+		return parent && parent.nodeType !== 11 ? parent : null;
+	},
+	parents: function( elem ) {
+		return dir( elem, "parentNode" );
+	},
+	parentsUntil: function( elem, i, until ) {
+		return dir( elem, "parentNode", until );
+	},
+	next: function( elem ) {
+		return sibling( elem, "nextSibling" );
+	},
+	prev: function( elem ) {
+		return sibling( elem, "previousSibling" );
+	},
+	nextAll: function( elem ) {
+		return dir( elem, "nextSibling" );
+	},
+	prevAll: function( elem ) {
+		return dir( elem, "previousSibling" );
+	},
+	nextUntil: function( elem, i, until ) {
+		return dir( elem, "nextSibling", until );
+	},
+	prevUntil: function( elem, i, until ) {
+		return dir( elem, "previousSibling", until );
+	},
+	siblings: function( elem ) {
+		return siblings( ( elem.parentNode || {} ).firstChild, elem );
+	},
+	children: function( elem ) {
+		return siblings( elem.firstChild );
+	},
+	contents: function( elem ) {
+		if ( typeof elem.contentDocument !== "undefined" ) {
+			return elem.contentDocument;
+		}
+
+		// Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only
+		// Treat the template element as a regular one in browsers that
+		// don't support it.
+		if ( nodeName( elem, "template" ) ) {
+			elem = elem.content || elem;
+		}
+
+		return jQuery.merge( [], elem.childNodes );
+	}
+}, function( name, fn ) {
+	jQuery.fn[ name ] = function( until, selector ) {
+		var matched = jQuery.map( this, fn, until );
+
+		if ( name.slice( -5 ) !== "Until" ) {
+			selector = until;
+		}
+
+		if ( selector && typeof selector === "string" ) {
+			matched = jQuery.filter( selector, matched );
+		}
+
+		if ( this.length > 1 ) {
+
+			// Remove duplicates
+			if ( !guaranteedUnique[ name ] ) {
+				jQuery.uniqueSort( matched );
+			}
+
+			// Reverse order for parents* and prev-derivatives
+			if ( rparentsprev.test( name ) ) {
+				matched.reverse();
+			}
+		}
+
+		return this.pushStack( matched );
+	};
+} );
+var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g );
+
+
+
+// Convert String-formatted options into Object-formatted ones
+function createOptions( options ) {
+	var object = {};
+	jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) {
+		object[ flag ] = true;
+	} );
+	return object;
+}
+
+/*
+ * Create a callback list using the following parameters:
+ *
+ *	options: an optional list of space-separated options that will change how
+ *			the callback list behaves or a more traditional option object
+ *
+ * By default a callback list will act like an event callback list and can be
+ * "fired" multiple times.
+ *
+ * Possible options:
+ *
+ *	once:			will ensure the callback list can only be fired once (like a Deferred)
+ *
+ *	memory:			will keep track of previous values and will call any callback added
+ *					after the list has been fired right away with the latest "memorized"
+ *					values (like a Deferred)
+ *
+ *	unique:			will ensure a callback can only be added once (no duplicate in the list)
+ *
+ *	stopOnFalse:	interrupt callings when a callback returns false
+ *
+ */
+jQuery.Callbacks = function( options ) {
+
+	// Convert options from String-formatted to Object-formatted if needed
+	// (we check in cache first)
+	options = typeof options === "string" ?
+		createOptions( options ) :
+		jQuery.extend( {}, options );
+
+	var // Flag to know if list is currently firing
+		firing,
+
+		// Last fire value for non-forgettable lists
+		memory,
+
+		// Flag to know if list was already fired
+		fired,
+
+		// Flag to prevent firing
+		locked,
+
+		// Actual callback list
+		list = [],
+
+		// Queue of execution data for repeatable lists
+		queue = [],
+
+		// Index of currently firing callback (modified by add/remove as needed)
+		firingIndex = -1,
+
+		// Fire callbacks
+		fire = function() {
+
+			// Enforce single-firing
+			locked = locked || options.once;
+
+			// Execute callbacks for all pending executions,
+			// respecting firingIndex overrides and runtime changes
+			fired = firing = true;
+			for ( ; queue.length; firingIndex = -1 ) {
+				memory = queue.shift();
+				while ( ++firingIndex < list.length ) {
+
+					// Run callback and check for early termination
+					if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false &&
+						options.stopOnFalse ) {
+
+						// Jump to end and forget the data so .add doesn't re-fire
+						firingIndex = list.length;
+						memory = false;
+					}
+				}
+			}
+
+			// Forget the data if we're done with it
+			if ( !options.memory ) {
+				memory = false;
+			}
+
+			firing = false;
+
+			// Clean up if we're done firing for good
+			if ( locked ) {
+
+				// Keep an empty list if we have data for future add calls
+				if ( memory ) {
+					list = [];
+
+				// Otherwise, this object is spent
+				} else {
+					list = "";
+				}
+			}
+		},
+
+		// Actual Callbacks object
+		self = {
+
+			// Add a callback or a collection of callbacks to the list
+			add: function() {
+				if ( list ) {
+
+					// If we have memory from a past run, we should fire after adding
+					if ( memory && !firing ) {
+						firingIndex = list.length - 1;
+						queue.push( memory );
+					}
+
+					( function add( args ) {
+						jQuery.each( args, function( _, arg ) {
+							if ( isFunction( arg ) ) {
+								if ( !options.unique || !self.has( arg ) ) {
+									list.push( arg );
+								}
+							} else if ( arg && arg.length && toType( arg ) !== "string" ) {
+
+								// Inspect recursively
+								add( arg );
+							}
+						} );
+					} )( arguments );
+
+					if ( memory && !firing ) {
+						fire();
+					}
+				}
+				return this;
+			},
+
+			// Remove a callback from the list
+			remove: function() {
+				jQuery.each( arguments, function( _, arg ) {
+					var index;
+					while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
+						list.splice( index, 1 );
+
+						// Handle firing indexes
+						if ( index <= firingIndex ) {
+							firingIndex--;
+						}
+					}
+				} );
+				return this;
+			},
+
+			// Check if a given callback is in the list.
+			// If no argument is given, return whether or not list has callbacks attached.
+			has: function( fn ) {
+				return fn ?
+					jQuery.inArray( fn, list ) > -1 :
+					list.length > 0;
+			},
+
+			// Remove all callbacks from the list
+			empty: function() {
+				if ( list ) {
+					list = [];
+				}
+				return this;
+			},
+
+			// Disable .fire and .add
+			// Abort any current/pending executions
+			// Clear all callbacks and values
+			disable: function() {
+				locked = queue = [];
+				list = memory = "";
+				return this;
+			},
+			disabled: function() {
+				return !list;
+			},
+
+			// Disable .fire
+			// Also disable .add unless we have memory (since it would have no effect)
+			// Abort any pending executions
+			lock: function() {
+				locked = queue = [];
+				if ( !memory && !firing ) {
+					list = memory = "";
+				}
+				return this;
+			},
+			locked: function() {
+				return !!locked;
+			},
+
+			// Call all callbacks with the given context and arguments
+			fireWith: function( context, args ) {
+				if ( !locked ) {
+					args = args || [];
+					args = [ context, args.slice ? args.slice() : args ];
+					queue.push( args );
+					if ( !firing ) {
+						fire();
+					}
+				}
+				return this;
+			},
+
+			// Call all the callbacks with the given arguments
+			fire: function() {
+				self.fireWith( this, arguments );
+				return this;
+			},
+
+			// To know if the callbacks have already been called at least once
+			fired: function() {
+				return !!fired;
+			}
+		};
+
+	return self;
+};
+
+
+function Identity( v ) {
+	return v;
+}
+function Thrower( ex ) {
+	throw ex;
+}
+
+function adoptValue( value, resolve, reject, noValue ) {
+	var method;
+
+	try {
+
+		// Check for promise aspect first to privilege synchronous behavior
+		if ( value && isFunction( ( method = value.promise ) ) ) {
+			method.call( value ).done( resolve ).fail( reject );
+
+		// Other thenables
+		} else if ( value && isFunction( ( method = value.then ) ) ) {
+			method.call( value, resolve, reject );
+
+		// Other non-thenables
+		} else {
+
+			// Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer:
+			// * false: [ value ].slice( 0 ) => resolve( value )
+			// * true: [ value ].slice( 1 ) => resolve()
+			resolve.apply( undefined, [ value ].slice( noValue ) );
+		}
+
+	// For Promises/A+, convert exceptions into rejections
+	// Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in
+	// Deferred#then to conditionally suppress rejection.
+	} catch ( value ) {
+
+		// Support: Android 4.0 only
+		// Strict mode functions invoked without .call/.apply get global-object context
+		reject.apply( undefined, [ value ] );
+	}
+}
+
+jQuery.extend( {
+
+	Deferred: function( func ) {
+		var tuples = [
+
+				// action, add listener, callbacks,
+				// ... .then handlers, argument index, [final state]
+				[ "notify", "progress", jQuery.Callbacks( "memory" ),
+					jQuery.Callbacks( "memory" ), 2 ],
+				[ "resolve", "done", jQuery.Callbacks( "once memory" ),
+					jQuery.Callbacks( "once memory" ), 0, "resolved" ],
+				[ "reject", "fail", jQuery.Callbacks( "once memory" ),
+					jQuery.Callbacks( "once memory" ), 1, "rejected" ]
+			],
+			state = "pending",
+			promise = {
+				state: function() {
+					return state;
+				},
+				always: function() {
+					deferred.done( arguments ).fail( arguments );
+					return this;
+				},
+				"catch": function( fn ) {
+					return promise.then( null, fn );
+				},
+
+				// Keep pipe for back-compat
+				pipe: function( /* fnDone, fnFail, fnProgress */ ) {
+					var fns = arguments;
+
+					return jQuery.Deferred( function( newDefer ) {
+						jQuery.each( tuples, function( i, tuple ) {
+
+							// Map tuples (progress, done, fail) to arguments (done, fail, progress)
+							var fn = isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ];
+
+							// deferred.progress(function() { bind to newDefer or newDefer.notify })
+							// deferred.done(function() { bind to newDefer or newDefer.resolve })
+							// deferred.fail(function() { bind to newDefer or newDefer.reject })
+							deferred[ tuple[ 1 ] ]( function() {
+								var returned = fn && fn.apply( this, arguments );
+								if ( returned && isFunction( returned.promise ) ) {
+									returned.promise()
+										.progress( newDefer.notify )
+										.done( newDefer.resolve )
+										.fail( newDefer.reject );
+								} else {
+									newDefer[ tuple[ 0 ] + "With" ](
+										this,
+										fn ? [ returned ] : arguments
+									);
+								}
+							} );
+						} );
+						fns = null;
+					} ).promise();
+				},
+				then: function( onFulfilled, onRejected, onProgress ) {
+					var maxDepth = 0;
+					function resolve( depth, deferred, handler, special ) {
+						return function() {
+							var that = this,
+								args = arguments,
+								mightThrow = function() {
+									var returned, then;
+
+									// Support: Promises/A+ section 2.3.3.3.3
+									// https://promisesaplus.com/#point-59
+									// Ignore double-resolution attempts
+									if ( depth < maxDepth ) {
+										return;
+									}
+
+									returned = handler.apply( that, args );
+
+									// Support: Promises/A+ section 2.3.1
+									// https://promisesaplus.com/#point-48
+									if ( returned === deferred.promise() ) {
+										throw new TypeError( "Thenable self-resolution" );
+									}
+
+									// Support: Promises/A+ sections 2.3.3.1, 3.5
+									// https://promisesaplus.com/#point-54
+									// https://promisesaplus.com/#point-75
+									// Retrieve `then` only once
+									then = returned &&
+
+										// Support: Promises/A+ section 2.3.4
+										// https://promisesaplus.com/#point-64
+										// Only check objects and functions for thenability
+										( typeof returned === "object" ||
+											typeof returned === "function" ) &&
+										returned.then;
+
+									// Handle a returned thenable
+									if ( isFunction( then ) ) {
+
+										// Special processors (notify) just wait for resolution
+										if ( special ) {
+											then.call(
+												returned,
+												resolve( maxDepth, deferred, Identity, special ),
+												resolve( maxDepth, deferred, Thrower, special )
+											);
+
+										// Normal processors (resolve) also hook into progress
+										} else {
+
+											// ...and disregard older resolution values
+											maxDepth++;
+
+											then.call(
+												returned,
+												resolve( maxDepth, deferred, Identity, special ),
+												resolve( maxDepth, deferred, Thrower, special ),
+												resolve( maxDepth, deferred, Identity,
+													deferred.notifyWith )
+											);
+										}
+
+									// Handle all other returned values
+									} else {
+
+										// Only substitute handlers pass on context
+										// and multiple values (non-spec behavior)
+										if ( handler !== Identity ) {
+											that = undefined;
+											args = [ returned ];
+										}
+
+										// Process the value(s)
+										// Default process is resolve
+										( special || deferred.resolveWith )( that, args );
+									}
+								},
+
+								// Only normal processors (resolve) catch and reject exceptions
+								process = special ?
+									mightThrow :
+									function() {
+										try {
+											mightThrow();
+										} catch ( e ) {
+
+											if ( jQuery.Deferred.exceptionHook ) {
+												jQuery.Deferred.exceptionHook( e,
+													process.stackTrace );
+											}
+
+											// Support: Promises/A+ section 2.3.3.3.4.1
+											// https://promisesaplus.com/#point-61
+											// Ignore post-resolution exceptions
+											if ( depth + 1 >= maxDepth ) {
+
+												// Only substitute handlers pass on context
+												// and multiple values (non-spec behavior)
+												if ( handler !== Thrower ) {
+													that = undefined;
+													args = [ e ];
+												}
+
+												deferred.rejectWith( that, args );
+											}
+										}
+									};
+
+							// Support: Promises/A+ section 2.3.3.3.1
+							// https://promisesaplus.com/#point-57
+							// Re-resolve promises immediately to dodge false rejection from
+							// subsequent errors
+							if ( depth ) {
+								process();
+							} else {
+
+								// Call an optional hook to record the stack, in case of exception
+								// since it's otherwise lost when execution goes async
+								if ( jQuery.Deferred.getStackHook ) {
+									process.stackTrace = jQuery.Deferred.getStackHook();
+								}
+								window.setTimeout( process );
+							}
+						};
+					}
+
+					return jQuery.Deferred( function( newDefer ) {
+
+						// progress_handlers.add( ... )
+						tuples[ 0 ][ 3 ].add(
+							resolve(
+								0,
+								newDefer,
+								isFunction( onProgress ) ?
+									onProgress :
+									Identity,
+								newDefer.notifyWith
+							)
+						);
+
+						// fulfilled_handlers.add( ... )
+						tuples[ 1 ][ 3 ].add(
+							resolve(
+								0,
+								newDefer,
+								isFunction( onFulfilled ) ?
+									onFulfilled :
+									Identity
+							)
+						);
+
+						// rejected_handlers.add( ... )
+						tuples[ 2 ][ 3 ].add(
+							resolve(
+								0,
+								newDefer,
+								isFunction( onRejected ) ?
+									onRejected :
+									Thrower
+							)
+						);
+					} ).promise();
+				},
+
+				// Get a promise for this deferred
+				// If obj is provided, the promise aspect is added to the object
+				promise: function( obj ) {
+					return obj != null ? jQuery.extend( obj, promise ) : promise;
+				}
+			},
+			deferred = {};
+
+		// Add list-specific methods
+		jQuery.each( tuples, function( i, tuple ) {
+			var list = tuple[ 2 ],
+				stateString = tuple[ 5 ];
+
+			// promise.progress = list.add
+			// promise.done = list.add
+			// promise.fail = list.add
+			promise[ tuple[ 1 ] ] = list.add;
+
+			// Handle state
+			if ( stateString ) {
+				list.add(
+					function() {
+
+						// state = "resolved" (i.e., fulfilled)
+						// state = "rejected"
+						state = stateString;
+					},
+
+					// rejected_callbacks.disable
+					// fulfilled_callbacks.disable
+					tuples[ 3 - i ][ 2 ].disable,
+
+					// rejected_handlers.disable
+					// fulfilled_handlers.disable
+					tuples[ 3 - i ][ 3 ].disable,
+
+					// progress_callbacks.lock
+					tuples[ 0 ][ 2 ].lock,
+
+					// progress_handlers.lock
+					tuples[ 0 ][ 3 ].lock
+				);
+			}
+
+			// progress_handlers.fire
+			// fulfilled_handlers.fire
+			// rejected_handlers.fire
+			list.add( tuple[ 3 ].fire );
+
+			// deferred.notify = function() { deferred.notifyWith(...) }
+			// deferred.resolve = function() { deferred.resolveWith(...) }
+			// deferred.reject = function() { deferred.rejectWith(...) }
+			deferred[ tuple[ 0 ] ] = function() {
+				deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments );
+				return this;
+			};
+
+			// deferred.notifyWith = list.fireWith
+			// deferred.resolveWith = list.fireWith
+			// deferred.rejectWith = list.fireWith
+			deferred[ tuple[ 0 ] + "With" ] = list.fireWith;
+		} );
+
+		// Make the deferred a promise
+		promise.promise( deferred );
+
+		// Call given func if any
+		if ( func ) {
+			func.call( deferred, deferred );
+		}
+
+		// All done!
+		return deferred;
+	},
+
+	// Deferred helper
+	when: function( singleValue ) {
+		var
+
+			// count of uncompleted subordinates
+			remaining = arguments.length,
+
+			// count of unprocessed arguments
+			i = remaining,
+
+			// subordinate fulfillment data
+			resolveContexts = Array( i ),
+			resolveValues = slice.call( arguments ),
+
+			// the master Deferred
+			master = jQuery.Deferred(),
+
+			// subordinate callback factory
+			updateFunc = function( i ) {
+				return function( value ) {
+					resolveContexts[ i ] = this;
+					resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
+					if ( !( --remaining ) ) {
+						master.resolveWith( resolveContexts, resolveValues );
+					}
+				};
+			};
+
+		// Single- and empty arguments are adopted like Promise.resolve
+		if ( remaining <= 1 ) {
+			adoptValue( singleValue, master.done( updateFunc( i ) ).resolve, master.reject,
+				!remaining );
+
+			// Use .then() to unwrap secondary thenables (cf. gh-3000)
+			if ( master.state() === "pending" ||
+				isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) {
+
+				return master.then();
+			}
+		}
+
+		// Multiple arguments are aggregated like Promise.all array elements
+		while ( i-- ) {
+			adoptValue( resolveValues[ i ], updateFunc( i ), master.reject );
+		}
+
+		return master.promise();
+	}
+} );
+
+
+// These usually indicate a programmer mistake during development,
+// warn about them ASAP rather than swallowing them by default.
+var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/;
+
+jQuery.Deferred.exceptionHook = function( error, stack ) {
+
+	// Support: IE 8 - 9 only
+	// Console exists when dev tools are open, which can happen at any time
+	if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) {
+		window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack );
+	}
+};
+
+
+
+
+jQuery.readyException = function( error ) {
+	window.setTimeout( function() {
+		throw error;
+	} );
+};
+
+
+
+
+// The deferred used on DOM ready
+var readyList = jQuery.Deferred();
+
+jQuery.fn.ready = function( fn ) {
+
+	readyList
+		.then( fn )
+
+		// Wrap jQuery.readyException in a function so that the lookup
+		// happens at the time of error handling instead of callback
+		// registration.
+		.catch( function( error ) {
+			jQuery.readyException( error );
+		} );
+
+	return this;
+};
+
+jQuery.extend( {
+
+	// Is the DOM ready to be used? Set to true once it occurs.
+	isReady: false,
+
+	// A counter to track how many items to wait for before
+	// the ready event fires. See #6781
+	readyWait: 1,
+
+	// Handle when the DOM is ready
+	ready: function( wait ) {
+
+		// Abort if there are pending holds or we're already ready
+		if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
+			return;
+		}
+
+		// Remember that the DOM is ready
+		jQuery.isReady = true;
+
+		// If a normal DOM Ready event fired, decrement, and wait if need be
+		if ( wait !== true && --jQuery.readyWait > 0 ) {
+			return;
+		}
+
+		// If there are functions bound, to execute
+		readyList.resolveWith( document, [ jQuery ] );
+	}
+} );
+
+jQuery.ready.then = readyList.then;
+
+// The ready event handler and self cleanup method
+function completed() {
+	document.removeEventListener( "DOMContentLoaded", completed );
+	window.removeEventListener( "load", completed );
+	jQuery.ready();
+}
+
+// Catch cases where $(document).ready() is called
+// after the browser event has already occurred.
+// Support: IE <=9 - 10 only
+// Older IE sometimes signals "interactive" too soon
+if ( document.readyState === "complete" ||
+	( document.readyState !== "loading" && !document.documentElement.doScroll ) ) {
+
+	// Handle it asynchronously to allow scripts the opportunity to delay ready
+	window.setTimeout( jQuery.ready );
+
+} else {
+
+	// Use the handy event callback
+	document.addEventListener( "DOMContentLoaded", completed );
+
+	// A fallback to window.onload, that will always work
+	window.addEventListener( "load", completed );
+}
+
+
+
+
+// Multifunctional method to get and set values of a collection
+// The value/s can optionally be executed if it's a function
+var access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
+	var i = 0,
+		len = elems.length,
+		bulk = key == null;
+
+	// Sets many values
+	if ( toType( key ) === "object" ) {
+		chainable = true;
+		for ( i in key ) {
+			access( elems, fn, i, key[ i ], true, emptyGet, raw );
+		}
+
+	// Sets one value
+	} else if ( value !== undefined ) {
+		chainable = true;
+
+		if ( !isFunction( value ) ) {
+			raw = true;
+		}
+
+		if ( bulk ) {
+
+			// Bulk operations run against the entire set
+			if ( raw ) {
+				fn.call( elems, value );
+				fn = null;
+
+			// ...except when executing function values
+			} else {
+				bulk = fn;
+				fn = function( elem, key, value ) {
+					return bulk.call( jQuery( elem ), value );
+				};
+			}
+		}
+
+		if ( fn ) {
+			for ( ; i < len; i++ ) {
+				fn(
+					elems[ i ], key, raw ?
+					value :
+					value.call( elems[ i ], i, fn( elems[ i ], key ) )
+				);
+			}
+		}
+	}
+
+	if ( chainable ) {
+		return elems;
+	}
+
+	// Gets
+	if ( bulk ) {
+		return fn.call( elems );
+	}
+
+	return len ? fn( elems[ 0 ], key ) : emptyGet;
+};
+
+
+// Matches dashed string for camelizing
+var rmsPrefix = /^-ms-/,
+	rdashAlpha = /-([a-z])/g;
+
+// Used by camelCase as callback to replace()
+function fcamelCase( all, letter ) {
+	return letter.toUpperCase();
+}
+
+// Convert dashed to camelCase; used by the css and data modules
+// Support: IE <=9 - 11, Edge 12 - 15
+// Microsoft forgot to hump their vendor prefix (#9572)
+function camelCase( string ) {
+	return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
+}
+var acceptData = function( owner ) {
+
+	// Accepts only:
+	//  - Node
+	//    - Node.ELEMENT_NODE
+	//    - Node.DOCUMENT_NODE
+	//  - Object
+	//    - Any
+	return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType );
+};
+
+
+
+
+function Data() {
+	this.expando = jQuery.expando + Data.uid++;
+}
+
+Data.uid = 1;
+
+Data.prototype = {
+
+	cache: function( owner ) {
+
+		// Check if the owner object already has a cache
+		var value = owner[ this.expando ];
+
+		// If not, create one
+		if ( !value ) {
+			value = {};
+
+			// We can accept data for non-element nodes in modern browsers,
+			// but we should not, see #8335.
+			// Always return an empty object.
+			if ( acceptData( owner ) ) {
+
+				// If it is a node unlikely to be stringify-ed or looped over
+				// use plain assignment
+				if ( owner.nodeType ) {
+					owner[ this.expando ] = value;
+
+				// Otherwise secure it in a non-enumerable property
+				// configurable must be true to allow the property to be
+				// deleted when data is removed
+				} else {
+					Object.defineProperty( owner, this.expando, {
+						value: value,
+						configurable: true
+					} );
+				}
+			}
+		}
+
+		return value;
+	},
+	set: function( owner, data, value ) {
+		var prop,
+			cache = this.cache( owner );
+
+		// Handle: [ owner, key, value ] args
+		// Always use camelCase key (gh-2257)
+		if ( typeof data === "string" ) {
+			cache[ camelCase( data ) ] = value;
+
+		// Handle: [ owner, { properties } ] args
+		} else {
+
+			// Copy the properties one-by-one to the cache object
+			for ( prop in data ) {
+				cache[ camelCase( prop ) ] = data[ prop ];
+			}
+		}
+		return cache;
+	},
+	get: function( owner, key ) {
+		return key === undefined ?
+			this.cache( owner ) :
+
+			// Always use camelCase key (gh-2257)
+			owner[ this.expando ] && owner[ this.expando ][ camelCase( key ) ];
+	},
+	access: function( owner, key, value ) {
+
+		// In cases where either:
+		//
+		//   1. No key was specified
+		//   2. A string key was specified, but no value provided
+		//
+		// Take the "read" path and allow the get method to determine
+		// which value to return, respectively either:
+		//
+		//   1. The entire cache object
+		//   2. The data stored at the key
+		//
+		if ( key === undefined ||
+				( ( key && typeof key === "string" ) && value === undefined ) ) {
+
+			return this.get( owner, key );
+		}
+
+		// When the key is not a string, or both a key and value
+		// are specified, set or extend (existing objects) with either:
+		//
+		//   1. An object of properties
+		//   2. A key and value
+		//
+		this.set( owner, key, value );
+
+		// Since the "set" path can have two possible entry points
+		// return the expected data based on which path was taken[*]
+		return value !== undefined ? value : key;
+	},
+	remove: function( owner, key ) {
+		var i,
+			cache = owner[ this.expando ];
+
+		if ( cache === undefined ) {
+			return;
+		}
+
+		if ( key !== undefined ) {
+
+			// Support array or space separated string of keys
+			if ( Array.isArray( key ) ) {
+
+				// If key is an array of keys...
+				// We always set camelCase keys, so remove that.
+				key = key.map( camelCase );
+			} else {
+				key = camelCase( key );
+
+				// If a key with the spaces exists, use it.
+				// Otherwise, create an array by matching non-whitespace
+				key = key in cache ?
+					[ key ] :
+					( key.match( rnothtmlwhite ) || [] );
+			}
+
+			i = key.length;
+
+			while ( i-- ) {
+				delete cache[ key[ i ] ];
+			}
+		}
+
+		// Remove the expando if there's no more data
+		if ( key === undefined || jQuery.isEmptyObject( cache ) ) {
+
+			// Support: Chrome <=35 - 45
+			// Webkit & Blink performance suffers when deleting properties
+			// from DOM nodes, so set to undefined instead
+			// https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted)
+			if ( owner.nodeType ) {
+				owner[ this.expando ] = undefined;
+			} else {
+				delete owner[ this.expando ];
+			}
+		}
+	},
+	hasData: function( owner ) {
+		var cache = owner[ this.expando ];
+		return cache !== undefined && !jQuery.isEmptyObject( cache );
+	}
+};
+var dataPriv = new Data();
+
+var dataUser = new Data();
+
+
+
+//	Implementation Summary
+//
+//	1. Enforce API surface and semantic compatibility with 1.9.x branch
+//	2. Improve the module's maintainability by reducing the storage
+//		paths to a single mechanism.
+//	3. Use the same single mechanism to support "private" and "user" data.
+//	4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData)
+//	5. Avoid exposing implementation details on user objects (eg. expando properties)
+//	6. Provide a clear path for implementation upgrade to WeakMap in 2014
+
+var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
+	rmultiDash = /[A-Z]/g;
+
+function getData( data ) {
+	if ( data === "true" ) {
+		return true;
+	}
+
+	if ( data === "false" ) {
+		return false;
+	}
+
+	if ( data === "null" ) {
+		return null;
+	}
+
+	// Only convert to a number if it doesn't change the string
+	if ( data === +data + "" ) {
+		return +data;
+	}
+
+	if ( rbrace.test( data ) ) {
+		return JSON.parse( data );
+	}
+
+	return data;
+}
+
+function dataAttr( elem, key, data ) {
+	var name;
+
+	// If nothing was found internally, try to fetch any
+	// data from the HTML5 data-* attribute
+	if ( data === undefined && elem.nodeType === 1 ) {
+		name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase();
+		data = elem.getAttribute( name );
+
+		if ( typeof data === "string" ) {
+			try {
+				data = getData( data );
+			} catch ( e ) {}
+
+			// Make sure we set the data so it isn't changed later
+			dataUser.set( elem, key, data );
+		} else {
+			data = undefined;
+		}
+	}
+	return data;
+}
+
+jQuery.extend( {
+	hasData: function( elem ) {
+		return dataUser.hasData( elem ) || dataPriv.hasData( elem );
+	},
+
+	data: function( elem, name, data ) {
+		return dataUser.access( elem, name, data );
+	},
+
+	removeData: function( elem, name ) {
+		dataUser.remove( elem, name );
+	},
+
+	// TODO: Now that all calls to _data and _removeData have been replaced
+	// with direct calls to dataPriv methods, these can be deprecated.
+	_data: function( elem, name, data ) {
+		return dataPriv.access( elem, name, data );
+	},
+
+	_removeData: function( elem, name ) {
+		dataPriv.remove( elem, name );
+	}
+} );
+
+jQuery.fn.extend( {
+	data: function( key, value ) {
+		var i, name, data,
+			elem = this[ 0 ],
+			attrs = elem && elem.attributes;
+
+		// Gets all values
+		if ( key === undefined ) {
+			if ( this.length ) {
+				data = dataUser.get( elem );
+
+				if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) {
+					i = attrs.length;
+					while ( i-- ) {
+
+						// Support: IE 11 only
+						// The attrs elements can be null (#14894)
+						if ( attrs[ i ] ) {
+							name = attrs[ i ].name;
+							if ( name.indexOf( "data-" ) === 0 ) {
+								name = camelCase( name.slice( 5 ) );
+								dataAttr( elem, name, data[ name ] );
+							}
+						}
+					}
+					dataPriv.set( elem, "hasDataAttrs", true );
+				}
+			}
+
+			return data;
+		}
+
+		// Sets multiple values
+		if ( typeof key === "object" ) {
+			return this.each( function() {
+				dataUser.set( this, key );
+			} );
+		}
+
+		return access( this, function( value ) {
+			var data;
+
+			// The calling jQuery object (element matches) is not empty
+			// (and therefore has an element appears at this[ 0 ]) and the
+			// `value` parameter was not undefined. An empty jQuery object
+			// will result in `undefined` for elem = this[ 0 ] which will
+			// throw an exception if an attempt to read a data cache is made.
+			if ( elem && value === undefined ) {
+
+				// Attempt to get data from the cache
+				// The key will always be camelCased in Data
+				data = dataUser.get( elem, key );
+				if ( data !== undefined ) {
+					return data;
+				}
+
+				// Attempt to "discover" the data in
+				// HTML5 custom data-* attrs
+				data = dataAttr( elem, key );
+				if ( data !== undefined ) {
+					return data;
+				}
+
+				// We tried really hard, but the data doesn't exist.
+				return;
+			}
+
+			// Set the data...
+			this.each( function() {
+
+				// We always store the camelCased key
+				dataUser.set( this, key, value );
+			} );
+		}, null, value, arguments.length > 1, null, true );
+	},
+
+	removeData: function( key ) {
+		return this.each( function() {
+			dataUser.remove( this, key );
+		} );
+	}
+} );
+
+
+jQuery.extend( {
+	queue: function( elem, type, data ) {
+		var queue;
+
+		if ( elem ) {
+			type = ( type || "fx" ) + "queue";
+			queue = dataPriv.get( elem, type );
+
+			// Speed up dequeue by getting out quickly if this is just a lookup
+			if ( data ) {
+				if ( !queue || Array.isArray( data ) ) {
+					queue = dataPriv.access( elem, type, jQuery.makeArray( data ) );
+				} else {
+					queue.push( data );
+				}
+			}
+			return queue || [];
+		}
+	},
+
+	dequeue: function( elem, type ) {
+		type = type || "fx";
+
+		var queue = jQuery.queue( elem, type ),
+			startLength = queue.length,
+			fn = queue.shift(),
+			hooks = jQuery._queueHooks( elem, type ),
+			next = function() {
+				jQuery.dequeue( elem, type );
+			};
+
+		// If the fx queue is dequeued, always remove the progress sentinel
+		if ( fn === "inprogress" ) {
+			fn = queue.shift();
+			startLength--;
+		}
+
+		if ( fn ) {
+
+			// Add a progress sentinel to prevent the fx queue from being
+			// automatically dequeued
+			if ( type === "fx" ) {
+				queue.unshift( "inprogress" );
+			}
+
+			// Clear up the last queue stop function
+			delete hooks.stop;
+			fn.call( elem, next, hooks );
+		}
+
+		if ( !startLength && hooks ) {
+			hooks.empty.fire();
+		}
+	},
+
+	// Not public - generate a queueHooks object, or return the current one
+	_queueHooks: function( elem, type ) {
+		var key = type + "queueHooks";
+		return dataPriv.get( elem, key ) || dataPriv.access( elem, key, {
+			empty: jQuery.Callbacks( "once memory" ).add( function() {
+				dataPriv.remove( elem, [ type + "queue", key ] );
+			} )
+		} );
+	}
+} );
+
+jQuery.fn.extend( {
+	queue: function( type, data ) {
+		var setter = 2;
+
+		if ( typeof type !== "string" ) {
+			data = type;
+			type = "fx";
+			setter--;
+		}
+
+		if ( arguments.length < setter ) {
+			return jQuery.queue( this[ 0 ], type );
+		}
+
+		return data === undefined ?
+			this :
+			this.each( function() {
+				var queue = jQuery.queue( this, type, data );
+
+				// Ensure a hooks for this queue
+				jQuery._queueHooks( this, type );
+
+				if ( type === "fx" && queue[ 0 ] !== "inprogress" ) {
+					jQuery.dequeue( this, type );
+				}
+			} );
+	},
+	dequeue: function( type ) {
+		return this.each( function() {
+			jQuery.dequeue( this, type );
+		} );
+	},
+	clearQueue: function( type ) {
+		return this.queue( type || "fx", [] );
+	},
+
+	// Get a promise resolved when queues of a certain type
+	// are emptied (fx is the type by default)
+	promise: function( type, obj ) {
+		var tmp,
+			count = 1,
+			defer = jQuery.Deferred(),
+			elements = this,
+			i = this.length,
+			resolve = function() {
+				if ( !( --count ) ) {
+					defer.resolveWith( elements, [ elements ] );
+				}
+			};
+
+		if ( typeof type !== "string" ) {
+			obj = type;
+			type = undefined;
+		}
+		type = type || "fx";
+
+		while ( i-- ) {
+			tmp = dataPriv.get( elements[ i ], type + "queueHooks" );
+			if ( tmp && tmp.empty ) {
+				count++;
+				tmp.empty.add( resolve );
+			}
+		}
+		resolve();
+		return defer.promise( obj );
+	}
+} );
+var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source;
+
+var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" );
+
+
+var cssExpand = [ "Top", "Right", "Bottom", "Left" ];
+
+var documentElement = document.documentElement;
+
+
+
+	var isAttached = function( elem ) {
+			return jQuery.contains( elem.ownerDocument, elem );
+		},
+		composed = { composed: true };
+
+	// Support: IE 9 - 11+, Edge 12 - 18+, iOS 10.0 - 10.2 only
+	// Check attachment across shadow DOM boundaries when possible (gh-3504)
+	// Support: iOS 10.0-10.2 only
+	// Early iOS 10 versions support `attachShadow` but not `getRootNode`,
+	// leading to errors. We need to check for `getRootNode`.
+	if ( documentElement.getRootNode ) {
+		isAttached = function( elem ) {
+			return jQuery.contains( elem.ownerDocument, elem ) ||
+				elem.getRootNode( composed ) === elem.ownerDocument;
+		};
+	}
+var isHiddenWithinTree = function( elem, el ) {
+
+		// isHiddenWithinTree might be called from jQuery#filter function;
+		// in that case, element will be second argument
+		elem = el || elem;
+
+		// Inline style trumps all
+		return elem.style.display === "none" ||
+			elem.style.display === "" &&
+
+			// Otherwise, check computed style
+			// Support: Firefox <=43 - 45
+			// Disconnected elements can have computed display: none, so first confirm that elem is
+			// in the document.
+			isAttached( elem ) &&
+
+			jQuery.css( elem, "display" ) === "none";
+	};
+
+var swap = function( elem, options, callback, args ) {
+	var ret, name,
+		old = {};
+
+	// Remember the old values, and insert the new ones
+	for ( name in options ) {
+		old[ name ] = elem.style[ name ];
+		elem.style[ name ] = options[ name ];
+	}
+
+	ret = callback.apply( elem, args || [] );
+
+	// Revert the old values
+	for ( name in options ) {
+		elem.style[ name ] = old[ name ];
+	}
+
+	return ret;
+};
+
+
+
+
+function adjustCSS( elem, prop, valueParts, tween ) {
+	var adjusted, scale,
+		maxIterations = 20,
+		currentValue = tween ?
+			function() {
+				return tween.cur();
+			} :
+			function() {
+				return jQuery.css( elem, prop, "" );
+			},
+		initial = currentValue(),
+		unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
+
+		// Starting value computation is required for potential unit mismatches
+		initialInUnit = elem.nodeType &&
+			( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) &&
+			rcssNum.exec( jQuery.css( elem, prop ) );
+
+	if ( initialInUnit && initialInUnit[ 3 ] !== unit ) {
+
+		// Support: Firefox <=54
+		// Halve the iteration target value to prevent interference from CSS upper bounds (gh-2144)
+		initial = initial / 2;
+
+		// Trust units reported by jQuery.css
+		unit = unit || initialInUnit[ 3 ];
+
+		// Iteratively approximate from a nonzero starting point
+		initialInUnit = +initial || 1;
+
+		while ( maxIterations-- ) {
+
+			// Evaluate and update our best guess (doubling guesses that zero out).
+			// Finish if the scale equals or crosses 1 (making the old*new product non-positive).
+			jQuery.style( elem, prop, initialInUnit + unit );
+			if ( ( 1 - scale ) * ( 1 - ( scale = currentValue() / initial || 0.5 ) ) <= 0 ) {
+				maxIterations = 0;
+			}
+			initialInUnit = initialInUnit / scale;
+
+		}
+
+		initialInUnit = initialInUnit * 2;
+		jQuery.style( elem, prop, initialInUnit + unit );
+
+		// Make sure we update the tween properties later on
+		valueParts = valueParts || [];
+	}
+
+	if ( valueParts ) {
+		initialInUnit = +initialInUnit || +initial || 0;
+
+		// Apply relative offset (+=/-=) if specified
+		adjusted = valueParts[ 1 ] ?
+			initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] :
+			+valueParts[ 2 ];
+		if ( tween ) {
+			tween.unit = unit;
+			tween.start = initialInUnit;
+			tween.end = adjusted;
+		}
+	}
+	return adjusted;
+}
+
+
+var defaultDisplayMap = {};
+
+function getDefaultDisplay( elem ) {
+	var temp,
+		doc = elem.ownerDocument,
+		nodeName = elem.nodeName,
+		display = defaultDisplayMap[ nodeName ];
+
+	if ( display ) {
+		return display;
+	}
+
+	temp = doc.body.appendChild( doc.createElement( nodeName ) );
+	display = jQuery.css( temp, "display" );
+
+	temp.parentNode.removeChild( temp );
+
+	if ( display === "none" ) {
+		display = "block";
+	}
+	defaultDisplayMap[ nodeName ] = display;
+
+	return display;
+}
+
+function showHide( elements, show ) {
+	var display, elem,
+		values = [],
+		index = 0,
+		length = elements.length;
+
+	// Determine new display value for elements that need to change
+	for ( ; index < length; index++ ) {
+		elem = elements[ index ];
+		if ( !elem.style ) {
+			continue;
+		}
+
+		display = elem.style.display;
+		if ( show ) {
+
+			// Since we force visibility upon cascade-hidden elements, an immediate (and slow)
+			// check is required in this first loop unless we have a nonempty display value (either
+			// inline or about-to-be-restored)
+			if ( display === "none" ) {
+				values[ index ] = dataPriv.get( elem, "display" ) || null;
+				if ( !values[ index ] ) {
+					elem.style.display = "";
+				}
+			}
+			if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) {
+				values[ index ] = getDefaultDisplay( elem );
+			}
+		} else {
+			if ( display !== "none" ) {
+				values[ index ] = "none";
+
+				// Remember what we're overwriting
+				dataPriv.set( elem, "display", display );
+			}
+		}
+	}
+
+	// Set the display of the elements in a second loop to avoid constant reflow
+	for ( index = 0; index < length; index++ ) {
+		if ( values[ index ] != null ) {
+			elements[ index ].style.display = values[ index ];
+		}
+	}
+
+	return elements;
+}
+
+jQuery.fn.extend( {
+	show: function() {
+		return showHide( this, true );
+	},
+	hide: function() {
+		return showHide( this );
+	},
+	toggle: function( state ) {
+		if ( typeof state === "boolean" ) {
+			return state ? this.show() : this.hide();
+		}
+
+		return this.each( function() {
+			if ( isHiddenWithinTree( this ) ) {
+				jQuery( this ).show();
+			} else {
+				jQuery( this ).hide();
+			}
+		} );
+	}
+} );
+var rcheckableType = ( /^(?:checkbox|radio)$/i );
+
+var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]*)/i );
+
+var rscriptType = ( /^$|^module$|\/(?:java|ecma)script/i );
+
+
+
+// We have to close these tags to support XHTML (#13200)
+var wrapMap = {
+
+	// Support: IE <=9 only
+	option: [ 1, "<select multiple='multiple'>", "</select>" ],
+
+	// XHTML parsers do not magically insert elements in the
+	// same way that tag soup parsers do. So we cannot shorten
+	// this by omitting <tbody> or other required elements.
+	thead: [ 1, "<table>", "</table>" ],
+	col: [ 2, "<table><colgroup>", "</colgroup></table>" ],
+	tr: [ 2, "<table><tbody>", "</tbody></table>" ],
+	td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ],
+
+	_default: [ 0, "", "" ]
+};
+
+// Support: IE <=9 only
+wrapMap.optgroup = wrapMap.option;
+
+wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
+wrapMap.th = wrapMap.td;
+
+
+function getAll( context, tag ) {
+
+	// Support: IE <=9 - 11 only
+	// Use typeof to avoid zero-argument method invocation on host objects (#15151)
+	var ret;
+
+	if ( typeof context.getElementsByTagName !== "undefined" ) {
+		ret = context.getElementsByTagName( tag || "*" );
+
+	} else if ( typeof context.querySelectorAll !== "undefined" ) {
+		ret = context.querySelectorAll( tag || "*" );
+
+	} else {
+		ret = [];
+	}
+
+	if ( tag === undefined || tag && nodeName( context, tag ) ) {
+		return jQuery.merge( [ context ], ret );
+	}
+
+	return ret;
+}
+
+
+// Mark scripts as having already been evaluated
+function setGlobalEval( elems, refElements ) {
+	var i = 0,
+		l = elems.length;
+
+	for ( ; i < l; i++ ) {
+		dataPriv.set(
+			elems[ i ],
+			"globalEval",
+			!refElements || dataPriv.get( refElements[ i ], "globalEval" )
+		);
+	}
+}
+
+
+var rhtml = /<|&#?\w+;/;
+
+function buildFragment( elems, context, scripts, selection, ignored ) {
+	var elem, tmp, tag, wrap, attached, j,
+		fragment = context.createDocumentFragment(),
+		nodes = [],
+		i = 0,
+		l = elems.length;
+
+	for ( ; i < l; i++ ) {
+		elem = elems[ i ];
+
+		if ( elem || elem === 0 ) {
+
+			// Add nodes directly
+			if ( toType( elem ) === "object" ) {
+
+				// Support: Android <=4.0 only, PhantomJS 1 only
+				// push.apply(_, arraylike) throws on ancient WebKit
+				jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );
+
+			// Convert non-html into a text node
+			} else if ( !rhtml.test( elem ) ) {
+				nodes.push( context.createTextNode( elem ) );
+
+			// Convert html into DOM nodes
+			} else {
+				tmp = tmp || fragment.appendChild( context.createElement( "div" ) );
+
+				// Deserialize a standard representation
+				tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase();
+				wrap = wrapMap[ tag ] || wrapMap._default;
+				tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ];
+
+				// Descend through wrappers to the right content
+				j = wrap[ 0 ];
+				while ( j-- ) {
+					tmp = tmp.lastChild;
+				}
+
+				// Support: Android <=4.0 only, PhantomJS 1 only
+				// push.apply(_, arraylike) throws on ancient WebKit
+				jQuery.merge( nodes, tmp.childNodes );
+
+				// Remember the top-level container
+				tmp = fragment.firstChild;
+
+				// Ensure the created nodes are orphaned (#12392)
+				tmp.textContent = "";
+			}
+		}
+	}
+
+	// Remove wrapper from fragment
+	fragment.textContent = "";
+
+	i = 0;
+	while ( ( elem = nodes[ i++ ] ) ) {
+
+		// Skip elements already in the context collection (trac-4087)
+		if ( selection && jQuery.inArray( elem, selection ) > -1 ) {
+			if ( ignored ) {
+				ignored.push( elem );
+			}
+			continue;
+		}
+
+		attached = isAttached( elem );
+
+		// Append to fragment
+		tmp = getAll( fragment.appendChild( elem ), "script" );
+
+		// Preserve script evaluation history
+		if ( attached ) {
+			setGlobalEval( tmp );
+		}
+
+		// Capture executables
+		if ( scripts ) {
+			j = 0;
+			while ( ( elem = tmp[ j++ ] ) ) {
+				if ( rscriptType.test( elem.type || "" ) ) {
+					scripts.push( elem );
+				}
+			}
+		}
+	}
+
+	return fragment;
+}
+
+
+( function() {
+	var fragment = document.createDocumentFragment(),
+		div = fragment.appendChild( document.createElement( "div" ) ),
+		input = document.createElement( "input" );
+
+	// Support: Android 4.0 - 4.3 only
+	// Check state lost if the name is set (#11217)
+	// Support: Windows Web Apps (WWA)
+	// `name` and `type` must use .setAttribute for WWA (#14901)
+	input.setAttribute( "type", "radio" );
+	input.setAttribute( "checked", "checked" );
+	input.setAttribute( "name", "t" );
+
+	div.appendChild( input );
+
+	// Support: Android <=4.1 only
+	// Older WebKit doesn't clone checked state correctly in fragments
+	support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
+
+	// Support: IE <=11 only
+	// Make sure textarea (and checkbox) defaultValue is properly cloned
+	div.innerHTML = "<textarea>x</textarea>";
+	support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
+} )();
+
+
+var
+	rkeyEvent = /^key/,
+	rmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/,
+	rtypenamespace = /^([^.]*)(?:\.(.+)|)/;
+
+function returnTrue() {
+	return true;
+}
+
+function returnFalse() {
+	return false;
+}
+
+// Support: IE <=9 - 11+
+// focus() and blur() are asynchronous, except when they are no-op.
+// So expect focus to be synchronous when the element is already active,
+// and blur to be synchronous when the element is not already active.
+// (focus and blur are always synchronous in other supported browsers,
+// this just defines when we can count on it).
+function expectSync( elem, type ) {
+	return ( elem === safeActiveElement() ) === ( type === "focus" );
+}
+
+// Support: IE <=9 only
+// Accessing document.activeElement can throw unexpectedly
+// https://bugs.jquery.com/ticket/13393
+function safeActiveElement() {
+	try {
+		return document.activeElement;
+	} catch ( err ) { }
+}
+
+function on( elem, types, selector, data, fn, one ) {
+	var origFn, type;
+
+	// Types can be a map of types/handlers
+	if ( typeof types === "object" ) {
+
+		// ( types-Object, selector, data )
+		if ( typeof selector !== "string" ) {
+
+			// ( types-Object, data )
+			data = data || selector;
+			selector = undefined;
+		}
+		for ( type in types ) {
+			on( elem, type, selector, data, types[ type ], one );
+		}
+		return elem;
+	}
+
+	if ( data == null && fn == null ) {
+
+		// ( types, fn )
+		fn = selector;
+		data = selector = undefined;
+	} else if ( fn == null ) {
+		if ( typeof selector === "string" ) {
+
+			// ( types, selector, fn )
+			fn = data;
+			data = undefined;
+		} else {
+
+			// ( types, data, fn )
+			fn = data;
+			data = selector;
+			selector = undefined;
+		}
+	}
+	if ( fn === false ) {
+		fn = returnFalse;
+	} else if ( !fn ) {
+		return elem;
+	}
+
+	if ( one === 1 ) {
+		origFn = fn;
+		fn = function( event ) {
+
+			// Can use an empty set, since event contains the info
+			jQuery().off( event );
+			return origFn.apply( this, arguments );
+		};
+
+		// Use same guid so caller can remove using origFn
+		fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
+	}
+	return elem.each( function() {
+		jQuery.event.add( this, types, fn, data, selector );
+	} );
+}
+
+/*
+ * Helper functions for managing events -- not part of the public interface.
+ * Props to Dean Edwards' addEvent library for many of the ideas.
+ */
+jQuery.event = {
+
+	global: {},
+
+	add: function( elem, types, handler, data, selector ) {
+
+		var handleObjIn, eventHandle, tmp,
+			events, t, handleObj,
+			special, handlers, type, namespaces, origType,
+			elemData = dataPriv.get( elem );
+
+		// Don't attach events to noData or text/comment nodes (but allow plain objects)
+		if ( !elemData ) {
+			return;
+		}
+
+		// Caller can pass in an object of custom data in lieu of the handler
+		if ( handler.handler ) {
+			handleObjIn = handler;
+			handler = handleObjIn.handler;
+			selector = handleObjIn.selector;
+		}
+
+		// Ensure that invalid selectors throw exceptions at attach time
+		// Evaluate against documentElement in case elem is a non-element node (e.g., document)
+		if ( selector ) {
+			jQuery.find.matchesSelector( documentElement, selector );
+		}
+
+		// Make sure that the handler has a unique ID, used to find/remove it later
+		if ( !handler.guid ) {
+			handler.guid = jQuery.guid++;
+		}
+
+		// Init the element's event structure and main handler, if this is the first
+		if ( !( events = elemData.events ) ) {
+			events = elemData.events = {};
+		}
+		if ( !( eventHandle = elemData.handle ) ) {
+			eventHandle = elemData.handle = function( e ) {
+
+				// Discard the second event of a jQuery.event.trigger() and
+				// when an event is called after a page has unloaded
+				return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ?
+					jQuery.event.dispatch.apply( elem, arguments ) : undefined;
+			};
+		}
+
+		// Handle multiple events separated by a space
+		types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
+		t = types.length;
+		while ( t-- ) {
+			tmp = rtypenamespace.exec( types[ t ] ) || [];
+			type = origType = tmp[ 1 ];
+			namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
+
+			// There *must* be a type, no attaching namespace-only handlers
+			if ( !type ) {
+				continue;
+			}
+
+			// If event changes its type, use the special event handlers for the changed type
+			special = jQuery.event.special[ type ] || {};
+
+			// If selector defined, determine special event api type, otherwise given type
+			type = ( selector ? special.delegateType : special.bindType ) || type;
+
+			// Update special based on newly reset type
+			special = jQuery.event.special[ type ] || {};
+
+			// handleObj is passed to all event handlers
+			handleObj = jQuery.extend( {
+				type: type,
+				origType: origType,
+				data: data,
+				handler: handler,
+				guid: handler.guid,
+				selector: selector,
+				needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
+				namespace: namespaces.join( "." )
+			}, handleObjIn );
+
+			// Init the event handler queue if we're the first
+			if ( !( handlers = events[ type ] ) ) {
+				handlers = events[ type ] = [];
+				handlers.delegateCount = 0;
+
+				// Only use addEventListener if the special events handler returns false
+				if ( !special.setup ||
+					special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
+
+					if ( elem.addEventListener ) {
+						elem.addEventListener( type, eventHandle );
+					}
+				}
+			}
+
+			if ( special.add ) {
+				special.add.call( elem, handleObj );
+
+				if ( !handleObj.handler.guid ) {
+					handleObj.handler.guid = handler.guid;
+				}
+			}
+
+			// Add to the element's handler list, delegates in front
+			if ( selector ) {
+				handlers.splice( handlers.delegateCount++, 0, handleObj );
+			} else {
+				handlers.push( handleObj );
+			}
+
+			// Keep track of which events have ever been used, for event optimization
+			jQuery.event.global[ type ] = true;
+		}
+
+	},
+
+	// Detach an event or set of events from an element
+	remove: function( elem, types, handler, selector, mappedTypes ) {
+
+		var j, origCount, tmp,
+			events, t, handleObj,
+			special, handlers, type, namespaces, origType,
+			elemData = dataPriv.hasData( elem ) && dataPriv.get( elem );
+
+		if ( !elemData || !( events = elemData.events ) ) {
+			return;
+		}
+
+		// Once for each type.namespace in types; type may be omitted
+		types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
+		t = types.length;
+		while ( t-- ) {
+			tmp = rtypenamespace.exec( types[ t ] ) || [];
+			type = origType = tmp[ 1 ];
+			namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
+
+			// Unbind all events (on this namespace, if provided) for the element
+			if ( !type ) {
+				for ( type in events ) {
+					jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
+				}
+				continue;
+			}
+
+			special = jQuery.event.special[ type ] || {};
+			type = ( selector ? special.delegateType : special.bindType ) || type;
+			handlers = events[ type ] || [];
+			tmp = tmp[ 2 ] &&
+				new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" );
+
+			// Remove matching events
+			origCount = j = handlers.length;
+			while ( j-- ) {
+				handleObj = handlers[ j ];
+
+				if ( ( mappedTypes || origType === handleObj.origType ) &&
+					( !handler || handler.guid === handleObj.guid ) &&
+					( !tmp || tmp.test( handleObj.namespace ) ) &&
+					( !selector || selector === handleObj.selector ||
+						selector === "**" && handleObj.selector ) ) {
+					handlers.splice( j, 1 );
+
+					if ( handleObj.selector ) {
+						handlers.delegateCount--;
+					}
+					if ( special.remove ) {
+						special.remove.call( elem, handleObj );
+					}
+				}
+			}
+
+			// Remove generic event handler if we removed something and no more handlers exist
+			// (avoids potential for endless recursion during removal of special event handlers)
+			if ( origCount && !handlers.length ) {
+				if ( !special.teardown ||
+					special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
+
+					jQuery.removeEvent( elem, type, elemData.handle );
+				}
+
+				delete events[ type ];
+			}
+		}
+
+		// Remove data and the expando if it's no longer used
+		if ( jQuery.isEmptyObject( events ) ) {
+			dataPriv.remove( elem, "handle events" );
+		}
+	},
+
+	dispatch: function( nativeEvent ) {
+
+		// Make a writable jQuery.Event from the native event object
+		var event = jQuery.event.fix( nativeEvent );
+
+		var i, j, ret, matched, handleObj, handlerQueue,
+			args = new Array( arguments.length ),
+			handlers = ( dataPriv.get( this, "events" ) || {} )[ event.type ] || [],
+			special = jQuery.event.special[ event.type ] || {};
+
+		// Use the fix-ed jQuery.Event rather than the (read-only) native event
+		args[ 0 ] = event;
+
+		for ( i = 1; i < arguments.length; i++ ) {
+			args[ i ] = arguments[ i ];
+		}
+
+		event.delegateTarget = this;
+
+		// Call the preDispatch hook for the mapped type, and let it bail if desired
+		if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
+			return;
+		}
+
+		// Determine handlers
+		handlerQueue = jQuery.event.handlers.call( this, event, handlers );
+
+		// Run delegates first; they may want to stop propagation beneath us
+		i = 0;
+		while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) {
+			event.currentTarget = matched.elem;
+
+			j = 0;
+			while ( ( handleObj = matched.handlers[ j++ ] ) &&
+				!event.isImmediatePropagationStopped() ) {
+
+				// If the event is namespaced, then each handler is only invoked if it is
+				// specially universal or its namespaces are a superset of the event's.
+				if ( !event.rnamespace || handleObj.namespace === false ||
+					event.rnamespace.test( handleObj.namespace ) ) {
+
+					event.handleObj = handleObj;
+					event.data = handleObj.data;
+
+					ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle ||
+						handleObj.handler ).apply( matched.elem, args );
+
+					if ( ret !== undefined ) {
+						if ( ( event.result = ret ) === false ) {
+							event.preventDefault();
+							event.stopPropagation();
+						}
+					}
+				}
+			}
+		}
+
+		// Call the postDispatch hook for the mapped type
+		if ( special.postDispatch ) {
+			special.postDispatch.call( this, event );
+		}
+
+		return event.result;
+	},
+
+	handlers: function( event, handlers ) {
+		var i, handleObj, sel, matchedHandlers, matchedSelectors,
+			handlerQueue = [],
+			delegateCount = handlers.delegateCount,
+			cur = event.target;
+
+		// Find delegate handlers
+		if ( delegateCount &&
+
+			// Support: IE <=9
+			// Black-hole SVG <use> instance trees (trac-13180)
+			cur.nodeType &&
+
+			// Support: Firefox <=42
+			// Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861)
+			// https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click
+			// Support: IE 11 only
+			// ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343)
+			!( event.type === "click" && event.button >= 1 ) ) {
+
+			for ( ; cur !== this; cur = cur.parentNode || this ) {
+
+				// Don't check non-elements (#13208)
+				// Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
+				if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) {
+					matchedHandlers = [];
+					matchedSelectors = {};
+					for ( i = 0; i < delegateCount; i++ ) {
+						handleObj = handlers[ i ];
+
+						// Don't conflict with Object.prototype properties (#13203)
+						sel = handleObj.selector + " ";
+
+						if ( matchedSelectors[ sel ] === undefined ) {
+							matchedSelectors[ sel ] = handleObj.needsContext ?
+								jQuery( sel, this ).index( cur ) > -1 :
+								jQuery.find( sel, this, null, [ cur ] ).length;
+						}
+						if ( matchedSelectors[ sel ] ) {
+							matchedHandlers.push( handleObj );
+						}
+					}
+					if ( matchedHandlers.length ) {
+						handlerQueue.push( { elem: cur, handlers: matchedHandlers } );
+					}
+				}
+			}
+		}
+
+		// Add the remaining (directly-bound) handlers
+		cur = this;
+		if ( delegateCount < handlers.length ) {
+			handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } );
+		}
+
+		return handlerQueue;
+	},
+
+	addProp: function( name, hook ) {
+		Object.defineProperty( jQuery.Event.prototype, name, {
+			enumerable: true,
+			configurable: true,
+
+			get: isFunction( hook ) ?
+				function() {
+					if ( this.originalEvent ) {
+							return hook( this.originalEvent );
+					}
+				} :
+				function() {
+					if ( this.originalEvent ) {
+							return this.originalEvent[ name ];
+					}
+				},
+
+			set: function( value ) {
+				Object.defineProperty( this, name, {
+					enumerable: true,
+					configurable: true,
+					writable: true,
+					value: value
+				} );
+			}
+		} );
+	},
+
+	fix: function( originalEvent ) {
+		return originalEvent[ jQuery.expando ] ?
+			originalEvent :
+			new jQuery.Event( originalEvent );
+	},
+
+	special: {
+		load: {
+
+			// Prevent triggered image.load events from bubbling to window.load
+			noBubble: true
+		},
+		click: {
+
+			// Utilize native event to ensure correct state for checkable inputs
+			setup: function( data ) {
+
+				// For mutual compressibility with _default, replace `this` access with a local var.
+				// `|| data` is dead code meant only to preserve the variable through minification.
+				var el = this || data;
+
+				// Claim the first handler
+				if ( rcheckableType.test( el.type ) &&
+					el.click && nodeName( el, "input" ) ) {
+
+					// dataPriv.set( el, "click", ... )
+					leverageNative( el, "click", returnTrue );
+				}
+
+				// Return false to allow normal processing in the caller
+				return false;
+			},
+			trigger: function( data ) {
+
+				// For mutual compressibility with _default, replace `this` access with a local var.
+				// `|| data` is dead code meant only to preserve the variable through minification.
+				var el = this || data;
+
+				// Force setup before triggering a click
+				if ( rcheckableType.test( el.type ) &&
+					el.click && nodeName( el, "input" ) ) {
+
+					leverageNative( el, "click" );
+				}
+
+				// Return non-false to allow normal event-path propagation
+				return true;
+			},
+
+			// For cross-browser consistency, suppress native .click() on links
+			// Also prevent it if we're currently inside a leveraged native-event stack
+			_default: function( event ) {
+				var target = event.target;
+				return rcheckableType.test( target.type ) &&
+					target.click && nodeName( target, "input" ) &&
+					dataPriv.get( target, "click" ) ||
+					nodeName( target, "a" );
+			}
+		},
+
+		beforeunload: {
+			postDispatch: function( event ) {
+
+				// Support: Firefox 20+
+				// Firefox doesn't alert if the returnValue field is not set.
+				if ( event.result !== undefined && event.originalEvent ) {
+					event.originalEvent.returnValue = event.result;
+				}
+			}
+		}
+	}
+};
+
+// Ensure the presence of an event listener that handles manually-triggered
+// synthetic events by interrupting progress until reinvoked in response to
+// *native* events that it fires directly, ensuring that state changes have
+// already occurred before other listeners are invoked.
+function leverageNative( el, type, expectSync ) {
+
+	// Missing expectSync indicates a trigger call, which must force setup through jQuery.event.add
+	if ( !expectSync ) {
+		if ( dataPriv.get( el, type ) === undefined ) {
+			jQuery.event.add( el, type, returnTrue );
+		}
+		return;
+	}
+
+	// Register the controller as a special universal handler for all event namespaces
+	dataPriv.set( el, type, false );
+	jQuery.event.add( el, type, {
+		namespace: false,
+		handler: function( event ) {
+			var notAsync, result,
+				saved = dataPriv.get( this, type );
+
+			if ( ( event.isTrigger & 1 ) && this[ type ] ) {
+
+				// Interrupt processing of the outer synthetic .trigger()ed event
+				// Saved data should be false in such cases, but might be a leftover capture object
+				// from an async native handler (gh-4350)
+				if ( !saved.length ) {
+
+					// Store arguments for use when handling the inner native event
+					// There will always be at least one argument (an event object), so this array
+					// will not be confused with a leftover capture object.
+					saved = slice.call( arguments );
+					dataPriv.set( this, type, saved );
+
+					// Trigger the native event and capture its result
+					// Support: IE <=9 - 11+
+					// focus() and blur() are asynchronous
+					notAsync = expectSync( this, type );
+					this[ type ]();
+					result = dataPriv.get( this, type );
+					if ( saved !== result || notAsync ) {
+						dataPriv.set( this, type, false );
+					} else {
+						result = {};
+					}
+					if ( saved !== result ) {
+
+						// Cancel the outer synthetic event
+						event.stopImmediatePropagation();
+						event.preventDefault();
+						return result.value;
+					}
+
+				// If this is an inner synthetic event for an event with a bubbling surrogate
+				// (focus or blur), assume that the surrogate already propagated from triggering the
+				// native event and prevent that from happening again here.
+				// This technically gets the ordering wrong w.r.t. to `.trigger()` (in which the
+				// bubbling surrogate propagates *after* the non-bubbling base), but that seems
+				// less bad than duplication.
+				} else if ( ( jQuery.event.special[ type ] || {} ).delegateType ) {
+					event.stopPropagation();
+				}
+
+			// If this is a native event triggered above, everything is now in order
+			// Fire an inner synthetic event with the original arguments
+			} else if ( saved.length ) {
+
+				// ...and capture the result
+				dataPriv.set( this, type, {
+					value: jQuery.event.trigger(
+
+						// Support: IE <=9 - 11+
+						// Extend with the prototype to reset the above stopImmediatePropagation()
+						jQuery.extend( saved[ 0 ], jQuery.Event.prototype ),
+						saved.slice( 1 ),
+						this
+					)
+				} );
+
+				// Abort handling of the native event
+				event.stopImmediatePropagation();
+			}
+		}
+	} );
+}
+
+jQuery.removeEvent = function( elem, type, handle ) {
+
+	// This "if" is needed for plain objects
+	if ( elem.removeEventListener ) {
+		elem.removeEventListener( type, handle );
+	}
+};
+
+jQuery.Event = function( src, props ) {
+
+	// Allow instantiation without the 'new' keyword
+	if ( !( this instanceof jQuery.Event ) ) {
+		return new jQuery.Event( src, props );
+	}
+
+	// Event object
+	if ( src && src.type ) {
+		this.originalEvent = src;
+		this.type = src.type;
+
+		// Events bubbling up the document may have been marked as prevented
+		// by a handler lower down the tree; reflect the correct value.
+		this.isDefaultPrevented = src.defaultPrevented ||
+				src.defaultPrevented === undefined &&
+
+				// Support: Android <=2.3 only
+				src.returnValue === false ?
+			returnTrue :
+			returnFalse;
+
+		// Create target properties
+		// Support: Safari <=6 - 7 only
+		// Target should not be a text node (#504, #13143)
+		this.target = ( src.target && src.target.nodeType === 3 ) ?
+			src.target.parentNode :
+			src.target;
+
+		this.currentTarget = src.currentTarget;
+		this.relatedTarget = src.relatedTarget;
+
+	// Event type
+	} else {
+		this.type = src;
+	}
+
+	// Put explicitly provided properties onto the event object
+	if ( props ) {
+		jQuery.extend( this, props );
+	}
+
+	// Create a timestamp if incoming event doesn't have one
+	this.timeStamp = src && src.timeStamp || Date.now();
+
+	// Mark it as fixed
+	this[ jQuery.expando ] = true;
+};
+
+// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
+// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
+jQuery.Event.prototype = {
+	constructor: jQuery.Event,
+	isDefaultPrevented: returnFalse,
+	isPropagationStopped: returnFalse,
+	isImmediatePropagationStopped: returnFalse,
+	isSimulated: false,
+
+	preventDefault: function() {
+		var e = this.originalEvent;
+
+		this.isDefaultPrevented = returnTrue;
+
+		if ( e && !this.isSimulated ) {
+			e.preventDefault();
+		}
+	},
+	stopPropagation: function() {
+		var e = this.originalEvent;
+
+		this.isPropagationStopped = returnTrue;
+
+		if ( e && !this.isSimulated ) {
+			e.stopPropagation();
+		}
+	},
+	stopImmediatePropagation: function() {
+		var e = this.originalEvent;
+
+		this.isImmediatePropagationStopped = returnTrue;
+
+		if ( e && !this.isSimulated ) {
+			e.stopImmediatePropagation();
+		}
+
+		this.stopPropagation();
+	}
+};
+
+// Includes all common event props including KeyEvent and MouseEvent specific props
+jQuery.each( {
+	altKey: true,
+	bubbles: true,
+	cancelable: true,
+	changedTouches: true,
+	ctrlKey: true,
+	detail: true,
+	eventPhase: true,
+	metaKey: true,
+	pageX: true,
+	pageY: true,
+	shiftKey: true,
+	view: true,
+	"char": true,
+	code: true,
+	charCode: true,
+	key: true,
+	keyCode: true,
+	button: true,
+	buttons: true,
+	clientX: true,
+	clientY: true,
+	offsetX: true,
+	offsetY: true,
+	pointerId: true,
+	pointerType: true,
+	screenX: true,
+	screenY: true,
+	targetTouches: true,
+	toElement: true,
+	touches: true,
+
+	which: function( event ) {
+		var button = event.button;
+
+		// Add which for key events
+		if ( event.which == null && rkeyEvent.test( event.type ) ) {
+			return event.charCode != null ? event.charCode : event.keyCode;
+		}
+
+		// Add which for click: 1 === left; 2 === middle; 3 === right
+		if ( !event.which && button !== undefined && rmouseEvent.test( event.type ) ) {
+			if ( button & 1 ) {
+				return 1;
+			}
+
+			if ( button & 2 ) {
+				return 3;
+			}
+
+			if ( button & 4 ) {
+				return 2;
+			}
+
+			return 0;
+		}
+
+		return event.which;
+	}
+}, jQuery.event.addProp );
+
+jQuery.each( { focus: "focusin", blur: "focusout" }, function( type, delegateType ) {
+	jQuery.event.special[ type ] = {
+
+		// Utilize native event if possible so blur/focus sequence is correct
+		setup: function() {
+
+			// Claim the first handler
+			// dataPriv.set( this, "focus", ... )
+			// dataPriv.set( this, "blur", ... )
+			leverageNative( this, type, expectSync );
+
+			// Return false to allow normal processing in the caller
+			return false;
+		},
+		trigger: function() {
+
+			// Force setup before trigger
+			leverageNative( this, type );
+
+			// Return non-false to allow normal event-path propagation
+			return true;
+		},
+
+		delegateType: delegateType
+	};
+} );
+
+// Create mouseenter/leave events using mouseover/out and event-time checks
+// so that event delegation works in jQuery.
+// Do the same for pointerenter/pointerleave and pointerover/pointerout
+//
+// Support: Safari 7 only
+// Safari sends mouseenter too often; see:
+// https://bugs.chromium.org/p/chromium/issues/detail?id=470258
+// for the description of the bug (it existed in older Chrome versions as well).
+jQuery.each( {
+	mouseenter: "mouseover",
+	mouseleave: "mouseout",
+	pointerenter: "pointerover",
+	pointerleave: "pointerout"
+}, function( orig, fix ) {
+	jQuery.event.special[ orig ] = {
+		delegateType: fix,
+		bindType: fix,
+
+		handle: function( event ) {
+			var ret,
+				target = this,
+				related = event.relatedTarget,
+				handleObj = event.handleObj;
+
+			// For mouseenter/leave call the handler if related is outside the target.
+			// NB: No relatedTarget if the mouse left/entered the browser window
+			if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) {
+				event.type = handleObj.origType;
+				ret = handleObj.handler.apply( this, arguments );
+				event.type = fix;
+			}
+			return ret;
+		}
+	};
+} );
+
+jQuery.fn.extend( {
+
+	on: function( types, selector, data, fn ) {
+		return on( this, types, selector, data, fn );
+	},
+	one: function( types, selector, data, fn ) {
+		return on( this, types, selector, data, fn, 1 );
+	},
+	off: function( types, selector, fn ) {
+		var handleObj, type;
+		if ( types && types.preventDefault && types.handleObj ) {
+
+			// ( event )  dispatched jQuery.Event
+			handleObj = types.handleObj;
+			jQuery( types.delegateTarget ).off(
+				handleObj.namespace ?
+					handleObj.origType + "." + handleObj.namespace :
+					handleObj.origType,
+				handleObj.selector,
+				handleObj.handler
+			);
+			return this;
+		}
+		if ( typeof types === "object" ) {
+
+			// ( types-object [, selector] )
+			for ( type in types ) {
+				this.off( type, selector, types[ type ] );
+			}
+			return this;
+		}
+		if ( selector === false || typeof selector === "function" ) {
+
+			// ( types [, fn] )
+			fn = selector;
+			selector = undefined;
+		}
+		if ( fn === false ) {
+			fn = returnFalse;
+		}
+		return this.each( function() {
+			jQuery.event.remove( this, types, fn, selector );
+		} );
+	}
+} );
+
+
+var
+
+	/* eslint-disable max-len */
+
+	// See https://github.com/eslint/eslint/issues/3229
+	rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([a-z][^\/\0>\x20\t\r\n\f]*)[^>]*)\/>/gi,
+
+	/* eslint-enable */
+
+	// Support: IE <=10 - 11, Edge 12 - 13 only
+	// In IE/Edge using regex groups here causes severe slowdowns.
+	// See https://connect.microsoft.com/IE/feedback/details/1736512/
+	rnoInnerhtml = /<script|<style|<link/i,
+
+	// checked="checked" or checked
+	rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i,
+	rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g;
+
+// Prefer a tbody over its parent table for containing new rows
+function manipulationTarget( elem, content ) {
+	if ( nodeName( elem, "table" ) &&
+		nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) {
+
+		return jQuery( elem ).children( "tbody" )[ 0 ] || elem;
+	}
+
+	return elem;
+}
+
+// Replace/restore the type attribute of script elements for safe DOM manipulation
+function disableScript( elem ) {
+	elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type;
+	return elem;
+}
+function restoreScript( elem ) {
+	if ( ( elem.type || "" ).slice( 0, 5 ) === "true/" ) {
+		elem.type = elem.type.slice( 5 );
+	} else {
+		elem.removeAttribute( "type" );
+	}
+
+	return elem;
+}
+
+function cloneCopyEvent( src, dest ) {
+	var i, l, type, pdataOld, pdataCur, udataOld, udataCur, events;
+
+	if ( dest.nodeType !== 1 ) {
+		return;
+	}
+
+	// 1. Copy private data: events, handlers, etc.
+	if ( dataPriv.hasData( src ) ) {
+		pdataOld = dataPriv.access( src );
+		pdataCur = dataPriv.set( dest, pdataOld );
+		events = pdataOld.events;
+
+		if ( events ) {
+			delete pdataCur.handle;
+			pdataCur.events = {};
+
+			for ( type in events ) {
+				for ( i = 0, l = events[ type ].length; i < l; i++ ) {
+					jQuery.event.add( dest, type, events[ type ][ i ] );
+				}
+			}
+		}
+	}
+
+	// 2. Copy user data
+	if ( dataUser.hasData( src ) ) {
+		udataOld = dataUser.access( src );
+		udataCur = jQuery.extend( {}, udataOld );
+
+		dataUser.set( dest, udataCur );
+	}
+}
+
+// Fix IE bugs, see support tests
+function fixInput( src, dest ) {
+	var nodeName = dest.nodeName.toLowerCase();
+
+	// Fails to persist the checked state of a cloned checkbox or radio button.
+	if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
+		dest.checked = src.checked;
+
+	// Fails to return the selected option to the default selected state when cloning options
+	} else if ( nodeName === "input" || nodeName === "textarea" ) {
+		dest.defaultValue = src.defaultValue;
+	}
+}
+
+function domManip( collection, args, callback, ignored ) {
+
+	// Flatten any nested arrays
+	args = concat.apply( [], args );
+
+	var fragment, first, scripts, hasScripts, node, doc,
+		i = 0,
+		l = collection.length,
+		iNoClone = l - 1,
+		value = args[ 0 ],
+		valueIsFunction = isFunction( value );
+
+	// We can't cloneNode fragments that contain checked, in WebKit
+	if ( valueIsFunction ||
+			( l > 1 && typeof value === "string" &&
+				!support.checkClone && rchecked.test( value ) ) ) {
+		return collection.each( function( index ) {
+			var self = collection.eq( index );
+			if ( valueIsFunction ) {
+				args[ 0 ] = value.call( this, index, self.html() );
+			}
+			domManip( self, args, callback, ignored );
+		} );
+	}
+
+	if ( l ) {
+		fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored );
+		first = fragment.firstChild;
+
+		if ( fragment.childNodes.length === 1 ) {
+			fragment = first;
+		}
+
+		// Require either new content or an interest in ignored elements to invoke the callback
+		if ( first || ignored ) {
+			scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
+			hasScripts = scripts.length;
+
+			// Use the original fragment for the last item
+			// instead of the first because it can end up
+			// being emptied incorrectly in certain situations (#8070).
+			for ( ; i < l; i++ ) {
+				node = fragment;
+
+				if ( i !== iNoClone ) {
+					node = jQuery.clone( node, true, true );
+
+					// Keep references to cloned scripts for later restoration
+					if ( hasScripts ) {
+
+						// Support: Android <=4.0 only, PhantomJS 1 only
+						// push.apply(_, arraylike) throws on ancient WebKit
+						jQuery.merge( scripts, getAll( node, "script" ) );
+					}
+				}
+
+				callback.call( collection[ i ], node, i );
+			}
+
+			if ( hasScripts ) {
+				doc = scripts[ scripts.length - 1 ].ownerDocument;
+
+				// Reenable scripts
+				jQuery.map( scripts, restoreScript );
+
+				// Evaluate executable scripts on first document insertion
+				for ( i = 0; i < hasScripts; i++ ) {
+					node = scripts[ i ];
+					if ( rscriptType.test( node.type || "" ) &&
+						!dataPriv.access( node, "globalEval" ) &&
+						jQuery.contains( doc, node ) ) {
+
+						if ( node.src && ( node.type || "" ).toLowerCase()  !== "module" ) {
+
+							// Optional AJAX dependency, but won't run scripts if not present
+							if ( jQuery._evalUrl && !node.noModule ) {
+								jQuery._evalUrl( node.src, {
+									nonce: node.nonce || node.getAttribute( "nonce" )
+								} );
+							}
+						} else {
+							DOMEval( node.textContent.replace( rcleanScript, "" ), node, doc );
+						}
+					}
+				}
+			}
+		}
+	}
+
+	return collection;
+}
+
+function remove( elem, selector, keepData ) {
+	var node,
+		nodes = selector ? jQuery.filter( selector, elem ) : elem,
+		i = 0;
+
+	for ( ; ( node = nodes[ i ] ) != null; i++ ) {
+		if ( !keepData && node.nodeType === 1 ) {
+			jQuery.cleanData( getAll( node ) );
+		}
+
+		if ( node.parentNode ) {
+			if ( keepData && isAttached( node ) ) {
+				setGlobalEval( getAll( node, "script" ) );
+			}
+			node.parentNode.removeChild( node );
+		}
+	}
+
+	return elem;
+}
+
+jQuery.extend( {
+	htmlPrefilter: function( html ) {
+		return html.replace( rxhtmlTag, "<$1></$2>" );
+	},
+
+	clone: function( elem, dataAndEvents, deepDataAndEvents ) {
+		var i, l, srcElements, destElements,
+			clone = elem.cloneNode( true ),
+			inPage = isAttached( elem );
+
+		// Fix IE cloning issues
+		if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) &&
+				!jQuery.isXMLDoc( elem ) ) {
+
+			// We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2
+			destElements = getAll( clone );
+			srcElements = getAll( elem );
+
+			for ( i = 0, l = srcElements.length; i < l; i++ ) {
+				fixInput( srcElements[ i ], destElements[ i ] );
+			}
+		}
+
+		// Copy the events from the original to the clone
+		if ( dataAndEvents ) {
+			if ( deepDataAndEvents ) {
+				srcElements = srcElements || getAll( elem );
+				destElements = destElements || getAll( clone );
+
+				for ( i = 0, l = srcElements.length; i < l; i++ ) {
+					cloneCopyEvent( srcElements[ i ], destElements[ i ] );
+				}
+			} else {
+				cloneCopyEvent( elem, clone );
+			}
+		}
+
+		// Preserve script evaluation history
+		destElements = getAll( clone, "script" );
+		if ( destElements.length > 0 ) {
+			setGlobalEval( destElements, !inPage && getAll( elem, "script" ) );
+		}
+
+		// Return the cloned set
+		return clone;
+	},
+
+	cleanData: function( elems ) {
+		var data, elem, type,
+			special = jQuery.event.special,
+			i = 0;
+
+		for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) {
+			if ( acceptData( elem ) ) {
+				if ( ( data = elem[ dataPriv.expando ] ) ) {
+					if ( data.events ) {
+						for ( type in data.events ) {
+							if ( special[ type ] ) {
+								jQuery.event.remove( elem, type );
+
+							// This is a shortcut to avoid jQuery.event.remove's overhead
+							} else {
+								jQuery.removeEvent( elem, type, data.handle );
+							}
+						}
+					}
+
+					// Support: Chrome <=35 - 45+
+					// Assign undefined instead of using delete, see Data#remove
+					elem[ dataPriv.expando ] = undefined;
+				}
+				if ( elem[ dataUser.expando ] ) {
+
+					// Support: Chrome <=35 - 45+
+					// Assign undefined instead of using delete, see Data#remove
+					elem[ dataUser.expando ] = undefined;
+				}
+			}
+		}
+	}
+} );
+
+jQuery.fn.extend( {
+	detach: function( selector ) {
+		return remove( this, selector, true );
+	},
+
+	remove: function( selector ) {
+		return remove( this, selector );
+	},
+
+	text: function( value ) {
+		return access( this, function( value ) {
+			return value === undefined ?
+				jQuery.text( this ) :
+				this.empty().each( function() {
+					if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+						this.textContent = value;
+					}
+				} );
+		}, null, value, arguments.length );
+	},
+
+	append: function() {
+		return domManip( this, arguments, function( elem ) {
+			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+				var target = manipulationTarget( this, elem );
+				target.appendChild( elem );
+			}
+		} );
+	},
+
+	prepend: function() {
+		return domManip( this, arguments, function( elem ) {
+			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
+				var target = manipulationTarget( this, elem );
+				target.insertBefore( elem, target.firstChild );
+			}
+		} );
+	},
+
+	before: function() {
+		return domManip( this, arguments, function( elem ) {
+			if ( this.parentNode ) {
+				this.parentNode.insertBefore( elem, this );
+			}
+		} );
+	},
+
+	after: function() {
+		return domManip( this, arguments, function( elem ) {
+			if ( this.parentNode ) {
+				this.parentNode.insertBefore( elem, this.nextSibling );
+			}
+		} );
+	},
+
+	empty: function() {
+		var elem,
+			i = 0;
+
+		for ( ; ( elem = this[ i ] ) != null; i++ ) {
+			if ( elem.nodeType === 1 ) {
+
+				// Prevent memory leaks
+				jQuery.cleanData( getAll( elem, false ) );
+
+				// Remove any remaining nodes
+				elem.textContent = "";
+			}
+		}
+
+		return this;
+	},
+
+	clone: function( dataAndEvents, deepDataAndEvents ) {
+		dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
+		deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
+
+		return this.map( function() {
+			return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
+		} );
+	},
+
+	html: function( value ) {
+		return access( this, function( value ) {
+			var elem = this[ 0 ] || {},
+				i = 0,
+				l = this.length;
+
+			if ( value === undefined && elem.nodeType === 1 ) {
+				return elem.innerHTML;
+			}
+
+			// See if we can take a shortcut and just use innerHTML
+			if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
+				!wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) {
+
+				value = jQuery.htmlPrefilter( value );
+
+				try {
+					for ( ; i < l; i++ ) {
+						elem = this[ i ] || {};
+
+						// Remove element nodes and prevent memory leaks
+						if ( elem.nodeType === 1 ) {
+							jQuery.cleanData( getAll( elem, false ) );
+							elem.innerHTML = value;
+						}
+					}
+
+					elem = 0;
+
+				// If using innerHTML throws an exception, use the fallback method
+				} catch ( e ) {}
+			}
+
+			if ( elem ) {
+				this.empty().append( value );
+			}
+		}, null, value, arguments.length );
+	},
+
+	replaceWith: function() {
+		var ignored = [];
+
+		// Make the changes, replacing each non-ignored context element with the new content
+		return domManip( this, arguments, function( elem ) {
+			var parent = this.parentNode;
+
+			if ( jQuery.inArray( this, ignored ) < 0 ) {
+				jQuery.cleanData( getAll( this ) );
+				if ( parent ) {
+					parent.replaceChild( elem, this );
+				}
+			}
+
+		// Force callback invocation
+		}, ignored );
+	}
+} );
+
+jQuery.each( {
+	appendTo: "append",
+	prependTo: "prepend",
+	insertBefore: "before",
+	insertAfter: "after",
+	replaceAll: "replaceWith"
+}, function( name, original ) {
+	jQuery.fn[ name ] = function( selector ) {
+		var elems,
+			ret = [],
+			insert = jQuery( selector ),
+			last = insert.length - 1,
+			i = 0;
+
+		for ( ; i <= last; i++ ) {
+			elems = i === last ? this : this.clone( true );
+			jQuery( insert[ i ] )[ original ]( elems );
+
+			// Support: Android <=4.0 only, PhantomJS 1 only
+			// .get() because push.apply(_, arraylike) throws on ancient WebKit
+			push.apply( ret, elems.get() );
+		}
+
+		return this.pushStack( ret );
+	};
+} );
+var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
+
+var getStyles = function( elem ) {
+
+		// Support: IE <=11 only, Firefox <=30 (#15098, #14150)
+		// IE throws on elements created in popups
+		// FF meanwhile throws on frame elements through "defaultView.getComputedStyle"
+		var view = elem.ownerDocument.defaultView;
+
+		if ( !view || !view.opener ) {
+			view = window;
+		}
+
+		return view.getComputedStyle( elem );
+	};
+
+var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" );
+
+
+
+( function() {
+
+	// Executing both pixelPosition & boxSizingReliable tests require only one layout
+	// so they're executed at the same time to save the second computation.
+	function computeStyleTests() {
+
+		// This is a singleton, we need to execute it only once
+		if ( !div ) {
+			return;
+		}
+
+		container.style.cssText = "position:absolute;left:-11111px;width:60px;" +
+			"margin-top:1px;padding:0;border:0";
+		div.style.cssText =
+			"position:relative;display:block;box-sizing:border-box;overflow:scroll;" +
+			"margin:auto;border:1px;padding:1px;" +
+			"width:60%;top:1%";
+		documentElement.appendChild( container ).appendChild( div );
+
+		var divStyle = window.getComputedStyle( div );
+		pixelPositionVal = divStyle.top !== "1%";
+
+		// Support: Android 4.0 - 4.3 only, Firefox <=3 - 44
+		reliableMarginLeftVal = roundPixelMeasures( divStyle.marginLeft ) === 12;
+
+		// Support: Android 4.0 - 4.3 only, Safari <=9.1 - 10.1, iOS <=7.0 - 9.3
+		// Some styles come back with percentage values, even though they shouldn't
+		div.style.right = "60%";
+		pixelBoxStylesVal = roundPixelMeasures( divStyle.right ) === 36;
+
+		// Support: IE 9 - 11 only
+		// Detect misreporting of content dimensions for box-sizing:border-box elements
+		boxSizingReliableVal = roundPixelMeasures( divStyle.width ) === 36;
+
+		// Support: IE 9 only
+		// Detect overflow:scroll screwiness (gh-3699)
+		// Support: Chrome <=64
+		// Don't get tricked when zoom affects offsetWidth (gh-4029)
+		div.style.position = "absolute";
+		scrollboxSizeVal = roundPixelMeasures( div.offsetWidth / 3 ) === 12;
+
+		documentElement.removeChild( container );
+
+		// Nullify the div so it wouldn't be stored in the memory and
+		// it will also be a sign that checks already performed
+		div = null;
+	}
+
+	function roundPixelMeasures( measure ) {
+		return Math.round( parseFloat( measure ) );
+	}
+
+	var pixelPositionVal, boxSizingReliableVal, scrollboxSizeVal, pixelBoxStylesVal,
+		reliableMarginLeftVal,
+		container = document.createElement( "div" ),
+		div = document.createElement( "div" );
+
+	// Finish early in limited (non-browser) environments
+	if ( !div.style ) {
+		return;
+	}
+
+	// Support: IE <=9 - 11 only
+	// Style of cloned element affects source element cloned (#8908)
+	div.style.backgroundClip = "content-box";
+	div.cloneNode( true ).style.backgroundClip = "";
+	support.clearCloneStyle = div.style.backgroundClip === "content-box";
+
+	jQuery.extend( support, {
+		boxSizingReliable: function() {
+			computeStyleTests();
+			return boxSizingReliableVal;
+		},
+		pixelBoxStyles: function() {
+			computeStyleTests();
+			return pixelBoxStylesVal;
+		},
+		pixelPosition: function() {
+			computeStyleTests();
+			return pixelPositionVal;
+		},
+		reliableMarginLeft: function() {
+			computeStyleTests();
+			return reliableMarginLeftVal;
+		},
+		scrollboxSize: function() {
+			computeStyleTests();
+			return scrollboxSizeVal;
+		}
+	} );
+} )();
+
+
+function curCSS( elem, name, computed ) {
+	var width, minWidth, maxWidth, ret,
+
+		// Support: Firefox 51+
+		// Retrieving style before computed somehow
+		// fixes an issue with getting wrong values
+		// on detached elements
+		style = elem.style;
+
+	computed = computed || getStyles( elem );
+
+	// getPropertyValue is needed for:
+	//   .css('filter') (IE 9 only, #12537)
+	//   .css('--customProperty) (#3144)
+	if ( computed ) {
+		ret = computed.getPropertyValue( name ) || computed[ name ];
+
+		if ( ret === "" && !isAttached( elem ) ) {
+			ret = jQuery.style( elem, name );
+		}
+
+		// A tribute to the "awesome hack by Dean Edwards"
+		// Android Browser returns percentage for some values,
+		// but width seems to be reliably pixels.
+		// This is against the CSSOM draft spec:
+		// https://drafts.csswg.org/cssom/#resolved-values
+		if ( !support.pixelBoxStyles() && rnumnonpx.test( ret ) && rboxStyle.test( name ) ) {
+
+			// Remember the original values
+			width = style.width;
+			minWidth = style.minWidth;
+			maxWidth = style.maxWidth;
+
+			// Put in the new values to get a computed value out
+			style.minWidth = style.maxWidth = style.width = ret;
+			ret = computed.width;
+
+			// Revert the changed values
+			style.width = width;
+			style.minWidth = minWidth;
+			style.maxWidth = maxWidth;
+		}
+	}
+
+	return ret !== undefined ?
+
+		// Support: IE <=9 - 11 only
+		// IE returns zIndex value as an integer.
+		ret + "" :
+		ret;
+}
+
+
+function addGetHookIf( conditionFn, hookFn ) {
+
+	// Define the hook, we'll check on the first run if it's really needed.
+	return {
+		get: function() {
+			if ( conditionFn() ) {
+
+				// Hook not needed (or it's not possible to use it due
+				// to missing dependency), remove it.
+				delete this.get;
+				return;
+			}
+
+			// Hook needed; redefine it so that the support test is not executed again.
+			return ( this.get = hookFn ).apply( this, arguments );
+		}
+	};
+}
+
+
+var cssPrefixes = [ "Webkit", "Moz", "ms" ],
+	emptyStyle = document.createElement( "div" ).style,
+	vendorProps = {};
+
+// Return a vendor-prefixed property or undefined
+function vendorPropName( name ) {
+
+	// Check for vendor prefixed names
+	var capName = name[ 0 ].toUpperCase() + name.slice( 1 ),
+		i = cssPrefixes.length;
+
+	while ( i-- ) {
+		name = cssPrefixes[ i ] + capName;
+		if ( name in emptyStyle ) {
+			return name;
+		}
+	}
+}
+
+// Return a potentially-mapped jQuery.cssProps or vendor prefixed property
+function finalPropName( name ) {
+	var final = jQuery.cssProps[ name ] || vendorProps[ name ];
+
+	if ( final ) {
+		return final;
+	}
+	if ( name in emptyStyle ) {
+		return name;
+	}
+	return vendorProps[ name ] = vendorPropName( name ) || name;
+}
+
+
+var
+
+	// Swappable if display is none or starts with table
+	// except "table", "table-cell", or "table-caption"
+	// See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
+	rdisplayswap = /^(none|table(?!-c[ea]).+)/,
+	rcustomProp = /^--/,
+	cssShow = { position: "absolute", visibility: "hidden", display: "block" },
+	cssNormalTransform = {
+		letterSpacing: "0",
+		fontWeight: "400"
+	};
+
+function setPositiveNumber( elem, value, subtract ) {
+
+	// Any relative (+/-) values have already been
+	// normalized at this point
+	var matches = rcssNum.exec( value );
+	return matches ?
+
+		// Guard against undefined "subtract", e.g., when used as in cssHooks
+		Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) :
+		value;
+}
+
+function boxModelAdjustment( elem, dimension, box, isBorderBox, styles, computedVal ) {
+	var i = dimension === "width" ? 1 : 0,
+		extra = 0,
+		delta = 0;
+
+	// Adjustment may not be necessary
+	if ( box === ( isBorderBox ? "border" : "content" ) ) {
+		return 0;
+	}
+
+	for ( ; i < 4; i += 2 ) {
+
+		// Both box models exclude margin
+		if ( box === "margin" ) {
+			delta += jQuery.css( elem, box + cssExpand[ i ], true, styles );
+		}
+
+		// If we get here with a content-box, we're seeking "padding" or "border" or "margin"
+		if ( !isBorderBox ) {
+
+			// Add padding
+			delta += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+
+			// For "border" or "margin", add border
+			if ( box !== "padding" ) {
+				delta += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+
+			// But still keep track of it otherwise
+			} else {
+				extra += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+			}
+
+		// If we get here with a border-box (content + padding + border), we're seeking "content" or
+		// "padding" or "margin"
+		} else {
+
+			// For "content", subtract padding
+			if ( box === "content" ) {
+				delta -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
+			}
+
+			// For "content" or "padding", subtract border
+			if ( box !== "margin" ) {
+				delta -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
+			}
+		}
+	}
+
+	// Account for positive content-box scroll gutter when requested by providing computedVal
+	if ( !isBorderBox && computedVal >= 0 ) {
+
+		// offsetWidth/offsetHeight is a rounded sum of content, padding, scroll gutter, and border
+		// Assuming integer scroll gutter, subtract the rest and round down
+		delta += Math.max( 0, Math.ceil(
+			elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] -
+			computedVal -
+			delta -
+			extra -
+			0.5
+
+		// If offsetWidth/offsetHeight is unknown, then we can't determine content-box scroll gutter
+		// Use an explicit zero to avoid NaN (gh-3964)
+		) ) || 0;
+	}
+
+	return delta;
+}
+
+function getWidthOrHeight( elem, dimension, extra ) {
+
+	// Start with computed style
+	var styles = getStyles( elem ),
+
+		// To avoid forcing a reflow, only fetch boxSizing if we need it (gh-4322).
+		// Fake content-box until we know it's needed to know the true value.
+		boxSizingNeeded = !support.boxSizingReliable() || extra,
+		isBorderBox = boxSizingNeeded &&
+			jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
+		valueIsBorderBox = isBorderBox,
+
+		val = curCSS( elem, dimension, styles ),
+		offsetProp = "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 );
+
+	// Support: Firefox <=54
+	// Return a confounding non-pixel value or feign ignorance, as appropriate.
+	if ( rnumnonpx.test( val ) ) {
+		if ( !extra ) {
+			return val;
+		}
+		val = "auto";
+	}
+
+
+	// Fall back to offsetWidth/offsetHeight when value is "auto"
+	// This happens for inline elements with no explicit setting (gh-3571)
+	// Support: Android <=4.1 - 4.3 only
+	// Also use offsetWidth/offsetHeight for misreported inline dimensions (gh-3602)
+	// Support: IE 9-11 only
+	// Also use offsetWidth/offsetHeight for when box sizing is unreliable
+	// We use getClientRects() to check for hidden/disconnected.
+	// In those cases, the computed value can be trusted to be border-box
+	if ( ( !support.boxSizingReliable() && isBorderBox ||
+		val === "auto" ||
+		!parseFloat( val ) && jQuery.css( elem, "display", false, styles ) === "inline" ) &&
+		elem.getClientRects().length ) {
+
+		isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
+
+		// Where available, offsetWidth/offsetHeight approximate border box dimensions.
+		// Where not available (e.g., SVG), assume unreliable box-sizing and interpret the
+		// retrieved value as a content box dimension.
+		valueIsBorderBox = offsetProp in elem;
+		if ( valueIsBorderBox ) {
+			val = elem[ offsetProp ];
+		}
+	}
+
+	// Normalize "" and auto
+	val = parseFloat( val ) || 0;
+
+	// Adjust for the element's box model
+	return ( val +
+		boxModelAdjustment(
+			elem,
+			dimension,
+			extra || ( isBorderBox ? "border" : "content" ),
+			valueIsBorderBox,
+			styles,
+
+			// Provide the current computed size to request scroll gutter calculation (gh-3589)
+			val
+		)
+	) + "px";
+}
+
+jQuery.extend( {
+
+	// Add in style property hooks for overriding the default
+	// behavior of getting and setting a style property
+	cssHooks: {
+		opacity: {
+			get: function( elem, computed ) {
+				if ( computed ) {
+
+					// We should always get a number back from opacity
+					var ret = curCSS( elem, "opacity" );
+					return ret === "" ? "1" : ret;
+				}
+			}
+		}
+	},
+
+	// Don't automatically add "px" to these possibly-unitless properties
+	cssNumber: {
+		"animationIterationCount": true,
+		"columnCount": true,
+		"fillOpacity": true,
+		"flexGrow": true,
+		"flexShrink": true,
+		"fontWeight": true,
+		"gridArea": true,
+		"gridColumn": true,
+		"gridColumnEnd": true,
+		"gridColumnStart": true,
+		"gridRow": true,
+		"gridRowEnd": true,
+		"gridRowStart": true,
+		"lineHeight": true,
+		"opacity": true,
+		"order": true,
+		"orphans": true,
+		"widows": true,
+		"zIndex": true,
+		"zoom": true
+	},
+
+	// Add in properties whose names you wish to fix before
+	// setting or getting the value
+	cssProps: {},
+
+	// Get and set the style property on a DOM Node
+	style: function( elem, name, value, extra ) {
+
+		// Don't set styles on text and comment nodes
+		if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
+			return;
+		}
+
+		// Make sure that we're working with the right name
+		var ret, type, hooks,
+			origName = camelCase( name ),
+			isCustomProp = rcustomProp.test( name ),
+			style = elem.style;
+
+		// Make sure that we're working with the right name. We don't
+		// want to query the value if it is a CSS custom property
+		// since they are user-defined.
+		if ( !isCustomProp ) {
+			name = finalPropName( origName );
+		}
+
+		// Gets hook for the prefixed version, then unprefixed version
+		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+		// Check if we're setting a value
+		if ( value !== undefined ) {
+			type = typeof value;
+
+			// Convert "+=" or "-=" to relative numbers (#7345)
+			if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) {
+				value = adjustCSS( elem, name, ret );
+
+				// Fixes bug #9237
+				type = "number";
+			}
+
+			// Make sure that null and NaN values aren't set (#7116)
+			if ( value == null || value !== value ) {
+				return;
+			}
+
+			// If a number was passed in, add the unit (except for certain CSS properties)
+			// The isCustomProp check can be removed in jQuery 4.0 when we only auto-append
+			// "px" to a few hardcoded values.
+			if ( type === "number" && !isCustomProp ) {
+				value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" );
+			}
+
+			// background-* props affect original clone's values
+			if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) {
+				style[ name ] = "inherit";
+			}
+
+			// If a hook was provided, use that value, otherwise just set the specified value
+			if ( !hooks || !( "set" in hooks ) ||
+				( value = hooks.set( elem, value, extra ) ) !== undefined ) {
+
+				if ( isCustomProp ) {
+					style.setProperty( name, value );
+				} else {
+					style[ name ] = value;
+				}
+			}
+
+		} else {
+
+			// If a hook was provided get the non-computed value from there
+			if ( hooks && "get" in hooks &&
+				( ret = hooks.get( elem, false, extra ) ) !== undefined ) {
+
+				return ret;
+			}
+
+			// Otherwise just get the value from the style object
+			return style[ name ];
+		}
+	},
+
+	css: function( elem, name, extra, styles ) {
+		var val, num, hooks,
+			origName = camelCase( name ),
+			isCustomProp = rcustomProp.test( name );
+
+		// Make sure that we're working with the right name. We don't
+		// want to modify the value if it is a CSS custom property
+		// since they are user-defined.
+		if ( !isCustomProp ) {
+			name = finalPropName( origName );
+		}
+
+		// Try prefixed name followed by the unprefixed name
+		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
+
+		// If a hook was provided get the computed value from there
+		if ( hooks && "get" in hooks ) {
+			val = hooks.get( elem, true, extra );
+		}
+
+		// Otherwise, if a way to get the computed value exists, use that
+		if ( val === undefined ) {
+			val = curCSS( elem, name, styles );
+		}
+
+		// Convert "normal" to computed value
+		if ( val === "normal" && name in cssNormalTransform ) {
+			val = cssNormalTransform[ name ];
+		}
+
+		// Make numeric if forced or a qualifier was provided and val looks numeric
+		if ( extra === "" || extra ) {
+			num = parseFloat( val );
+			return extra === true || isFinite( num ) ? num || 0 : val;
+		}
+
+		return val;
+	}
+} );
+
+jQuery.each( [ "height", "width" ], function( i, dimension ) {
+	jQuery.cssHooks[ dimension ] = {
+		get: function( elem, computed, extra ) {
+			if ( computed ) {
+
+				// Certain elements can have dimension info if we invisibly show them
+				// but it must have a current display style that would benefit
+				return rdisplayswap.test( jQuery.css( elem, "display" ) ) &&
+
+					// Support: Safari 8+
+					// Table columns in Safari have non-zero offsetWidth & zero
+					// getBoundingClientRect().width unless display is changed.
+					// Support: IE <=11 only
+					// Running getBoundingClientRect on a disconnected node
+					// in IE throws an error.
+					( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ?
+						swap( elem, cssShow, function() {
+							return getWidthOrHeight( elem, dimension, extra );
+						} ) :
+						getWidthOrHeight( elem, dimension, extra );
+			}
+		},
+
+		set: function( elem, value, extra ) {
+			var matches,
+				styles = getStyles( elem ),
+
+				// Only read styles.position if the test has a chance to fail
+				// to avoid forcing a reflow.
+				scrollboxSizeBuggy = !support.scrollboxSize() &&
+					styles.position === "absolute",
+
+				// To avoid forcing a reflow, only fetch boxSizing if we need it (gh-3991)
+				boxSizingNeeded = scrollboxSizeBuggy || extra,
+				isBorderBox = boxSizingNeeded &&
+					jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
+				subtract = extra ?
+					boxModelAdjustment(
+						elem,
+						dimension,
+						extra,
+						isBorderBox,
+						styles
+					) :
+					0;
+
+			// Account for unreliable border-box dimensions by comparing offset* to computed and
+			// faking a content-box to get border and padding (gh-3699)
+			if ( isBorderBox && scrollboxSizeBuggy ) {
+				subtract -= Math.ceil(
+					elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] -
+					parseFloat( styles[ dimension ] ) -
+					boxModelAdjustment( elem, dimension, "border", false, styles ) -
+					0.5
+				);
+			}
+
+			// Convert to pixels if value adjustment is needed
+			if ( subtract && ( matches = rcssNum.exec( value ) ) &&
+				( matches[ 3 ] || "px" ) !== "px" ) {
+
+				elem.style[ dimension ] = value;
+				value = jQuery.css( elem, dimension );
+			}
+
+			return setPositiveNumber( elem, value, subtract );
+		}
+	};
+} );
+
+jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft,
+	function( elem, computed ) {
+		if ( computed ) {
+			return ( parseFloat( curCSS( elem, "marginLeft" ) ) ||
+				elem.getBoundingClientRect().left -
+					swap( elem, { marginLeft: 0 }, function() {
+						return elem.getBoundingClientRect().left;
+					} )
+				) + "px";
+		}
+	}
+);
+
+// These hooks are used by animate to expand properties
+jQuery.each( {
+	margin: "",
+	padding: "",
+	border: "Width"
+}, function( prefix, suffix ) {
+	jQuery.cssHooks[ prefix + suffix ] = {
+		expand: function( value ) {
+			var i = 0,
+				expanded = {},
+
+				// Assumes a single number if not a string
+				parts = typeof value === "string" ? value.split( " " ) : [ value ];
+
+			for ( ; i < 4; i++ ) {
+				expanded[ prefix + cssExpand[ i ] + suffix ] =
+					parts[ i ] || parts[ i - 2 ] || parts[ 0 ];
+			}
+
+			return expanded;
+		}
+	};
+
+	if ( prefix !== "margin" ) {
+		jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
+	}
+} );
+
+jQuery.fn.extend( {
+	css: function( name, value ) {
+		return access( this, function( elem, name, value ) {
+			var styles, len,
+				map = {},
+				i = 0;
+
+			if ( Array.isArray( name ) ) {
+				styles = getStyles( elem );
+				len = name.length;
+
+				for ( ; i < len; i++ ) {
+					map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles );
+				}
+
+				return map;
+			}
+
+			return value !== undefined ?
+				jQuery.style( elem, name, value ) :
+				jQuery.css( elem, name );
+		}, name, value, arguments.length > 1 );
+	}
+} );
+
+
+function Tween( elem, options, prop, end, easing ) {
+	return new Tween.prototype.init( elem, options, prop, end, easing );
+}
+jQuery.Tween = Tween;
+
+Tween.prototype = {
+	constructor: Tween,
+	init: function( elem, options, prop, end, easing, unit ) {
+		this.elem = elem;
+		this.prop = prop;
+		this.easing = easing || jQuery.easing._default;
+		this.options = options;
+		this.start = this.now = this.cur();
+		this.end = end;
+		this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
+	},
+	cur: function() {
+		var hooks = Tween.propHooks[ this.prop ];
+
+		return hooks && hooks.get ?
+			hooks.get( this ) :
+			Tween.propHooks._default.get( this );
+	},
+	run: function( percent ) {
+		var eased,
+			hooks = Tween.propHooks[ this.prop ];
+
+		if ( this.options.duration ) {
+			this.pos = eased = jQuery.easing[ this.easing ](
+				percent, this.options.duration * percent, 0, 1, this.options.duration
+			);
+		} else {
+			this.pos = eased = percent;
+		}
+		this.now = ( this.end - this.start ) * eased + this.start;
+
+		if ( this.options.step ) {
+			this.options.step.call( this.elem, this.now, this );
+		}
+
+		if ( hooks && hooks.set ) {
+			hooks.set( this );
+		} else {
+			Tween.propHooks._default.set( this );
+		}
+		return this;
+	}
+};
+
+Tween.prototype.init.prototype = Tween.prototype;
+
+Tween.propHooks = {
+	_default: {
+		get: function( tween ) {
+			var result;
+
+			// Use a property on the element directly when it is not a DOM element,
+			// or when there is no matching style property that exists.
+			if ( tween.elem.nodeType !== 1 ||
+				tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) {
+				return tween.elem[ tween.prop ];
+			}
+
+			// Passing an empty string as a 3rd parameter to .css will automatically
+			// attempt a parseFloat and fallback to a string if the parse fails.
+			// Simple values such as "10px" are parsed to Float;
+			// complex values such as "rotate(1rad)" are returned as-is.
+			result = jQuery.css( tween.elem, tween.prop, "" );
+
+			// Empty strings, null, undefined and "auto" are converted to 0.
+			return !result || result === "auto" ? 0 : result;
+		},
+		set: function( tween ) {
+
+			// Use step hook for back compat.
+			// Use cssHook if its there.
+			// Use .style if available and use plain properties where available.
+			if ( jQuery.fx.step[ tween.prop ] ) {
+				jQuery.fx.step[ tween.prop ]( tween );
+			} else if ( tween.elem.nodeType === 1 && (
+					jQuery.cssHooks[ tween.prop ] ||
+					tween.elem.style[ finalPropName( tween.prop ) ] != null ) ) {
+				jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
+			} else {
+				tween.elem[ tween.prop ] = tween.now;
+			}
+		}
+	}
+};
+
+// Support: IE <=9 only
+// Panic based approach to setting things on disconnected nodes
+Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
+	set: function( tween ) {
+		if ( tween.elem.nodeType && tween.elem.parentNode ) {
+			tween.elem[ tween.prop ] = tween.now;
+		}
+	}
+};
+
+jQuery.easing = {
+	linear: function( p ) {
+		return p;
+	},
+	swing: function( p ) {
+		return 0.5 - Math.cos( p * Math.PI ) / 2;
+	},
+	_default: "swing"
+};
+
+jQuery.fx = Tween.prototype.init;
+
+// Back compat <1.8 extension point
+jQuery.fx.step = {};
+
+
+
+
+var
+	fxNow, inProgress,
+	rfxtypes = /^(?:toggle|show|hide)$/,
+	rrun = /queueHooks$/;
+
+function schedule() {
+	if ( inProgress ) {
+		if ( document.hidden === false && window.requestAnimationFrame ) {
+			window.requestAnimationFrame( schedule );
+		} else {
+			window.setTimeout( schedule, jQuery.fx.interval );
+		}
+
+		jQuery.fx.tick();
+	}
+}
+
+// Animations created synchronously will run synchronously
+function createFxNow() {
+	window.setTimeout( function() {
+		fxNow = undefined;
+	} );
+	return ( fxNow = Date.now() );
+}
+
+// Generate parameters to create a standard animation
+function genFx( type, includeWidth ) {
+	var which,
+		i = 0,
+		attrs = { height: type };
+
+	// If we include width, step value is 1 to do all cssExpand values,
+	// otherwise step value is 2 to skip over Left and Right
+	includeWidth = includeWidth ? 1 : 0;
+	for ( ; i < 4; i += 2 - includeWidth ) {
+		which = cssExpand[ i ];
+		attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
+	}
+
+	if ( includeWidth ) {
+		attrs.opacity = attrs.width = type;
+	}
+
+	return attrs;
+}
+
+function createTween( value, prop, animation ) {
+	var tween,
+		collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ),
+		index = 0,
+		length = collection.length;
+	for ( ; index < length; index++ ) {
+		if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) {
+
+			// We're done with this property
+			return tween;
+		}
+	}
+}
+
+function defaultPrefilter( elem, props, opts ) {
+	var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display,
+		isBox = "width" in props || "height" in props,
+		anim = this,
+		orig = {},
+		style = elem.style,
+		hidden = elem.nodeType && isHiddenWithinTree( elem ),
+		dataShow = dataPriv.get( elem, "fxshow" );
+
+	// Queue-skipping animations hijack the fx hooks
+	if ( !opts.queue ) {
+		hooks = jQuery._queueHooks( elem, "fx" );
+		if ( hooks.unqueued == null ) {
+			hooks.unqueued = 0;
+			oldfire = hooks.empty.fire;
+			hooks.empty.fire = function() {
+				if ( !hooks.unqueued ) {
+					oldfire();
+				}
+			};
+		}
+		hooks.unqueued++;
+
+		anim.always( function() {
+
+			// Ensure the complete handler is called before this completes
+			anim.always( function() {
+				hooks.unqueued--;
+				if ( !jQuery.queue( elem, "fx" ).length ) {
+					hooks.empty.fire();
+				}
+			} );
+		} );
+	}
+
+	// Detect show/hide animations
+	for ( prop in props ) {
+		value = props[ prop ];
+		if ( rfxtypes.test( value ) ) {
+			delete props[ prop ];
+			toggle = toggle || value === "toggle";
+			if ( value === ( hidden ? "hide" : "show" ) ) {
+
+				// Pretend to be hidden if this is a "show" and
+				// there is still data from a stopped show/hide
+				if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) {
+					hidden = true;
+
+				// Ignore all other no-op show/hide data
+				} else {
+					continue;
+				}
+			}
+			orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop );
+		}
+	}
+
+	// Bail out if this is a no-op like .hide().hide()
+	propTween = !jQuery.isEmptyObject( props );
+	if ( !propTween && jQuery.isEmptyObject( orig ) ) {
+		return;
+	}
+
+	// Restrict "overflow" and "display" styles during box animations
+	if ( isBox && elem.nodeType === 1 ) {
+
+		// Support: IE <=9 - 11, Edge 12 - 15
+		// Record all 3 overflow attributes because IE does not infer the shorthand
+		// from identically-valued overflowX and overflowY and Edge just mirrors
+		// the overflowX value there.
+		opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
+
+		// Identify a display type, preferring old show/hide data over the CSS cascade
+		restoreDisplay = dataShow && dataShow.display;
+		if ( restoreDisplay == null ) {
+			restoreDisplay = dataPriv.get( elem, "display" );
+		}
+		display = jQuery.css( elem, "display" );
+		if ( display === "none" ) {
+			if ( restoreDisplay ) {
+				display = restoreDisplay;
+			} else {
+
+				// Get nonempty value(s) by temporarily forcing visibility
+				showHide( [ elem ], true );
+				restoreDisplay = elem.style.display || restoreDisplay;
+				display = jQuery.css( elem, "display" );
+				showHide( [ elem ] );
+			}
+		}
+
+		// Animate inline elements as inline-block
+		if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) {
+			if ( jQuery.css( elem, "float" ) === "none" ) {
+
+				// Restore the original display value at the end of pure show/hide animations
+				if ( !propTween ) {
+					anim.done( function() {
+						style.display = restoreDisplay;
+					} );
+					if ( restoreDisplay == null ) {
+						display = style.display;
+						restoreDisplay = display === "none" ? "" : display;
+					}
+				}
+				style.display = "inline-block";
+			}
+		}
+	}
+
+	if ( opts.overflow ) {
+		style.overflow = "hidden";
+		anim.always( function() {
+			style.overflow = opts.overflow[ 0 ];
+			style.overflowX = opts.overflow[ 1 ];
+			style.overflowY = opts.overflow[ 2 ];
+		} );
+	}
+
+	// Implement show/hide animations
+	propTween = false;
+	for ( prop in orig ) {
+
+		// General show/hide setup for this element animation
+		if ( !propTween ) {
+			if ( dataShow ) {
+				if ( "hidden" in dataShow ) {
+					hidden = dataShow.hidden;
+				}
+			} else {
+				dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } );
+			}
+
+			// Store hidden/visible for toggle so `.stop().toggle()` "reverses"
+			if ( toggle ) {
+				dataShow.hidden = !hidden;
+			}
+
+			// Show elements before animating them
+			if ( hidden ) {
+				showHide( [ elem ], true );
+			}
+
+			/* eslint-disable no-loop-func */
+
+			anim.done( function() {
+
+			/* eslint-enable no-loop-func */
+
+				// The final step of a "hide" animation is actually hiding the element
+				if ( !hidden ) {
+					showHide( [ elem ] );
+				}
+				dataPriv.remove( elem, "fxshow" );
+				for ( prop in orig ) {
+					jQuery.style( elem, prop, orig[ prop ] );
+				}
+			} );
+		}
+
+		// Per-property setup
+		propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
+		if ( !( prop in dataShow ) ) {
+			dataShow[ prop ] = propTween.start;
+			if ( hidden ) {
+				propTween.end = propTween.start;
+				propTween.start = 0;
+			}
+		}
+	}
+}
+
+function propFilter( props, specialEasing ) {
+	var index, name, easing, value, hooks;
+
+	// camelCase, specialEasing and expand cssHook pass
+	for ( index in props ) {
+		name = camelCase( index );
+		easing = specialEasing[ name ];
+		value = props[ index ];
+		if ( Array.isArray( value ) ) {
+			easing = value[ 1 ];
+			value = props[ index ] = value[ 0 ];
+		}
+
+		if ( index !== name ) {
+			props[ name ] = value;
+			delete props[ index ];
+		}
+
+		hooks = jQuery.cssHooks[ name ];
+		if ( hooks && "expand" in hooks ) {
+			value = hooks.expand( value );
+			delete props[ name ];
+
+			// Not quite $.extend, this won't overwrite existing keys.
+			// Reusing 'index' because we have the correct "name"
+			for ( index in value ) {
+				if ( !( index in props ) ) {
+					props[ index ] = value[ index ];
+					specialEasing[ index ] = easing;
+				}
+			}
+		} else {
+			specialEasing[ name ] = easing;
+		}
+	}
+}
+
+function Animation( elem, properties, options ) {
+	var result,
+		stopped,
+		index = 0,
+		length = Animation.prefilters.length,
+		deferred = jQuery.Deferred().always( function() {
+
+			// Don't match elem in the :animated selector
+			delete tick.elem;
+		} ),
+		tick = function() {
+			if ( stopped ) {
+				return false;
+			}
+			var currentTime = fxNow || createFxNow(),
+				remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
+
+				// Support: Android 2.3 only
+				// Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497)
+				temp = remaining / animation.duration || 0,
+				percent = 1 - temp,
+				index = 0,
+				length = animation.tweens.length;
+
+			for ( ; index < length; index++ ) {
+				animation.tweens[ index ].run( percent );
+			}
+
+			deferred.notifyWith( elem, [ animation, percent, remaining ] );
+
+			// If there's more to do, yield
+			if ( percent < 1 && length ) {
+				return remaining;
+			}
+
+			// If this was an empty animation, synthesize a final progress notification
+			if ( !length ) {
+				deferred.notifyWith( elem, [ animation, 1, 0 ] );
+			}
+
+			// Resolve the animation and report its conclusion
+			deferred.resolveWith( elem, [ animation ] );
+			return false;
+		},
+		animation = deferred.promise( {
+			elem: elem,
+			props: jQuery.extend( {}, properties ),
+			opts: jQuery.extend( true, {
+				specialEasing: {},
+				easing: jQuery.easing._default
+			}, options ),
+			originalProperties: properties,
+			originalOptions: options,
+			startTime: fxNow || createFxNow(),
+			duration: options.duration,
+			tweens: [],
+			createTween: function( prop, end ) {
+				var tween = jQuery.Tween( elem, animation.opts, prop, end,
+						animation.opts.specialEasing[ prop ] || animation.opts.easing );
+				animation.tweens.push( tween );
+				return tween;
+			},
+			stop: function( gotoEnd ) {
+				var index = 0,
+
+					// If we are going to the end, we want to run all the tweens
+					// otherwise we skip this part
+					length = gotoEnd ? animation.tweens.length : 0;
+				if ( stopped ) {
+					return this;
+				}
+				stopped = true;
+				for ( ; index < length; index++ ) {
+					animation.tweens[ index ].run( 1 );
+				}
+
+				// Resolve when we played the last frame; otherwise, reject
+				if ( gotoEnd ) {
+					deferred.notifyWith( elem, [ animation, 1, 0 ] );
+					deferred.resolveWith( elem, [ animation, gotoEnd ] );
+				} else {
+					deferred.rejectWith( elem, [ animation, gotoEnd ] );
+				}
+				return this;
+			}
+		} ),
+		props = animation.props;
+
+	propFilter( props, animation.opts.specialEasing );
+
+	for ( ; index < length; index++ ) {
+		result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts );
+		if ( result ) {
+			if ( isFunction( result.stop ) ) {
+				jQuery._queueHooks( animation.elem, animation.opts.queue ).stop =
+					result.stop.bind( result );
+			}
+			return result;
+		}
+	}
+
+	jQuery.map( props, createTween, animation );
+
+	if ( isFunction( animation.opts.start ) ) {
+		animation.opts.start.call( elem, animation );
+	}
+
+	// Attach callbacks from options
+	animation
+		.progress( animation.opts.progress )
+		.done( animation.opts.done, animation.opts.complete )
+		.fail( animation.opts.fail )
+		.always( animation.opts.always );
+
+	jQuery.fx.timer(
+		jQuery.extend( tick, {
+			elem: elem,
+			anim: animation,
+			queue: animation.opts.queue
+		} )
+	);
+
+	return animation;
+}
+
+jQuery.Animation = jQuery.extend( Animation, {
+
+	tweeners: {
+		"*": [ function( prop, value ) {
+			var tween = this.createTween( prop, value );
+			adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween );
+			return tween;
+		} ]
+	},
+
+	tweener: function( props, callback ) {
+		if ( isFunction( props ) ) {
+			callback = props;
+			props = [ "*" ];
+		} else {
+			props = props.match( rnothtmlwhite );
+		}
+
+		var prop,
+			index = 0,
+			length = props.length;
+
+		for ( ; index < length; index++ ) {
+			prop = props[ index ];
+			Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || [];
+			Animation.tweeners[ prop ].unshift( callback );
+		}
+	},
+
+	prefilters: [ defaultPrefilter ],
+
+	prefilter: function( callback, prepend ) {
+		if ( prepend ) {
+			Animation.prefilters.unshift( callback );
+		} else {
+			Animation.prefilters.push( callback );
+		}
+	}
+} );
+
+jQuery.speed = function( speed, easing, fn ) {
+	var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
+		complete: fn || !fn && easing ||
+			isFunction( speed ) && speed,
+		duration: speed,
+		easing: fn && easing || easing && !isFunction( easing ) && easing
+	};
+
+	// Go to the end state if fx are off
+	if ( jQuery.fx.off ) {
+		opt.duration = 0;
+
+	} else {
+		if ( typeof opt.duration !== "number" ) {
+			if ( opt.duration in jQuery.fx.speeds ) {
+				opt.duration = jQuery.fx.speeds[ opt.duration ];
+
+			} else {
+				opt.duration = jQuery.fx.speeds._default;
+			}
+		}
+	}
+
+	// Normalize opt.queue - true/undefined/null -> "fx"
+	if ( opt.queue == null || opt.queue === true ) {
+		opt.queue = "fx";
+	}
+
+	// Queueing
+	opt.old = opt.complete;
+
+	opt.complete = function() {
+		if ( isFunction( opt.old ) ) {
+			opt.old.call( this );
+		}
+
+		if ( opt.queue ) {
+			jQuery.dequeue( this, opt.queue );
+		}
+	};
+
+	return opt;
+};
+
+jQuery.fn.extend( {
+	fadeTo: function( speed, to, easing, callback ) {
+
+		// Show any hidden elements after setting opacity to 0
+		return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show()
+
+			// Animate to the value specified
+			.end().animate( { opacity: to }, speed, easing, callback );
+	},
+	animate: function( prop, speed, easing, callback ) {
+		var empty = jQuery.isEmptyObject( prop ),
+			optall = jQuery.speed( speed, easing, callback ),
+			doAnimation = function() {
+
+				// Operate on a copy of prop so per-property easing won't be lost
+				var anim = Animation( this, jQuery.extend( {}, prop ), optall );
+
+				// Empty animations, or finishing resolves immediately
+				if ( empty || dataPriv.get( this, "finish" ) ) {
+					anim.stop( true );
+				}
+			};
+			doAnimation.finish = doAnimation;
+
+		return empty || optall.queue === false ?
+			this.each( doAnimation ) :
+			this.queue( optall.queue, doAnimation );
+	},
+	stop: function( type, clearQueue, gotoEnd ) {
+		var stopQueue = function( hooks ) {
+			var stop = hooks.stop;
+			delete hooks.stop;
+			stop( gotoEnd );
+		};
+
+		if ( typeof type !== "string" ) {
+			gotoEnd = clearQueue;
+			clearQueue = type;
+			type = undefined;
+		}
+		if ( clearQueue && type !== false ) {
+			this.queue( type || "fx", [] );
+		}
+
+		return this.each( function() {
+			var dequeue = true,
+				index = type != null && type + "queueHooks",
+				timers = jQuery.timers,
+				data = dataPriv.get( this );
+
+			if ( index ) {
+				if ( data[ index ] && data[ index ].stop ) {
+					stopQueue( data[ index ] );
+				}
+			} else {
+				for ( index in data ) {
+					if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
+						stopQueue( data[ index ] );
+					}
+				}
+			}
+
+			for ( index = timers.length; index--; ) {
+				if ( timers[ index ].elem === this &&
+					( type == null || timers[ index ].queue === type ) ) {
+
+					timers[ index ].anim.stop( gotoEnd );
+					dequeue = false;
+					timers.splice( index, 1 );
+				}
+			}
+
+			// Start the next in the queue if the last step wasn't forced.
+			// Timers currently will call their complete callbacks, which
+			// will dequeue but only if they were gotoEnd.
+			if ( dequeue || !gotoEnd ) {
+				jQuery.dequeue( this, type );
+			}
+		} );
+	},
+	finish: function( type ) {
+		if ( type !== false ) {
+			type = type || "fx";
+		}
+		return this.each( function() {
+			var index,
+				data = dataPriv.get( this ),
+				queue = data[ type + "queue" ],
+				hooks = data[ type + "queueHooks" ],
+				timers = jQuery.timers,
+				length = queue ? queue.length : 0;
+
+			// Enable finishing flag on private data
+			data.finish = true;
+
+			// Empty the queue first
+			jQuery.queue( this, type, [] );
+
+			if ( hooks && hooks.stop ) {
+				hooks.stop.call( this, true );
+			}
+
+			// Look for any active animations, and finish them
+			for ( index = timers.length; index--; ) {
+				if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
+					timers[ index ].anim.stop( true );
+					timers.splice( index, 1 );
+				}
+			}
+
+			// Look for any animations in the old queue and finish them
+			for ( index = 0; index < length; index++ ) {
+				if ( queue[ index ] && queue[ index ].finish ) {
+					queue[ index ].finish.call( this );
+				}
+			}
+
+			// Turn off finishing flag
+			delete data.finish;
+		} );
+	}
+} );
+
+jQuery.each( [ "toggle", "show", "hide" ], function( i, name ) {
+	var cssFn = jQuery.fn[ name ];
+	jQuery.fn[ name ] = function( speed, easing, callback ) {
+		return speed == null || typeof speed === "boolean" ?
+			cssFn.apply( this, arguments ) :
+			this.animate( genFx( name, true ), speed, easing, callback );
+	};
+} );
+
+// Generate shortcuts for custom animations
+jQuery.each( {
+	slideDown: genFx( "show" ),
+	slideUp: genFx( "hide" ),
+	slideToggle: genFx( "toggle" ),
+	fadeIn: { opacity: "show" },
+	fadeOut: { opacity: "hide" },
+	fadeToggle: { opacity: "toggle" }
+}, function( name, props ) {
+	jQuery.fn[ name ] = function( speed, easing, callback ) {
+		return this.animate( props, speed, easing, callback );
+	};
+} );
+
+jQuery.timers = [];
+jQuery.fx.tick = function() {
+	var timer,
+		i = 0,
+		timers = jQuery.timers;
+
+	fxNow = Date.now();
+
+	for ( ; i < timers.length; i++ ) {
+		timer = timers[ i ];
+
+		// Run the timer and safely remove it when done (allowing for external removal)
+		if ( !timer() && timers[ i ] === timer ) {
+			timers.splice( i--, 1 );
+		}
+	}
+
+	if ( !timers.length ) {
+		jQuery.fx.stop();
+	}
+	fxNow = undefined;
+};
+
+jQuery.fx.timer = function( timer ) {
+	jQuery.timers.push( timer );
+	jQuery.fx.start();
+};
+
+jQuery.fx.interval = 13;
+jQuery.fx.start = function() {
+	if ( inProgress ) {
+		return;
+	}
+
+	inProgress = true;
+	schedule();
+};
+
+jQuery.fx.stop = function() {
+	inProgress = null;
+};
+
+jQuery.fx.speeds = {
+	slow: 600,
+	fast: 200,
+
+	// Default speed
+	_default: 400
+};
+
+
+// Based off of the plugin by Clint Helfers, with permission.
+// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/
+jQuery.fn.delay = function( time, type ) {
+	time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
+	type = type || "fx";
+
+	return this.queue( type, function( next, hooks ) {
+		var timeout = window.setTimeout( next, time );
+		hooks.stop = function() {
+			window.clearTimeout( timeout );
+		};
+	} );
+};
+
+
+( function() {
+	var input = document.createElement( "input" ),
+		select = document.createElement( "select" ),
+		opt = select.appendChild( document.createElement( "option" ) );
+
+	input.type = "checkbox";
+
+	// Support: Android <=4.3 only
+	// Default value for a checkbox should be "on"
+	support.checkOn = input.value !== "";
+
+	// Support: IE <=11 only
+	// Must access selectedIndex to make default options select
+	support.optSelected = opt.selected;
+
+	// Support: IE <=11 only
+	// An input loses its value after becoming a radio
+	input = document.createElement( "input" );
+	input.value = "t";
+	input.type = "radio";
+	support.radioValue = input.value === "t";
+} )();
+
+
+var boolHook,
+	attrHandle = jQuery.expr.attrHandle;
+
+jQuery.fn.extend( {
+	attr: function( name, value ) {
+		return access( this, jQuery.attr, name, value, arguments.length > 1 );
+	},
+
+	removeAttr: function( name ) {
+		return this.each( function() {
+			jQuery.removeAttr( this, name );
+		} );
+	}
+} );
+
+jQuery.extend( {
+	attr: function( elem, name, value ) {
+		var ret, hooks,
+			nType = elem.nodeType;
+
+		// Don't get/set attributes on text, comment and attribute nodes
+		if ( nType === 3 || nType === 8 || nType === 2 ) {
+			return;
+		}
+
+		// Fallback to prop when attributes are not supported
+		if ( typeof elem.getAttribute === "undefined" ) {
+			return jQuery.prop( elem, name, value );
+		}
+
+		// Attribute hooks are determined by the lowercase version
+		// Grab necessary hook if one is defined
+		if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
+			hooks = jQuery.attrHooks[ name.toLowerCase() ] ||
+				( jQuery.expr.match.bool.test( name ) ? boolHook : undefined );
+		}
+
+		if ( value !== undefined ) {
+			if ( value === null ) {
+				jQuery.removeAttr( elem, name );
+				return;
+			}
+
+			if ( hooks && "set" in hooks &&
+				( ret = hooks.set( elem, value, name ) ) !== undefined ) {
+				return ret;
+			}
+
+			elem.setAttribute( name, value + "" );
+			return value;
+		}
+
+		if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
+			return ret;
+		}
+
+		ret = jQuery.find.attr( elem, name );
+
+		// Non-existent attributes return null, we normalize to undefined
+		return ret == null ? undefined : ret;
+	},
+
+	attrHooks: {
+		type: {
+			set: function( elem, value ) {
+				if ( !support.radioValue && value === "radio" &&
+					nodeName( elem, "input" ) ) {
+					var val = elem.value;
+					elem.setAttribute( "type", value );
+					if ( val ) {
+						elem.value = val;
+					}
+					return value;
+				}
+			}
+		}
+	},
+
+	removeAttr: function( elem, value ) {
+		var name,
+			i = 0,
+
+			// Attribute names can contain non-HTML whitespace characters
+			// https://html.spec.whatwg.org/multipage/syntax.html#attributes-2
+			attrNames = value && value.match( rnothtmlwhite );
+
+		if ( attrNames && elem.nodeType === 1 ) {
+			while ( ( name = attrNames[ i++ ] ) ) {
+				elem.removeAttribute( name );
+			}
+		}
+	}
+} );
+
+// Hooks for boolean attributes
+boolHook = {
+	set: function( elem, value, name ) {
+		if ( value === false ) {
+
+			// Remove boolean attributes when set to false
+			jQuery.removeAttr( elem, name );
+		} else {
+			elem.setAttribute( name, name );
+		}
+		return name;
+	}
+};
+
+jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) {
+	var getter = attrHandle[ name ] || jQuery.find.attr;
+
+	attrHandle[ name ] = function( elem, name, isXML ) {
+		var ret, handle,
+			lowercaseName = name.toLowerCase();
+
+		if ( !isXML ) {
+
+			// Avoid an infinite loop by temporarily removing this function from the getter
+			handle = attrHandle[ lowercaseName ];
+			attrHandle[ lowercaseName ] = ret;
+			ret = getter( elem, name, isXML ) != null ?
+				lowercaseName :
+				null;
+			attrHandle[ lowercaseName ] = handle;
+		}
+		return ret;
+	};
+} );
+
+
+
+
+var rfocusable = /^(?:input|select|textarea|button)$/i,
+	rclickable = /^(?:a|area)$/i;
+
+jQuery.fn.extend( {
+	prop: function( name, value ) {
+		return access( this, jQuery.prop, name, value, arguments.length > 1 );
+	},
+
+	removeProp: function( name ) {
+		return this.each( function() {
+			delete this[ jQuery.propFix[ name ] || name ];
+		} );
+	}
+} );
+
+jQuery.extend( {
+	prop: function( elem, name, value ) {
+		var ret, hooks,
+			nType = elem.nodeType;
+
+		// Don't get/set properties on text, comment and attribute nodes
+		if ( nType === 3 || nType === 8 || nType === 2 ) {
+			return;
+		}
+
+		if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
+
+			// Fix name and attach hooks
+			name = jQuery.propFix[ name ] || name;
+			hooks = jQuery.propHooks[ name ];
+		}
+
+		if ( value !== undefined ) {
+			if ( hooks && "set" in hooks &&
+				( ret = hooks.set( elem, value, name ) ) !== undefined ) {
+				return ret;
+			}
+
+			return ( elem[ name ] = value );
+		}
+
+		if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
+			return ret;
+		}
+
+		return elem[ name ];
+	},
+
+	propHooks: {
+		tabIndex: {
+			get: function( elem ) {
+
+				// Support: IE <=9 - 11 only
+				// elem.tabIndex doesn't always return the
+				// correct value when it hasn't been explicitly set
+				// https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
+				// Use proper attribute retrieval(#12072)
+				var tabindex = jQuery.find.attr( elem, "tabindex" );
+
+				if ( tabindex ) {
+					return parseInt( tabindex, 10 );
+				}
+
+				if (
+					rfocusable.test( elem.nodeName ) ||
+					rclickable.test( elem.nodeName ) &&
+					elem.href
+				) {
+					return 0;
+				}
+
+				return -1;
+			}
+		}
+	},
+
+	propFix: {
+		"for": "htmlFor",
+		"class": "className"
+	}
+} );
+
+// Support: IE <=11 only
+// Accessing the selectedIndex property
+// forces the browser to respect setting selected
+// on the option
+// The getter ensures a default option is selected
+// when in an optgroup
+// eslint rule "no-unused-expressions" is disabled for this code
+// since it considers such accessions noop
+if ( !support.optSelected ) {
+	jQuery.propHooks.selected = {
+		get: function( elem ) {
+
+			/* eslint no-unused-expressions: "off" */
+
+			var parent = elem.parentNode;
+			if ( parent && parent.parentNode ) {
+				parent.parentNode.selectedIndex;
+			}
+			return null;
+		},
+		set: function( elem ) {
+
+			/* eslint no-unused-expressions: "off" */
+
+			var parent = elem.parentNode;
+			if ( parent ) {
+				parent.selectedIndex;
+
+				if ( parent.parentNode ) {
+					parent.parentNode.selectedIndex;
+				}
+			}
+		}
+	};
+}
+
+jQuery.each( [
+	"tabIndex",
+	"readOnly",
+	"maxLength",
+	"cellSpacing",
+	"cellPadding",
+	"rowSpan",
+	"colSpan",
+	"useMap",
+	"frameBorder",
+	"contentEditable"
+], function() {
+	jQuery.propFix[ this.toLowerCase() ] = this;
+} );
+
+
+
+
+	// Strip and collapse whitespace according to HTML spec
+	// https://infra.spec.whatwg.org/#strip-and-collapse-ascii-whitespace
+	function stripAndCollapse( value ) {
+		var tokens = value.match( rnothtmlwhite ) || [];
+		return tokens.join( " " );
+	}
+
+
+function getClass( elem ) {
+	return elem.getAttribute && elem.getAttribute( "class" ) || "";
+}
+
+function classesToArray( value ) {
+	if ( Array.isArray( value ) ) {
+		return value;
+	}
+	if ( typeof value === "string" ) {
+		return value.match( rnothtmlwhite ) || [];
+	}
+	return [];
+}
+
+jQuery.fn.extend( {
+	addClass: function( value ) {
+		var classes, elem, cur, curValue, clazz, j, finalValue,
+			i = 0;
+
+		if ( isFunction( value ) ) {
+			return this.each( function( j ) {
+				jQuery( this ).addClass( value.call( this, j, getClass( this ) ) );
+			} );
+		}
+
+		classes = classesToArray( value );
+
+		if ( classes.length ) {
+			while ( ( elem = this[ i++ ] ) ) {
+				curValue = getClass( elem );
+				cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
+
+				if ( cur ) {
+					j = 0;
+					while ( ( clazz = classes[ j++ ] ) ) {
+						if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
+							cur += clazz + " ";
+						}
+					}
+
+					// Only assign if different to avoid unneeded rendering.
+					finalValue = stripAndCollapse( cur );
+					if ( curValue !== finalValue ) {
+						elem.setAttribute( "class", finalValue );
+					}
+				}
+			}
+		}
+
+		return this;
+	},
+
+	removeClass: function( value ) {
+		var classes, elem, cur, curValue, clazz, j, finalValue,
+			i = 0;
+
+		if ( isFunction( value ) ) {
+			return this.each( function( j ) {
+				jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) );
+			} );
+		}
+
+		if ( !arguments.length ) {
+			return this.attr( "class", "" );
+		}
+
+		classes = classesToArray( value );
+
+		if ( classes.length ) {
+			while ( ( elem = this[ i++ ] ) ) {
+				curValue = getClass( elem );
+
+				// This expression is here for better compressibility (see addClass)
+				cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
+
+				if ( cur ) {
+					j = 0;
+					while ( ( clazz = classes[ j++ ] ) ) {
+
+						// Remove *all* instances
+						while ( cur.indexOf( " " + clazz + " " ) > -1 ) {
+							cur = cur.replace( " " + clazz + " ", " " );
+						}
+					}
+
+					// Only assign if different to avoid unneeded rendering.
+					finalValue = stripAndCollapse( cur );
+					if ( curValue !== finalValue ) {
+						elem.setAttribute( "class", finalValue );
+					}
+				}
+			}
+		}
+
+		return this;
+	},
+
+	toggleClass: function( value, stateVal ) {
+		var type = typeof value,
+			isValidValue = type === "string" || Array.isArray( value );
+
+		if ( typeof stateVal === "boolean" && isValidValue ) {
+			return stateVal ? this.addClass( value ) : this.removeClass( value );
+		}
+
+		if ( isFunction( value ) ) {
+			return this.each( function( i ) {
+				jQuery( this ).toggleClass(
+					value.call( this, i, getClass( this ), stateVal ),
+					stateVal
+				);
+			} );
+		}
+
+		return this.each( function() {
+			var className, i, self, classNames;
+
+			if ( isValidValue ) {
+
+				// Toggle individual class names
+				i = 0;
+				self = jQuery( this );
+				classNames = classesToArray( value );
+
+				while ( ( className = classNames[ i++ ] ) ) {
+
+					// Check each className given, space separated list
+					if ( self.hasClass( className ) ) {
+						self.removeClass( className );
+					} else {
+						self.addClass( className );
+					}
+				}
+
+			// Toggle whole class name
+			} else if ( value === undefined || type === "boolean" ) {
+				className = getClass( this );
+				if ( className ) {
+
+					// Store className if set
+					dataPriv.set( this, "__className__", className );
+				}
+
+				// If the element has a class name or if we're passed `false`,
+				// then remove the whole classname (if there was one, the above saved it).
+				// Otherwise bring back whatever was previously saved (if anything),
+				// falling back to the empty string if nothing was stored.
+				if ( this.setAttribute ) {
+					this.setAttribute( "class",
+						className || value === false ?
+						"" :
+						dataPriv.get( this, "__className__" ) || ""
+					);
+				}
+			}
+		} );
+	},
+
+	hasClass: function( selector ) {
+		var className, elem,
+			i = 0;
+
+		className = " " + selector + " ";
+		while ( ( elem = this[ i++ ] ) ) {
+			if ( elem.nodeType === 1 &&
+				( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) {
+					return true;
+			}
+		}
+
+		return false;
+	}
+} );
+
+
+
+
+var rreturn = /\r/g;
+
+jQuery.fn.extend( {
+	val: function( value ) {
+		var hooks, ret, valueIsFunction,
+			elem = this[ 0 ];
+
+		if ( !arguments.length ) {
+			if ( elem ) {
+				hooks = jQuery.valHooks[ elem.type ] ||
+					jQuery.valHooks[ elem.nodeName.toLowerCase() ];
+
+				if ( hooks &&
+					"get" in hooks &&
+					( ret = hooks.get( elem, "value" ) ) !== undefined
+				) {
+					return ret;
+				}
+
+				ret = elem.value;
+
+				// Handle most common string cases
+				if ( typeof ret === "string" ) {
+					return ret.replace( rreturn, "" );
+				}
+
+				// Handle cases where value is null/undef or number
+				return ret == null ? "" : ret;
+			}
+
+			return;
+		}
+
+		valueIsFunction = isFunction( value );
+
+		return this.each( function( i ) {
+			var val;
+
+			if ( this.nodeType !== 1 ) {
+				return;
+			}
+
+			if ( valueIsFunction ) {
+				val = value.call( this, i, jQuery( this ).val() );
+			} else {
+				val = value;
+			}
+
+			// Treat null/undefined as ""; convert numbers to string
+			if ( val == null ) {
+				val = "";
+
+			} else if ( typeof val === "number" ) {
+				val += "";
+
+			} else if ( Array.isArray( val ) ) {
+				val = jQuery.map( val, function( value ) {
+					return value == null ? "" : value + "";
+				} );
+			}
+
+			hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
+
+			// If set returns undefined, fall back to normal setting
+			if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) {
+				this.value = val;
+			}
+		} );
+	}
+} );
+
+jQuery.extend( {
+	valHooks: {
+		option: {
+			get: function( elem ) {
+
+				var val = jQuery.find.attr( elem, "value" );
+				return val != null ?
+					val :
+
+					// Support: IE <=10 - 11 only
+					// option.text throws exceptions (#14686, #14858)
+					// Strip and collapse whitespace
+					// https://html.spec.whatwg.org/#strip-and-collapse-whitespace
+					stripAndCollapse( jQuery.text( elem ) );
+			}
+		},
+		select: {
+			get: function( elem ) {
+				var value, option, i,
+					options = elem.options,
+					index = elem.selectedIndex,
+					one = elem.type === "select-one",
+					values = one ? null : [],
+					max = one ? index + 1 : options.length;
+
+				if ( index < 0 ) {
+					i = max;
+
+				} else {
+					i = one ? index : 0;
+				}
+
+				// Loop through all the selected options
+				for ( ; i < max; i++ ) {
+					option = options[ i ];
+
+					// Support: IE <=9 only
+					// IE8-9 doesn't update selected after form reset (#2551)
+					if ( ( option.selected || i === index ) &&
+
+							// Don't return options that are disabled or in a disabled optgroup
+							!option.disabled &&
+							( !option.parentNode.disabled ||
+								!nodeName( option.parentNode, "optgroup" ) ) ) {
+
+						// Get the specific value for the option
+						value = jQuery( option ).val();
+
+						// We don't need an array for one selects
+						if ( one ) {
+							return value;
+						}
+
+						// Multi-Selects return an array
+						values.push( value );
+					}
+				}
+
+				return values;
+			},
+
+			set: function( elem, value ) {
+				var optionSet, option,
+					options = elem.options,
+					values = jQuery.makeArray( value ),
+					i = options.length;
+
+				while ( i-- ) {
+					option = options[ i ];
+
+					/* eslint-disable no-cond-assign */
+
+					if ( option.selected =
+						jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1
+					) {
+						optionSet = true;
+					}
+
+					/* eslint-enable no-cond-assign */
+				}
+
+				// Force browsers to behave consistently when non-matching value is set
+				if ( !optionSet ) {
+					elem.selectedIndex = -1;
+				}
+				return values;
+			}
+		}
+	}
+} );
+
+// Radios and checkboxes getter/setter
+jQuery.each( [ "radio", "checkbox" ], function() {
+	jQuery.valHooks[ this ] = {
+		set: function( elem, value ) {
+			if ( Array.isArray( value ) ) {
+				return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 );
+			}
+		}
+	};
+	if ( !support.checkOn ) {
+		jQuery.valHooks[ this ].get = function( elem ) {
+			return elem.getAttribute( "value" ) === null ? "on" : elem.value;
+		};
+	}
+} );
+
+
+
+
+// Return jQuery for attributes-only inclusion
+
+
+support.focusin = "onfocusin" in window;
+
+
+var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
+	stopPropagationCallback = function( e ) {
+		e.stopPropagation();
+	};
+
+jQuery.extend( jQuery.event, {
+
+	trigger: function( event, data, elem, onlyHandlers ) {
+
+		var i, cur, tmp, bubbleType, ontype, handle, special, lastElement,
+			eventPath = [ elem || document ],
+			type = hasOwn.call( event, "type" ) ? event.type : event,
+			namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : [];
+
+		cur = lastElement = tmp = elem = elem || document;
+
+		// Don't do events on text and comment nodes
+		if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
+			return;
+		}
+
+		// focus/blur morphs to focusin/out; ensure we're not firing them right now
+		if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
+			return;
+		}
+
+		if ( type.indexOf( "." ) > -1 ) {
+
+			// Namespaced trigger; create a regexp to match event type in handle()
+			namespaces = type.split( "." );
+			type = namespaces.shift();
+			namespaces.sort();
+		}
+		ontype = type.indexOf( ":" ) < 0 && "on" + type;
+
+		// Caller can pass in a jQuery.Event object, Object, or just an event type string
+		event = event[ jQuery.expando ] ?
+			event :
+			new jQuery.Event( type, typeof event === "object" && event );
+
+		// Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
+		event.isTrigger = onlyHandlers ? 2 : 3;
+		event.namespace = namespaces.join( "." );
+		event.rnamespace = event.namespace ?
+			new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) :
+			null;
+
+		// Clean up the event in case it is being reused
+		event.result = undefined;
+		if ( !event.target ) {
+			event.target = elem;
+		}
+
+		// Clone any incoming data and prepend the event, creating the handler arg list
+		data = data == null ?
+			[ event ] :
+			jQuery.makeArray( data, [ event ] );
+
+		// Allow special events to draw outside the lines
+		special = jQuery.event.special[ type ] || {};
+		if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
+			return;
+		}
+
+		// Determine event propagation path in advance, per W3C events spec (#9951)
+		// Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
+		if ( !onlyHandlers && !special.noBubble && !isWindow( elem ) ) {
+
+			bubbleType = special.delegateType || type;
+			if ( !rfocusMorph.test( bubbleType + type ) ) {
+				cur = cur.parentNode;
+			}
+			for ( ; cur; cur = cur.parentNode ) {
+				eventPath.push( cur );
+				tmp = cur;
+			}
+
+			// Only add window if we got to document (e.g., not plain obj or detached DOM)
+			if ( tmp === ( elem.ownerDocument || document ) ) {
+				eventPath.push( tmp.defaultView || tmp.parentWindow || window );
+			}
+		}
+
+		// Fire handlers on the event path
+		i = 0;
+		while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) {
+			lastElement = cur;
+			event.type = i > 1 ?
+				bubbleType :
+				special.bindType || type;
+
+			// jQuery handler
+			handle = ( dataPriv.get( cur, "events" ) || {} )[ event.type ] &&
+				dataPriv.get( cur, "handle" );
+			if ( handle ) {
+				handle.apply( cur, data );
+			}
+
+			// Native handler
+			handle = ontype && cur[ ontype ];
+			if ( handle && handle.apply && acceptData( cur ) ) {
+				event.result = handle.apply( cur, data );
+				if ( event.result === false ) {
+					event.preventDefault();
+				}
+			}
+		}
+		event.type = type;
+
+		// If nobody prevented the default action, do it now
+		if ( !onlyHandlers && !event.isDefaultPrevented() ) {
+
+			if ( ( !special._default ||
+				special._default.apply( eventPath.pop(), data ) === false ) &&
+				acceptData( elem ) ) {
+
+				// Call a native DOM method on the target with the same name as the event.
+				// Don't do default actions on window, that's where global variables be (#6170)
+				if ( ontype && isFunction( elem[ type ] ) && !isWindow( elem ) ) {
+
+					// Don't re-trigger an onFOO event when we call its FOO() method
+					tmp = elem[ ontype ];
+
+					if ( tmp ) {
+						elem[ ontype ] = null;
+					}
+
+					// Prevent re-triggering of the same event, since we already bubbled it above
+					jQuery.event.triggered = type;
+
+					if ( event.isPropagationStopped() ) {
+						lastElement.addEventListener( type, stopPropagationCallback );
+					}
+
+					elem[ type ]();
+
+					if ( event.isPropagationStopped() ) {
+						lastElement.removeEventListener( type, stopPropagationCallback );
+					}
+
+					jQuery.event.triggered = undefined;
+
+					if ( tmp ) {
+						elem[ ontype ] = tmp;
+					}
+				}
+			}
+		}
+
+		return event.result;
+	},
+
+	// Piggyback on a donor event to simulate a different one
+	// Used only for `focus(in | out)` events
+	simulate: function( type, elem, event ) {
+		var e = jQuery.extend(
+			new jQuery.Event(),
+			event,
+			{
+				type: type,
+				isSimulated: true
+			}
+		);
+
+		jQuery.event.trigger( e, null, elem );
+	}
+
+} );
+
+jQuery.fn.extend( {
+
+	trigger: function( type, data ) {
+		return this.each( function() {
+			jQuery.event.trigger( type, data, this );
+		} );
+	},
+	triggerHandler: function( type, data ) {
+		var elem = this[ 0 ];
+		if ( elem ) {
+			return jQuery.event.trigger( type, data, elem, true );
+		}
+	}
+} );
+
+
+// Support: Firefox <=44
+// Firefox doesn't have focus(in | out) events
+// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787
+//
+// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1
+// focus(in | out) events fire after focus & blur events,
+// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order
+// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857
+if ( !support.focusin ) {
+	jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) {
+
+		// Attach a single capturing handler on the document while someone wants focusin/focusout
+		var handler = function( event ) {
+			jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) );
+		};
+
+		jQuery.event.special[ fix ] = {
+			setup: function() {
+				var doc = this.ownerDocument || this,
+					attaches = dataPriv.access( doc, fix );
+
+				if ( !attaches ) {
+					doc.addEventListener( orig, handler, true );
+				}
+				dataPriv.access( doc, fix, ( attaches || 0 ) + 1 );
+			},
+			teardown: function() {
+				var doc = this.ownerDocument || this,
+					attaches = dataPriv.access( doc, fix ) - 1;
+
+				if ( !attaches ) {
+					doc.removeEventListener( orig, handler, true );
+					dataPriv.remove( doc, fix );
+
+				} else {
+					dataPriv.access( doc, fix, attaches );
+				}
+			}
+		};
+	} );
+}
+var location = window.location;
+
+var nonce = Date.now();
+
+var rquery = ( /\?/ );
+
+
+
+// Cross-browser xml parsing
+jQuery.parseXML = function( data ) {
+	var xml;
+	if ( !data || typeof data !== "string" ) {
+		return null;
+	}
+
+	// Support: IE 9 - 11 only
+	// IE throws on parseFromString with invalid input.
+	try {
+		xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" );
+	} catch ( e ) {
+		xml = undefined;
+	}
+
+	if ( !xml || xml.getElementsByTagName( "parsererror" ).length ) {
+		jQuery.error( "Invalid XML: " + data );
+	}
+	return xml;
+};
+
+
+var
+	rbracket = /\[\]$/,
+	rCRLF = /\r?\n/g,
+	rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
+	rsubmittable = /^(?:input|select|textarea|keygen)/i;
+
+function buildParams( prefix, obj, traditional, add ) {
+	var name;
+
+	if ( Array.isArray( obj ) ) {
+
+		// Serialize array item.
+		jQuery.each( obj, function( i, v ) {
+			if ( traditional || rbracket.test( prefix ) ) {
+
+				// Treat each array item as a scalar.
+				add( prefix, v );
+
+			} else {
+
+				// Item is non-scalar (array or object), encode its numeric index.
+				buildParams(
+					prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]",
+					v,
+					traditional,
+					add
+				);
+			}
+		} );
+
+	} else if ( !traditional && toType( obj ) === "object" ) {
+
+		// Serialize object item.
+		for ( name in obj ) {
+			buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
+		}
+
+	} else {
+
+		// Serialize scalar item.
+		add( prefix, obj );
+	}
+}
+
+// Serialize an array of form elements or a set of
+// key/values into a query string
+jQuery.param = function( a, traditional ) {
+	var prefix,
+		s = [],
+		add = function( key, valueOrFunction ) {
+
+			// If value is a function, invoke it and use its return value
+			var value = isFunction( valueOrFunction ) ?
+				valueOrFunction() :
+				valueOrFunction;
+
+			s[ s.length ] = encodeURIComponent( key ) + "=" +
+				encodeURIComponent( value == null ? "" : value );
+		};
+
+	if ( a == null ) {
+		return "";
+	}
+
+	// If an array was passed in, assume that it is an array of form elements.
+	if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
+
+		// Serialize the form elements
+		jQuery.each( a, function() {
+			add( this.name, this.value );
+		} );
+
+	} else {
+
+		// If traditional, encode the "old" way (the way 1.3.2 or older
+		// did it), otherwise encode params recursively.
+		for ( prefix in a ) {
+			buildParams( prefix, a[ prefix ], traditional, add );
+		}
+	}
+
+	// Return the resulting serialization
+	return s.join( "&" );
+};
+
+jQuery.fn.extend( {
+	serialize: function() {
+		return jQuery.param( this.serializeArray() );
+	},
+	serializeArray: function() {
+		return this.map( function() {
+
+			// Can add propHook for "elements" to filter or add form elements
+			var elements = jQuery.prop( this, "elements" );
+			return elements ? jQuery.makeArray( elements ) : this;
+		} )
+		.filter( function() {
+			var type = this.type;
+
+			// Use .is( ":disabled" ) so that fieldset[disabled] works
+			return this.name && !jQuery( this ).is( ":disabled" ) &&
+				rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
+				( this.checked || !rcheckableType.test( type ) );
+		} )
+		.map( function( i, elem ) {
+			var val = jQuery( this ).val();
+
+			if ( val == null ) {
+				return null;
+			}
+
+			if ( Array.isArray( val ) ) {
+				return jQuery.map( val, function( val ) {
+					return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+				} );
+			}
+
+			return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
+		} ).get();
+	}
+} );
+
+
+var
+	r20 = /%20/g,
+	rhash = /#.*$/,
+	rantiCache = /([?&])_=[^&]*/,
+	rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg,
+
+	// #7653, #8125, #8152: local protocol detection
+	rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
+	rnoContent = /^(?:GET|HEAD)$/,
+	rprotocol = /^\/\//,
+
+	/* Prefilters
+	 * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
+	 * 2) These are called:
+	 *    - BEFORE asking for a transport
+	 *    - AFTER param serialization (s.data is a string if s.processData is true)
+	 * 3) key is the dataType
+	 * 4) the catchall symbol "*" can be used
+	 * 5) execution will start with transport dataType and THEN continue down to "*" if needed
+	 */
+	prefilters = {},
+
+	/* Transports bindings
+	 * 1) key is the dataType
+	 * 2) the catchall symbol "*" can be used
+	 * 3) selection will start with transport dataType and THEN go to "*" if needed
+	 */
+	transports = {},
+
+	// Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
+	allTypes = "*/".concat( "*" ),
+
+	// Anchor tag for parsing the document origin
+	originAnchor = document.createElement( "a" );
+	originAnchor.href = location.href;
+
+// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
+function addToPrefiltersOrTransports( structure ) {
+
+	// dataTypeExpression is optional and defaults to "*"
+	return function( dataTypeExpression, func ) {
+
+		if ( typeof dataTypeExpression !== "string" ) {
+			func = dataTypeExpression;
+			dataTypeExpression = "*";
+		}
+
+		var dataType,
+			i = 0,
+			dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || [];
+
+		if ( isFunction( func ) ) {
+
+			// For each dataType in the dataTypeExpression
+			while ( ( dataType = dataTypes[ i++ ] ) ) {
+
+				// Prepend if requested
+				if ( dataType[ 0 ] === "+" ) {
+					dataType = dataType.slice( 1 ) || "*";
+					( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func );
+
+				// Otherwise append
+				} else {
+					( structure[ dataType ] = structure[ dataType ] || [] ).push( func );
+				}
+			}
+		}
+	};
+}
+
+// Base inspection function for prefilters and transports
+function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) {
+
+	var inspected = {},
+		seekingTransport = ( structure === transports );
+
+	function inspect( dataType ) {
+		var selected;
+		inspected[ dataType ] = true;
+		jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
+			var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
+			if ( typeof dataTypeOrTransport === "string" &&
+				!seekingTransport && !inspected[ dataTypeOrTransport ] ) {
+
+				options.dataTypes.unshift( dataTypeOrTransport );
+				inspect( dataTypeOrTransport );
+				return false;
+			} else if ( seekingTransport ) {
+				return !( selected = dataTypeOrTransport );
+			}
+		} );
+		return selected;
+	}
+
+	return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" );
+}
+
+// A special extend for ajax options
+// that takes "flat" options (not to be deep extended)
+// Fixes #9887
+function ajaxExtend( target, src ) {
+	var key, deep,
+		flatOptions = jQuery.ajaxSettings.flatOptions || {};
+
+	for ( key in src ) {
+		if ( src[ key ] !== undefined ) {
+			( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ];
+		}
+	}
+	if ( deep ) {
+		jQuery.extend( true, target, deep );
+	}
+
+	return target;
+}
+
+/* Handles responses to an ajax request:
+ * - finds the right dataType (mediates between content-type and expected dataType)
+ * - returns the corresponding response
+ */
+function ajaxHandleResponses( s, jqXHR, responses ) {
+
+	var ct, type, finalDataType, firstDataType,
+		contents = s.contents,
+		dataTypes = s.dataTypes;
+
+	// Remove auto dataType and get content-type in the process
+	while ( dataTypes[ 0 ] === "*" ) {
+		dataTypes.shift();
+		if ( ct === undefined ) {
+			ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" );
+		}
+	}
+
+	// Check if we're dealing with a known content-type
+	if ( ct ) {
+		for ( type in contents ) {
+			if ( contents[ type ] && contents[ type ].test( ct ) ) {
+				dataTypes.unshift( type );
+				break;
+			}
+		}
+	}
+
+	// Check to see if we have a response for the expected dataType
+	if ( dataTypes[ 0 ] in responses ) {
+		finalDataType = dataTypes[ 0 ];
+	} else {
+
+		// Try convertible dataTypes
+		for ( type in responses ) {
+			if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) {
+				finalDataType = type;
+				break;
+			}
+			if ( !firstDataType ) {
+				firstDataType = type;
+			}
+		}
+
+		// Or just use first one
+		finalDataType = finalDataType || firstDataType;
+	}
+
+	// If we found a dataType
+	// We add the dataType to the list if needed
+	// and return the corresponding response
+	if ( finalDataType ) {
+		if ( finalDataType !== dataTypes[ 0 ] ) {
+			dataTypes.unshift( finalDataType );
+		}
+		return responses[ finalDataType ];
+	}
+}
+
+/* Chain conversions given the request and the original response
+ * Also sets the responseXXX fields on the jqXHR instance
+ */
+function ajaxConvert( s, response, jqXHR, isSuccess ) {
+	var conv2, current, conv, tmp, prev,
+		converters = {},
+
+		// Work with a copy of dataTypes in case we need to modify it for conversion
+		dataTypes = s.dataTypes.slice();
+
+	// Create converters map with lowercased keys
+	if ( dataTypes[ 1 ] ) {
+		for ( conv in s.converters ) {
+			converters[ conv.toLowerCase() ] = s.converters[ conv ];
+		}
+	}
+
+	current = dataTypes.shift();
+
+	// Convert to each sequential dataType
+	while ( current ) {
+
+		if ( s.responseFields[ current ] ) {
+			jqXHR[ s.responseFields[ current ] ] = response;
+		}
+
+		// Apply the dataFilter if provided
+		if ( !prev && isSuccess && s.dataFilter ) {
+			response = s.dataFilter( response, s.dataType );
+		}
+
+		prev = current;
+		current = dataTypes.shift();
+
+		if ( current ) {
+
+			// There's only work to do if current dataType is non-auto
+			if ( current === "*" ) {
+
+				current = prev;
+
+			// Convert response if prev dataType is non-auto and differs from current
+			} else if ( prev !== "*" && prev !== current ) {
+
+				// Seek a direct converter
+				conv = converters[ prev + " " + current ] || converters[ "* " + current ];
+
+				// If none found, seek a pair
+				if ( !conv ) {
+					for ( conv2 in converters ) {
+
+						// If conv2 outputs current
+						tmp = conv2.split( " " );
+						if ( tmp[ 1 ] === current ) {
+
+							// If prev can be converted to accepted input
+							conv = converters[ prev + " " + tmp[ 0 ] ] ||
+								converters[ "* " + tmp[ 0 ] ];
+							if ( conv ) {
+
+								// Condense equivalence converters
+								if ( conv === true ) {
+									conv = converters[ conv2 ];
+
+								// Otherwise, insert the intermediate dataType
+								} else if ( converters[ conv2 ] !== true ) {
+									current = tmp[ 0 ];
+									dataTypes.unshift( tmp[ 1 ] );
+								}
+								break;
+							}
+						}
+					}
+				}
+
+				// Apply converter (if not an equivalence)
+				if ( conv !== true ) {
+
+					// Unless errors are allowed to bubble, catch and return them
+					if ( conv && s.throws ) {
+						response = conv( response );
+					} else {
+						try {
+							response = conv( response );
+						} catch ( e ) {
+							return {
+								state: "parsererror",
+								error: conv ? e : "No conversion from " + prev + " to " + current
+							};
+						}
+					}
+				}
+			}
+		}
+	}
+
+	return { state: "success", data: response };
+}
+
+jQuery.extend( {
+
+	// Counter for holding the number of active queries
+	active: 0,
+
+	// Last-Modified header cache for next request
+	lastModified: {},
+	etag: {},
+
+	ajaxSettings: {
+		url: location.href,
+		type: "GET",
+		isLocal: rlocalProtocol.test( location.protocol ),
+		global: true,
+		processData: true,
+		async: true,
+		contentType: "application/x-www-form-urlencoded; charset=UTF-8",
+
+		/*
+		timeout: 0,
+		data: null,
+		dataType: null,
+		username: null,
+		password: null,
+		cache: null,
+		throws: false,
+		traditional: false,
+		headers: {},
+		*/
+
+		accepts: {
+			"*": allTypes,
+			text: "text/plain",
+			html: "text/html",
+			xml: "application/xml, text/xml",
+			json: "application/json, text/javascript"
+		},
+
+		contents: {
+			xml: /\bxml\b/,
+			html: /\bhtml/,
+			json: /\bjson\b/
+		},
+
+		responseFields: {
+			xml: "responseXML",
+			text: "responseText",
+			json: "responseJSON"
+		},
+
+		// Data converters
+		// Keys separate source (or catchall "*") and destination types with a single space
+		converters: {
+
+			// Convert anything to text
+			"* text": String,
+
+			// Text to html (true = no transformation)
+			"text html": true,
+
+			// Evaluate text as a json expression
+			"text json": JSON.parse,
+
+			// Parse text as xml
+			"text xml": jQuery.parseXML
+		},
+
+		// For options that shouldn't be deep extended:
+		// you can add your own custom options here if
+		// and when you create one that shouldn't be
+		// deep extended (see ajaxExtend)
+		flatOptions: {
+			url: true,
+			context: true
+		}
+	},
+
+	// Creates a full fledged settings object into target
+	// with both ajaxSettings and settings fields.
+	// If target is omitted, writes into ajaxSettings.
+	ajaxSetup: function( target, settings ) {
+		return settings ?
+
+			// Building a settings object
+			ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) :
+
+			// Extending ajaxSettings
+			ajaxExtend( jQuery.ajaxSettings, target );
+	},
+
+	ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
+	ajaxTransport: addToPrefiltersOrTransports( transports ),
+
+	// Main method
+	ajax: function( url, options ) {
+
+		// If url is an object, simulate pre-1.5 signature
+		if ( typeof url === "object" ) {
+			options = url;
+			url = undefined;
+		}
+
+		// Force options to be an object
+		options = options || {};
+
+		var transport,
+
+			// URL without anti-cache param
+			cacheURL,
+
+			// Response headers
+			responseHeadersString,
+			responseHeaders,
+
+			// timeout handle
+			timeoutTimer,
+
+			// Url cleanup var
+			urlAnchor,
+
+			// Request state (becomes false upon send and true upon completion)
+			completed,
+
+			// To know if global events are to be dispatched
+			fireGlobals,
+
+			// Loop variable
+			i,
+
+			// uncached part of the url
+			uncached,
+
+			// Create the final options object
+			s = jQuery.ajaxSetup( {}, options ),
+
+			// Callbacks context
+			callbackContext = s.context || s,
+
+			// Context for global events is callbackContext if it is a DOM node or jQuery collection
+			globalEventContext = s.context &&
+				( callbackContext.nodeType || callbackContext.jquery ) ?
+					jQuery( callbackContext ) :
+					jQuery.event,
+
+			// Deferreds
+			deferred = jQuery.Deferred(),
+			completeDeferred = jQuery.Callbacks( "once memory" ),
+
+			// Status-dependent callbacks
+			statusCode = s.statusCode || {},
+
+			// Headers (they are sent all at once)
+			requestHeaders = {},
+			requestHeadersNames = {},
+
+			// Default abort message
+			strAbort = "canceled",
+
+			// Fake xhr
+			jqXHR = {
+				readyState: 0,
+
+				// Builds headers hashtable if needed
+				getResponseHeader: function( key ) {
+					var match;
+					if ( completed ) {
+						if ( !responseHeaders ) {
+							responseHeaders = {};
+							while ( ( match = rheaders.exec( responseHeadersString ) ) ) {
+								responseHeaders[ match[ 1 ].toLowerCase() + " " ] =
+									( responseHeaders[ match[ 1 ].toLowerCase() + " " ] || [] )
+										.concat( match[ 2 ] );
+							}
+						}
+						match = responseHeaders[ key.toLowerCase() + " " ];
+					}
+					return match == null ? null : match.join( ", " );
+				},
+
+				// Raw string
+				getAllResponseHeaders: function() {
+					return completed ? responseHeadersString : null;
+				},
+
+				// Caches the header
+				setRequestHeader: function( name, value ) {
+					if ( completed == null ) {
+						name = requestHeadersNames[ name.toLowerCase() ] =
+							requestHeadersNames[ name.toLowerCase() ] || name;
+						requestHeaders[ name ] = value;
+					}
+					return this;
+				},
+
+				// Overrides response content-type header
+				overrideMimeType: function( type ) {
+					if ( completed == null ) {
+						s.mimeType = type;
+					}
+					return this;
+				},
+
+				// Status-dependent callbacks
+				statusCode: function( map ) {
+					var code;
+					if ( map ) {
+						if ( completed ) {
+
+							// Execute the appropriate callbacks
+							jqXHR.always( map[ jqXHR.status ] );
+						} else {
+
+							// Lazy-add the new callbacks in a way that preserves old ones
+							for ( code in map ) {
+								statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
+							}
+						}
+					}
+					return this;
+				},
+
+				// Cancel the request
+				abort: function( statusText ) {
+					var finalText = statusText || strAbort;
+					if ( transport ) {
+						transport.abort( finalText );
+					}
+					done( 0, finalText );
+					return this;
+				}
+			};
+
+		// Attach deferreds
+		deferred.promise( jqXHR );
+
+		// Add protocol if not provided (prefilters might expect it)
+		// Handle falsy url in the settings object (#10093: consistency with old signature)
+		// We also use the url parameter if available
+		s.url = ( ( url || s.url || location.href ) + "" )
+			.replace( rprotocol, location.protocol + "//" );
+
+		// Alias method option to type as per ticket #12004
+		s.type = options.method || options.type || s.method || s.type;
+
+		// Extract dataTypes list
+		s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ];
+
+		// A cross-domain request is in order when the origin doesn't match the current origin.
+		if ( s.crossDomain == null ) {
+			urlAnchor = document.createElement( "a" );
+
+			// Support: IE <=8 - 11, Edge 12 - 15
+			// IE throws exception on accessing the href property if url is malformed,
+			// e.g. http://example.com:80x/
+			try {
+				urlAnchor.href = s.url;
+
+				// Support: IE <=8 - 11 only
+				// Anchor's host property isn't correctly set when s.url is relative
+				urlAnchor.href = urlAnchor.href;
+				s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !==
+					urlAnchor.protocol + "//" + urlAnchor.host;
+			} catch ( e ) {
+
+				// If there is an error parsing the URL, assume it is crossDomain,
+				// it can be rejected by the transport if it is invalid
+				s.crossDomain = true;
+			}
+		}
+
+		// Convert data if not already a string
+		if ( s.data && s.processData && typeof s.data !== "string" ) {
+			s.data = jQuery.param( s.data, s.traditional );
+		}
+
+		// Apply prefilters
+		inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
+
+		// If request was aborted inside a prefilter, stop there
+		if ( completed ) {
+			return jqXHR;
+		}
+
+		// We can fire global events as of now if asked to
+		// Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118)
+		fireGlobals = jQuery.event && s.global;
+
+		// Watch for a new set of requests
+		if ( fireGlobals && jQuery.active++ === 0 ) {
+			jQuery.event.trigger( "ajaxStart" );
+		}
+
+		// Uppercase the type
+		s.type = s.type.toUpperCase();
+
+		// Determine if request has content
+		s.hasContent = !rnoContent.test( s.type );
+
+		// Save the URL in case we're toying with the If-Modified-Since
+		// and/or If-None-Match header later on
+		// Remove hash to simplify url manipulation
+		cacheURL = s.url.replace( rhash, "" );
+
+		// More options handling for requests with no content
+		if ( !s.hasContent ) {
+
+			// Remember the hash so we can put it back
+			uncached = s.url.slice( cacheURL.length );
+
+			// If data is available and should be processed, append data to url
+			if ( s.data && ( s.processData || typeof s.data === "string" ) ) {
+				cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data;
+
+				// #9682: remove data so that it's not used in an eventual retry
+				delete s.data;
+			}
+
+			// Add or update anti-cache param if needed
+			if ( s.cache === false ) {
+				cacheURL = cacheURL.replace( rantiCache, "$1" );
+				uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce++ ) + uncached;
+			}
+
+			// Put hash and anti-cache on the URL that will be requested (gh-1732)
+			s.url = cacheURL + uncached;
+
+		// Change '%20' to '+' if this is encoded form body content (gh-2658)
+		} else if ( s.data && s.processData &&
+			( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) {
+			s.data = s.data.replace( r20, "+" );
+		}
+
+		// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+		if ( s.ifModified ) {
+			if ( jQuery.lastModified[ cacheURL ] ) {
+				jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] );
+			}
+			if ( jQuery.etag[ cacheURL ] ) {
+				jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] );
+			}
+		}
+
+		// Set the correct header, if data is being sent
+		if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
+			jqXHR.setRequestHeader( "Content-Type", s.contentType );
+		}
+
+		// Set the Accepts header for the server, depending on the dataType
+		jqXHR.setRequestHeader(
+			"Accept",
+			s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ?
+				s.accepts[ s.dataTypes[ 0 ] ] +
+					( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
+				s.accepts[ "*" ]
+		);
+
+		// Check for headers option
+		for ( i in s.headers ) {
+			jqXHR.setRequestHeader( i, s.headers[ i ] );
+		}
+
+		// Allow custom headers/mimetypes and early abort
+		if ( s.beforeSend &&
+			( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) {
+
+			// Abort if not done already and return
+			return jqXHR.abort();
+		}
+
+		// Aborting is no longer a cancellation
+		strAbort = "abort";
+
+		// Install callbacks on deferreds
+		completeDeferred.add( s.complete );
+		jqXHR.done( s.success );
+		jqXHR.fail( s.error );
+
+		// Get transport
+		transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
+
+		// If no transport, we auto-abort
+		if ( !transport ) {
+			done( -1, "No Transport" );
+		} else {
+			jqXHR.readyState = 1;
+
+			// Send global event
+			if ( fireGlobals ) {
+				globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
+			}
+
+			// If request was aborted inside ajaxSend, stop there
+			if ( completed ) {
+				return jqXHR;
+			}
+
+			// Timeout
+			if ( s.async && s.timeout > 0 ) {
+				timeoutTimer = window.setTimeout( function() {
+					jqXHR.abort( "timeout" );
+				}, s.timeout );
+			}
+
+			try {
+				completed = false;
+				transport.send( requestHeaders, done );
+			} catch ( e ) {
+
+				// Rethrow post-completion exceptions
+				if ( completed ) {
+					throw e;
+				}
+
+				// Propagate others as results
+				done( -1, e );
+			}
+		}
+
+		// Callback for when everything is done
+		function done( status, nativeStatusText, responses, headers ) {
+			var isSuccess, success, error, response, modified,
+				statusText = nativeStatusText;
+
+			// Ignore repeat invocations
+			if ( completed ) {
+				return;
+			}
+
+			completed = true;
+
+			// Clear timeout if it exists
+			if ( timeoutTimer ) {
+				window.clearTimeout( timeoutTimer );
+			}
+
+			// Dereference transport for early garbage collection
+			// (no matter how long the jqXHR object will be used)
+			transport = undefined;
+
+			// Cache response headers
+			responseHeadersString = headers || "";
+
+			// Set readyState
+			jqXHR.readyState = status > 0 ? 4 : 0;
+
+			// Determine if successful
+			isSuccess = status >= 200 && status < 300 || status === 304;
+
+			// Get response data
+			if ( responses ) {
+				response = ajaxHandleResponses( s, jqXHR, responses );
+			}
+
+			// Convert no matter what (that way responseXXX fields are always set)
+			response = ajaxConvert( s, response, jqXHR, isSuccess );
+
+			// If successful, handle type chaining
+			if ( isSuccess ) {
+
+				// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
+				if ( s.ifModified ) {
+					modified = jqXHR.getResponseHeader( "Last-Modified" );
+					if ( modified ) {
+						jQuery.lastModified[ cacheURL ] = modified;
+					}
+					modified = jqXHR.getResponseHeader( "etag" );
+					if ( modified ) {
+						jQuery.etag[ cacheURL ] = modified;
+					}
+				}
+
+				// if no content
+				if ( status === 204 || s.type === "HEAD" ) {
+					statusText = "nocontent";
+
+				// if not modified
+				} else if ( status === 304 ) {
+					statusText = "notmodified";
+
+				// If we have data, let's convert it
+				} else {
+					statusText = response.state;
+					success = response.data;
+					error = response.error;
+					isSuccess = !error;
+				}
+			} else {
+
+				// Extract error from statusText and normalize for non-aborts
+				error = statusText;
+				if ( status || !statusText ) {
+					statusText = "error";
+					if ( status < 0 ) {
+						status = 0;
+					}
+				}
+			}
+
+			// Set data for the fake xhr object
+			jqXHR.status = status;
+			jqXHR.statusText = ( nativeStatusText || statusText ) + "";
+
+			// Success/Error
+			if ( isSuccess ) {
+				deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
+			} else {
+				deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
+			}
+
+			// Status-dependent callbacks
+			jqXHR.statusCode( statusCode );
+			statusCode = undefined;
+
+			if ( fireGlobals ) {
+				globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError",
+					[ jqXHR, s, isSuccess ? success : error ] );
+			}
+
+			// Complete
+			completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
+
+			if ( fireGlobals ) {
+				globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
+
+				// Handle the global AJAX counter
+				if ( !( --jQuery.active ) ) {
+					jQuery.event.trigger( "ajaxStop" );
+				}
+			}
+		}
+
+		return jqXHR;
+	},
+
+	getJSON: function( url, data, callback ) {
+		return jQuery.get( url, data, callback, "json" );
+	},
+
+	getScript: function( url, callback ) {
+		return jQuery.get( url, undefined, callback, "script" );
+	}
+} );
+
+jQuery.each( [ "get", "post" ], function( i, method ) {
+	jQuery[ method ] = function( url, data, callback, type ) {
+
+		// Shift arguments if data argument was omitted
+		if ( isFunction( data ) ) {
+			type = type || callback;
+			callback = data;
+			data = undefined;
+		}
+
+		// The url can be an options object (which then must have .url)
+		return jQuery.ajax( jQuery.extend( {
+			url: url,
+			type: method,
+			dataType: type,
+			data: data,
+			success: callback
+		}, jQuery.isPlainObject( url ) && url ) );
+	};
+} );
+
+
+jQuery._evalUrl = function( url, options ) {
+	return jQuery.ajax( {
+		url: url,
+
+		// Make this explicit, since user can override this through ajaxSetup (#11264)
+		type: "GET",
+		dataType: "script",
+		cache: true,
+		async: false,
+		global: false,
+
+		// Only evaluate the response if it is successful (gh-4126)
+		// dataFilter is not invoked for failure responses, so using it instead
+		// of the default converter is kludgy but it works.
+		converters: {
+			"text script": function() {}
+		},
+		dataFilter: function( response ) {
+			jQuery.globalEval( response, options );
+		}
+	} );
+};
+
+
+jQuery.fn.extend( {
+	wrapAll: function( html ) {
+		var wrap;
+
+		if ( this[ 0 ] ) {
+			if ( isFunction( html ) ) {
+				html = html.call( this[ 0 ] );
+			}
+
+			// The elements to wrap the target around
+			wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true );
+
+			if ( this[ 0 ].parentNode ) {
+				wrap.insertBefore( this[ 0 ] );
+			}
+
+			wrap.map( function() {
+				var elem = this;
+
+				while ( elem.firstElementChild ) {
+					elem = elem.firstElementChild;
+				}
+
+				return elem;
+			} ).append( this );
+		}
+
+		return this;
+	},
+
+	wrapInner: function( html ) {
+		if ( isFunction( html ) ) {
+			return this.each( function( i ) {
+				jQuery( this ).wrapInner( html.call( this, i ) );
+			} );
+		}
+
+		return this.each( function() {
+			var self = jQuery( this ),
+				contents = self.contents();
+
+			if ( contents.length ) {
+				contents.wrapAll( html );
+
+			} else {
+				self.append( html );
+			}
+		} );
+	},
+
+	wrap: function( html ) {
+		var htmlIsFunction = isFunction( html );
+
+		return this.each( function( i ) {
+			jQuery( this ).wrapAll( htmlIsFunction ? html.call( this, i ) : html );
+		} );
+	},
+
+	unwrap: function( selector ) {
+		this.parent( selector ).not( "body" ).each( function() {
+			jQuery( this ).replaceWith( this.childNodes );
+		} );
+		return this;
+	}
+} );
+
+
+jQuery.expr.pseudos.hidden = function( elem ) {
+	return !jQuery.expr.pseudos.visible( elem );
+};
+jQuery.expr.pseudos.visible = function( elem ) {
+	return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length );
+};
+
+
+
+
+jQuery.ajaxSettings.xhr = function() {
+	try {
+		return new window.XMLHttpRequest();
+	} catch ( e ) {}
+};
+
+var xhrSuccessStatus = {
+
+		// File protocol always yields status code 0, assume 200
+		0: 200,
+
+		// Support: IE <=9 only
+		// #1450: sometimes IE returns 1223 when it should be 204
+		1223: 204
+	},
+	xhrSupported = jQuery.ajaxSettings.xhr();
+
+support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
+support.ajax = xhrSupported = !!xhrSupported;
+
+jQuery.ajaxTransport( function( options ) {
+	var callback, errorCallback;
+
+	// Cross domain only allowed if supported through XMLHttpRequest
+	if ( support.cors || xhrSupported && !options.crossDomain ) {
+		return {
+			send: function( headers, complete ) {
+				var i,
+					xhr = options.xhr();
+
+				xhr.open(
+					options.type,
+					options.url,
+					options.async,
+					options.username,
+					options.password
+				);
+
+				// Apply custom fields if provided
+				if ( options.xhrFields ) {
+					for ( i in options.xhrFields ) {
+						xhr[ i ] = options.xhrFields[ i ];
+					}
+				}
+
+				// Override mime type if needed
+				if ( options.mimeType && xhr.overrideMimeType ) {
+					xhr.overrideMimeType( options.mimeType );
+				}
+
+				// X-Requested-With header
+				// For cross-domain requests, seeing as conditions for a preflight are
+				// akin to a jigsaw puzzle, we simply never set it to be sure.
+				// (it can always be set on a per-request basis or even using ajaxSetup)
+				// For same-domain requests, won't change header if already provided.
+				if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) {
+					headers[ "X-Requested-With" ] = "XMLHttpRequest";
+				}
+
+				// Set headers
+				for ( i in headers ) {
+					xhr.setRequestHeader( i, headers[ i ] );
+				}
+
+				// Callback
+				callback = function( type ) {
+					return function() {
+						if ( callback ) {
+							callback = errorCallback = xhr.onload =
+								xhr.onerror = xhr.onabort = xhr.ontimeout =
+									xhr.onreadystatechange = null;
+
+							if ( type === "abort" ) {
+								xhr.abort();
+							} else if ( type === "error" ) {
+
+								// Support: IE <=9 only
+								// On a manual native abort, IE9 throws
+								// errors on any property access that is not readyState
+								if ( typeof xhr.status !== "number" ) {
+									complete( 0, "error" );
+								} else {
+									complete(
+
+										// File: protocol always yields status 0; see #8605, #14207
+										xhr.status,
+										xhr.statusText
+									);
+								}
+							} else {
+								complete(
+									xhrSuccessStatus[ xhr.status ] || xhr.status,
+									xhr.statusText,
+
+									// Support: IE <=9 only
+									// IE9 has no XHR2 but throws on binary (trac-11426)
+									// For XHR2 non-text, let the caller handle it (gh-2498)
+									( xhr.responseType || "text" ) !== "text"  ||
+									typeof xhr.responseText !== "string" ?
+										{ binary: xhr.response } :
+										{ text: xhr.responseText },
+									xhr.getAllResponseHeaders()
+								);
+							}
+						}
+					};
+				};
+
+				// Listen to events
+				xhr.onload = callback();
+				errorCallback = xhr.onerror = xhr.ontimeout = callback( "error" );
+
+				// Support: IE 9 only
+				// Use onreadystatechange to replace onabort
+				// to handle uncaught aborts
+				if ( xhr.onabort !== undefined ) {
+					xhr.onabort = errorCallback;
+				} else {
+					xhr.onreadystatechange = function() {
+
+						// Check readyState before timeout as it changes
+						if ( xhr.readyState === 4 ) {
+
+							// Allow onerror to be called first,
+							// but that will not handle a native abort
+							// Also, save errorCallback to a variable
+							// as xhr.onerror cannot be accessed
+							window.setTimeout( function() {
+								if ( callback ) {
+									errorCallback();
+								}
+							} );
+						}
+					};
+				}
+
+				// Create the abort callback
+				callback = callback( "abort" );
+
+				try {
+
+					// Do send the request (this may raise an exception)
+					xhr.send( options.hasContent && options.data || null );
+				} catch ( e ) {
+
+					// #14683: Only rethrow if this hasn't been notified as an error yet
+					if ( callback ) {
+						throw e;
+					}
+				}
+			},
+
+			abort: function() {
+				if ( callback ) {
+					callback();
+				}
+			}
+		};
+	}
+} );
+
+
+
+
+// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432)
+jQuery.ajaxPrefilter( function( s ) {
+	if ( s.crossDomain ) {
+		s.contents.script = false;
+	}
+} );
+
+// Install script dataType
+jQuery.ajaxSetup( {
+	accepts: {
+		script: "text/javascript, application/javascript, " +
+			"application/ecmascript, application/x-ecmascript"
+	},
+	contents: {
+		script: /\b(?:java|ecma)script\b/
+	},
+	converters: {
+		"text script": function( text ) {
+			jQuery.globalEval( text );
+			return text;
+		}
+	}
+} );
+
+// Handle cache's special case and crossDomain
+jQuery.ajaxPrefilter( "script", function( s ) {
+	if ( s.cache === undefined ) {
+		s.cache = false;
+	}
+	if ( s.crossDomain ) {
+		s.type = "GET";
+	}
+} );
+
+// Bind script tag hack transport
+jQuery.ajaxTransport( "script", function( s ) {
+
+	// This transport only deals with cross domain or forced-by-attrs requests
+	if ( s.crossDomain || s.scriptAttrs ) {
+		var script, callback;
+		return {
+			send: function( _, complete ) {
+				script = jQuery( "<script>" )
+					.attr( s.scriptAttrs || {} )
+					.prop( { charset: s.scriptCharset, src: s.url } )
+					.on( "load error", callback = function( evt ) {
+						script.remove();
+						callback = null;
+						if ( evt ) {
+							complete( evt.type === "error" ? 404 : 200, evt.type );
+						}
+					} );
+
+				// Use native DOM manipulation to avoid our domManip AJAX trickery
+				document.head.appendChild( script[ 0 ] );
+			},
+			abort: function() {
+				if ( callback ) {
+					callback();
+				}
+			}
+		};
+	}
+} );
+
+
+
+
+var oldCallbacks = [],
+	rjsonp = /(=)\?(?=&|$)|\?\?/;
+
+// Default jsonp settings
+jQuery.ajaxSetup( {
+	jsonp: "callback",
+	jsonpCallback: function() {
+		var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce++ ) );
+		this[ callback ] = true;
+		return callback;
+	}
+} );
+
+// Detect, normalize options and install callbacks for jsonp requests
+jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) {
+
+	var callbackName, overwritten, responseContainer,
+		jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ?
+			"url" :
+			typeof s.data === "string" &&
+				( s.contentType || "" )
+					.indexOf( "application/x-www-form-urlencoded" ) === 0 &&
+				rjsonp.test( s.data ) && "data"
+		);
+
+	// Handle iff the expected data type is "jsonp" or we have a parameter to set
+	if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) {
+
+		// Get callback name, remembering preexisting value associated with it
+		callbackName = s.jsonpCallback = isFunction( s.jsonpCallback ) ?
+			s.jsonpCallback() :
+			s.jsonpCallback;
+
+		// Insert callback into url or form data
+		if ( jsonProp ) {
+			s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName );
+		} else if ( s.jsonp !== false ) {
+			s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName;
+		}
+
+		// Use data converter to retrieve json after script execution
+		s.converters[ "script json" ] = function() {
+			if ( !responseContainer ) {
+				jQuery.error( callbackName + " was not called" );
+			}
+			return responseContainer[ 0 ];
+		};
+
+		// Force json dataType
+		s.dataTypes[ 0 ] = "json";
+
+		// Install callback
+		overwritten = window[ callbackName ];
+		window[ callbackName ] = function() {
+			responseContainer = arguments;
+		};
+
+		// Clean-up function (fires after converters)
+		jqXHR.always( function() {
+
+			// If previous value didn't exist - remove it
+			if ( overwritten === undefined ) {
+				jQuery( window ).removeProp( callbackName );
+
+			// Otherwise restore preexisting value
+			} else {
+				window[ callbackName ] = overwritten;
+			}
+
+			// Save back as free
+			if ( s[ callbackName ] ) {
+
+				// Make sure that re-using the options doesn't screw things around
+				s.jsonpCallback = originalSettings.jsonpCallback;
+
+				// Save the callback name for future use
+				oldCallbacks.push( callbackName );
+			}
+
+			// Call if it was a function and we have a response
+			if ( responseContainer && isFunction( overwritten ) ) {
+				overwritten( responseContainer[ 0 ] );
+			}
+
+			responseContainer = overwritten = undefined;
+		} );
+
+		// Delegate to script
+		return "script";
+	}
+} );
+
+
+
+
+// Support: Safari 8 only
+// In Safari 8 documents created via document.implementation.createHTMLDocument
+// collapse sibling forms: the second one becomes a child of the first one.
+// Because of that, this security measure has to be disabled in Safari 8.
+// https://bugs.webkit.org/show_bug.cgi?id=137337
+support.createHTMLDocument = ( function() {
+	var body = document.implementation.createHTMLDocument( "" ).body;
+	body.innerHTML = "<form></form><form></form>";
+	return body.childNodes.length === 2;
+} )();
+
+
+// Argument "data" should be string of html
+// context (optional): If specified, the fragment will be created in this context,
+// defaults to document
+// keepScripts (optional): If true, will include scripts passed in the html string
+jQuery.parseHTML = function( data, context, keepScripts ) {
+	if ( typeof data !== "string" ) {
+		return [];
+	}
+	if ( typeof context === "boolean" ) {
+		keepScripts = context;
+		context = false;
+	}
+
+	var base, parsed, scripts;
+
+	if ( !context ) {
+
+		// Stop scripts or inline event handlers from being executed immediately
+		// by using document.implementation
+		if ( support.createHTMLDocument ) {
+			context = document.implementation.createHTMLDocument( "" );
+
+			// Set the base href for the created document
+			// so any parsed elements with URLs
+			// are based on the document's URL (gh-2965)
+			base = context.createElement( "base" );
+			base.href = document.location.href;
+			context.head.appendChild( base );
+		} else {
+			context = document;
+		}
+	}
+
+	parsed = rsingleTag.exec( data );
+	scripts = !keepScripts && [];
+
+	// Single tag
+	if ( parsed ) {
+		return [ context.createElement( parsed[ 1 ] ) ];
+	}
+
+	parsed = buildFragment( [ data ], context, scripts );
+
+	if ( scripts && scripts.length ) {
+		jQuery( scripts ).remove();
+	}
+
+	return jQuery.merge( [], parsed.childNodes );
+};
+
+
+/**
+ * Load a url into a page
+ */
+jQuery.fn.load = function( url, params, callback ) {
+	var selector, type, response,
+		self = this,
+		off = url.indexOf( " " );
+
+	if ( off > -1 ) {
+		selector = stripAndCollapse( url.slice( off ) );
+		url = url.slice( 0, off );
+	}
+
+	// If it's a function
+	if ( isFunction( params ) ) {
+
+		// We assume that it's the callback
+		callback = params;
+		params = undefined;
+
+	// Otherwise, build a param string
+	} else if ( params && typeof params === "object" ) {
+		type = "POST";
+	}
+
+	// If we have elements to modify, make the request
+	if ( self.length > 0 ) {
+		jQuery.ajax( {
+			url: url,
+
+			// If "type" variable is undefined, then "GET" method will be used.
+			// Make value of this field explicit since
+			// user can override it through ajaxSetup method
+			type: type || "GET",
+			dataType: "html",
+			data: params
+		} ).done( function( responseText ) {
+
+			// Save response for use in complete callback
+			response = arguments;
+
+			self.html( selector ?
+
+				// If a selector was specified, locate the right elements in a dummy div
+				// Exclude scripts to avoid IE 'Permission Denied' errors
+				jQuery( "<div>" ).append( jQuery.parseHTML( responseText ) ).find( selector ) :
+
+				// Otherwise use the full result
+				responseText );
+
+		// If the request succeeds, this function gets "data", "status", "jqXHR"
+		// but they are ignored because response was set above.
+		// If it fails, this function gets "jqXHR", "status", "error"
+		} ).always( callback && function( jqXHR, status ) {
+			self.each( function() {
+				callback.apply( this, response || [ jqXHR.responseText, status, jqXHR ] );
+			} );
+		} );
+	}
+
+	return this;
+};
+
+
+
+
+// Attach a bunch of functions for handling common AJAX events
+jQuery.each( [
+	"ajaxStart",
+	"ajaxStop",
+	"ajaxComplete",
+	"ajaxError",
+	"ajaxSuccess",
+	"ajaxSend"
+], function( i, type ) {
+	jQuery.fn[ type ] = function( fn ) {
+		return this.on( type, fn );
+	};
+} );
+
+
+
+
+jQuery.expr.pseudos.animated = function( elem ) {
+	return jQuery.grep( jQuery.timers, function( fn ) {
+		return elem === fn.elem;
+	} ).length;
+};
+
+
+
+
+jQuery.offset = {
+	setOffset: function( elem, options, i ) {
+		var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition,
+			position = jQuery.css( elem, "position" ),
+			curElem = jQuery( elem ),
+			props = {};
+
+		// Set position first, in-case top/left are set even on static elem
+		if ( position === "static" ) {
+			elem.style.position = "relative";
+		}
+
+		curOffset = curElem.offset();
+		curCSSTop = jQuery.css( elem, "top" );
+		curCSSLeft = jQuery.css( elem, "left" );
+		calculatePosition = ( position === "absolute" || position === "fixed" ) &&
+			( curCSSTop + curCSSLeft ).indexOf( "auto" ) > -1;
+
+		// Need to be able to calculate position if either
+		// top or left is auto and position is either absolute or fixed
+		if ( calculatePosition ) {
+			curPosition = curElem.position();
+			curTop = curPosition.top;
+			curLeft = curPosition.left;
+
+		} else {
+			curTop = parseFloat( curCSSTop ) || 0;
+			curLeft = parseFloat( curCSSLeft ) || 0;
+		}
+
+		if ( isFunction( options ) ) {
+
+			// Use jQuery.extend here to allow modification of coordinates argument (gh-1848)
+			options = options.call( elem, i, jQuery.extend( {}, curOffset ) );
+		}
+
+		if ( options.top != null ) {
+			props.top = ( options.top - curOffset.top ) + curTop;
+		}
+		if ( options.left != null ) {
+			props.left = ( options.left - curOffset.left ) + curLeft;
+		}
+
+		if ( "using" in options ) {
+			options.using.call( elem, props );
+
+		} else {
+			curElem.css( props );
+		}
+	}
+};
+
+jQuery.fn.extend( {
+
+	// offset() relates an element's border box to the document origin
+	offset: function( options ) {
+
+		// Preserve chaining for setter
+		if ( arguments.length ) {
+			return options === undefined ?
+				this :
+				this.each( function( i ) {
+					jQuery.offset.setOffset( this, options, i );
+				} );
+		}
+
+		var rect, win,
+			elem = this[ 0 ];
+
+		if ( !elem ) {
+			return;
+		}
+
+		// Return zeros for disconnected and hidden (display: none) elements (gh-2310)
+		// Support: IE <=11 only
+		// Running getBoundingClientRect on a
+		// disconnected node in IE throws an error
+		if ( !elem.getClientRects().length ) {
+			return { top: 0, left: 0 };
+		}
+
+		// Get document-relative position by adding viewport scroll to viewport-relative gBCR
+		rect = elem.getBoundingClientRect();
+		win = elem.ownerDocument.defaultView;
+		return {
+			top: rect.top + win.pageYOffset,
+			left: rect.left + win.pageXOffset
+		};
+	},
+
+	// position() relates an element's margin box to its offset parent's padding box
+	// This corresponds to the behavior of CSS absolute positioning
+	position: function() {
+		if ( !this[ 0 ] ) {
+			return;
+		}
+
+		var offsetParent, offset, doc,
+			elem = this[ 0 ],
+			parentOffset = { top: 0, left: 0 };
+
+		// position:fixed elements are offset from the viewport, which itself always has zero offset
+		if ( jQuery.css( elem, "position" ) === "fixed" ) {
+
+			// Assume position:fixed implies availability of getBoundingClientRect
+			offset = elem.getBoundingClientRect();
+
+		} else {
+			offset = this.offset();
+
+			// Account for the *real* offset parent, which can be the document or its root element
+			// when a statically positioned element is identified
+			doc = elem.ownerDocument;
+			offsetParent = elem.offsetParent || doc.documentElement;
+			while ( offsetParent &&
+				( offsetParent === doc.body || offsetParent === doc.documentElement ) &&
+				jQuery.css( offsetParent, "position" ) === "static" ) {
+
+				offsetParent = offsetParent.parentNode;
+			}
+			if ( offsetParent && offsetParent !== elem && offsetParent.nodeType === 1 ) {
+
+				// Incorporate borders into its offset, since they are outside its content origin
+				parentOffset = jQuery( offsetParent ).offset();
+				parentOffset.top += jQuery.css( offsetParent, "borderTopWidth", true );
+				parentOffset.left += jQuery.css( offsetParent, "borderLeftWidth", true );
+			}
+		}
+
+		// Subtract parent offsets and element margins
+		return {
+			top: offset.top - parentOffset.top - jQuery.css( elem, "marginTop", true ),
+			left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true )
+		};
+	},
+
+	// This method will return documentElement in the following cases:
+	// 1) For the element inside the iframe without offsetParent, this method will return
+	//    documentElement of the parent window
+	// 2) For the hidden or detached element
+	// 3) For body or html element, i.e. in case of the html node - it will return itself
+	//
+	// but those exceptions were never presented as a real life use-cases
+	// and might be considered as more preferable results.
+	//
+	// This logic, however, is not guaranteed and can change at any point in the future
+	offsetParent: function() {
+		return this.map( function() {
+			var offsetParent = this.offsetParent;
+
+			while ( offsetParent && jQuery.css( offsetParent, "position" ) === "static" ) {
+				offsetParent = offsetParent.offsetParent;
+			}
+
+			return offsetParent || documentElement;
+		} );
+	}
+} );
+
+// Create scrollLeft and scrollTop methods
+jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) {
+	var top = "pageYOffset" === prop;
+
+	jQuery.fn[ method ] = function( val ) {
+		return access( this, function( elem, method, val ) {
+
+			// Coalesce documents and windows
+			var win;
+			if ( isWindow( elem ) ) {
+				win = elem;
+			} else if ( elem.nodeType === 9 ) {
+				win = elem.defaultView;
+			}
+
+			if ( val === undefined ) {
+				return win ? win[ prop ] : elem[ method ];
+			}
+
+			if ( win ) {
+				win.scrollTo(
+					!top ? val : win.pageXOffset,
+					top ? val : win.pageYOffset
+				);
+
+			} else {
+				elem[ method ] = val;
+			}
+		}, method, val, arguments.length );
+	};
+} );
+
+// Support: Safari <=7 - 9.1, Chrome <=37 - 49
+// Add the top/left cssHooks using jQuery.fn.position
+// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084
+// Blink bug: https://bugs.chromium.org/p/chromium/issues/detail?id=589347
+// getComputedStyle returns percent when specified for top/left/bottom/right;
+// rather than make the css module depend on the offset module, just check for it here
+jQuery.each( [ "top", "left" ], function( i, prop ) {
+	jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition,
+		function( elem, computed ) {
+			if ( computed ) {
+				computed = curCSS( elem, prop );
+
+				// If curCSS returns percentage, fallback to offset
+				return rnumnonpx.test( computed ) ?
+					jQuery( elem ).position()[ prop ] + "px" :
+					computed;
+			}
+		}
+	);
+} );
+
+
+// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods
+jQuery.each( { Height: "height", Width: "width" }, function( name, type ) {
+	jQuery.each( { padding: "inner" + name, content: type, "": "outer" + name },
+		function( defaultExtra, funcName ) {
+
+		// Margin is only for outerHeight, outerWidth
+		jQuery.fn[ funcName ] = function( margin, value ) {
+			var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ),
+				extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" );
+
+			return access( this, function( elem, type, value ) {
+				var doc;
+
+				if ( isWindow( elem ) ) {
+
+					// $( window ).outerWidth/Height return w/h including scrollbars (gh-1729)
+					return funcName.indexOf( "outer" ) === 0 ?
+						elem[ "inner" + name ] :
+						elem.document.documentElement[ "client" + name ];
+				}
+
+				// Get document width or height
+				if ( elem.nodeType === 9 ) {
+					doc = elem.documentElement;
+
+					// Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height],
+					// whichever is greatest
+					return Math.max(
+						elem.body[ "scroll" + name ], doc[ "scroll" + name ],
+						elem.body[ "offset" + name ], doc[ "offset" + name ],
+						doc[ "client" + name ]
+					);
+				}
+
+				return value === undefined ?
+
+					// Get width or height on the element, requesting but not forcing parseFloat
+					jQuery.css( elem, type, extra ) :
+
+					// Set width or height on the element
+					jQuery.style( elem, type, value, extra );
+			}, type, chainable ? margin : undefined, chainable );
+		};
+	} );
+} );
+
+
+jQuery.each( ( "blur focus focusin focusout resize scroll click dblclick " +
+	"mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
+	"change select submit keydown keypress keyup contextmenu" ).split( " " ),
+	function( i, name ) {
+
+	// Handle event binding
+	jQuery.fn[ name ] = function( data, fn ) {
+		return arguments.length > 0 ?
+			this.on( name, null, data, fn ) :
+			this.trigger( name );
+	};
+} );
+
+jQuery.fn.extend( {
+	hover: function( fnOver, fnOut ) {
+		return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
+	}
+} );
+
+
+
+
+jQuery.fn.extend( {
+
+	bind: function( types, data, fn ) {
+		return this.on( types, null, data, fn );
+	},
+	unbind: function( types, fn ) {
+		return this.off( types, null, fn );
+	},
+
+	delegate: function( selector, types, data, fn ) {
+		return this.on( types, selector, data, fn );
+	},
+	undelegate: function( selector, types, fn ) {
+
+		// ( namespace ) or ( selector, types [, fn] )
+		return arguments.length === 1 ?
+			this.off( selector, "**" ) :
+			this.off( types, selector || "**", fn );
+	}
+} );
+
+// Bind a function to a context, optionally partially applying any
+// arguments.
+// jQuery.proxy is deprecated to promote standards (specifically Function#bind)
+// However, it is not slated for removal any time soon
+jQuery.proxy = function( fn, context ) {
+	var tmp, args, proxy;
+
+	if ( typeof context === "string" ) {
+		tmp = fn[ context ];
+		context = fn;
+		fn = tmp;
+	}
+
+	// Quick check to determine if target is callable, in the spec
+	// this throws a TypeError, but we will just return undefined.
+	if ( !isFunction( fn ) ) {
+		return undefined;
+	}
+
+	// Simulated bind
+	args = slice.call( arguments, 2 );
+	proxy = function() {
+		return fn.apply( context || this, args.concat( slice.call( arguments ) ) );
+	};
+
+	// Set the guid of unique handler to the same of original handler, so it can be removed
+	proxy.guid = fn.guid = fn.guid || jQuery.guid++;
+
+	return proxy;
+};
+
+jQuery.holdReady = function( hold ) {
+	if ( hold ) {
+		jQuery.readyWait++;
+	} else {
+		jQuery.ready( true );
+	}
+};
+jQuery.isArray = Array.isArray;
+jQuery.parseJSON = JSON.parse;
+jQuery.nodeName = nodeName;
+jQuery.isFunction = isFunction;
+jQuery.isWindow = isWindow;
+jQuery.camelCase = camelCase;
+jQuery.type = toType;
+
+jQuery.now = Date.now;
+
+jQuery.isNumeric = function( obj ) {
+
+	// As of jQuery 3.0, isNumeric is limited to
+	// strings and numbers (primitives or objects)
+	// that can be coerced to finite numbers (gh-2662)
+	var type = jQuery.type( obj );
+	return ( type === "number" || type === "string" ) &&
+
+		// parseFloat NaNs numeric-cast false positives ("")
+		// ...but misinterprets leading-number strings, particularly hex literals ("0x...")
+		// subtraction forces infinities to NaN
+		!isNaN( obj - parseFloat( obj ) );
+};
+
+
+
+
+// Register as a named AMD module, since jQuery can be concatenated with other
+// files that may use define, but not via a proper concatenation script that
+// understands anonymous AMD modules. A named AMD is safest and most robust
+// way to register. Lowercase jquery is used because AMD module names are
+// derived from file names, and jQuery is normally delivered in a lowercase
+// file name. Do this after creating the global so that if an AMD module wants
+// to call noConflict to hide this version of jQuery, it will work.
+
+// Note that for maximum portability, libraries that are not jQuery should
+// declare themselves as anonymous modules, and avoid setting a global if an
+// AMD loader is present. jQuery is a special case. For more information, see
+// https://github.com/jrburke/requirejs/wiki/Updating-existing-libraries#wiki-anon
+
+if ( typeof define === "function" && define.amd ) {
+	define( "jquery", [], function() {
+		return jQuery;
+	} );
+}
+
+
+
+
+var
+
+	// Map over jQuery in case of overwrite
+	_jQuery = window.jQuery,
+
+	// Map over the $ in case of overwrite
+	_$ = window.$;
+
+jQuery.noConflict = function( deep ) {
+	if ( window.$ === jQuery ) {
+		window.$ = _$;
+	}
+
+	if ( deep && window.jQuery === jQuery ) {
+		window.jQuery = _jQuery;
+	}
+
+	return jQuery;
+};
+
+// Expose jQuery and $ identifiers, even in AMD
+// (#7102#comment:10, https://github.com/jquery/jquery/pull/557)
+// and CommonJS for browser emulators (#13566)
+if ( !noGlobal ) {
+	window.jQuery = window.$ = jQuery;
+}
+
+
+
+
+return jQuery;
+} );
diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js
new file mode 100644
index 0000000..d2b4ee9
--- /dev/null
+++ b/docs/_static/language_data.js
@@ -0,0 +1,297 @@
+/*
+ * language_data.js
+ * ~~~~~~~~~~~~~~~~
+ *
+ * This script contains the language-specific data used by searchtools.js,
+ * namely the list of stopwords, stemmer, scorer and splitter.
+ *
+ * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :license: BSD, see LICENSE for details.
+ *
+ */
+
+var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
+
+
+/* Non-minified version JS is _stemmer.js if file is provided */ 
+/**
+ * Porter Stemmer
+ */
+var Stemmer = function() {
+
+  var step2list = {
+    ational: 'ate',
+    tional: 'tion',
+    enci: 'ence',
+    anci: 'ance',
+    izer: 'ize',
+    bli: 'ble',
+    alli: 'al',
+    entli: 'ent',
+    eli: 'e',
+    ousli: 'ous',
+    ization: 'ize',
+    ation: 'ate',
+    ator: 'ate',
+    alism: 'al',
+    iveness: 'ive',
+    fulness: 'ful',
+    ousness: 'ous',
+    aliti: 'al',
+    iviti: 'ive',
+    biliti: 'ble',
+    logi: 'log'
+  };
+
+  var step3list = {
+    icate: 'ic',
+    ative: '',
+    alize: 'al',
+    iciti: 'ic',
+    ical: 'ic',
+    ful: '',
+    ness: ''
+  };
+
+  var c = "[^aeiou]";          // consonant
+  var v = "[aeiouy]";          // vowel
+  var C = c + "[^aeiouy]*";    // consonant sequence
+  var V = v + "[aeiou]*";      // vowel sequence
+
+  var mgr0 = "^(" + C + ")?" + V + C;                      // [C]VC... is m>0
+  var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$";    // [C]VC[V] is m=1
+  var mgr1 = "^(" + C + ")?" + V + C + V + C;              // [C]VCVC... is m>1
+  var s_v   = "^(" + C + ")?" + v;                         // vowel in stem
+
+  this.stemWord = function (w) {
+    var stem;
+    var suffix;
+    var firstch;
+    var origword = w;
+
+    if (w.length < 3)
+      return w;
+
+    var re;
+    var re2;
+    var re3;
+    var re4;
+
+    firstch = w.substr(0,1);
+    if (firstch == "y")
+      w = firstch.toUpperCase() + w.substr(1);
+
+    // Step 1a
+    re = /^(.+?)(ss|i)es$/;
+    re2 = /^(.+?)([^s])s$/;
+
+    if (re.test(w))
+      w = w.replace(re,"$1$2");
+    else if (re2.test(w))
+      w = w.replace(re2,"$1$2");
+
+    // Step 1b
+    re = /^(.+?)eed$/;
+    re2 = /^(.+?)(ed|ing)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      re = new RegExp(mgr0);
+      if (re.test(fp[1])) {
+        re = /.$/;
+        w = w.replace(re,"");
+      }
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1];
+      re2 = new RegExp(s_v);
+      if (re2.test(stem)) {
+        w = stem;
+        re2 = /(at|bl|iz)$/;
+        re3 = new RegExp("([^aeiouylsz])\\1$");
+        re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+        if (re2.test(w))
+          w = w + "e";
+        else if (re3.test(w)) {
+          re = /.$/;
+          w = w.replace(re,"");
+        }
+        else if (re4.test(w))
+          w = w + "e";
+      }
+    }
+
+    // Step 1c
+    re = /^(.+?)y$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(s_v);
+      if (re.test(stem))
+        w = stem + "i";
+    }
+
+    // Step 2
+    re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step2list[suffix];
+    }
+
+    // Step 3
+    re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      suffix = fp[2];
+      re = new RegExp(mgr0);
+      if (re.test(stem))
+        w = stem + step3list[suffix];
+    }
+
+    // Step 4
+    re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
+    re2 = /^(.+?)(s|t)(ion)$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      if (re.test(stem))
+        w = stem;
+    }
+    else if (re2.test(w)) {
+      var fp = re2.exec(w);
+      stem = fp[1] + fp[2];
+      re2 = new RegExp(mgr1);
+      if (re2.test(stem))
+        w = stem;
+    }
+
+    // Step 5
+    re = /^(.+?)e$/;
+    if (re.test(w)) {
+      var fp = re.exec(w);
+      stem = fp[1];
+      re = new RegExp(mgr1);
+      re2 = new RegExp(meq1);
+      re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
+      if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
+        w = stem;
+    }
+    re = /ll$/;
+    re2 = new RegExp(mgr1);
+    if (re.test(w) && re2.test(w)) {
+      re = /.$/;
+      w = w.replace(re,"");
+    }
+
+    // and turn initial Y back to y
+    if (firstch == "y")
+      w = firstch.toLowerCase() + w.substr(1);
+    return w;
+  }
+}
+
+
+
+
+
+var splitChars = (function() {
+    var result = {};
+    var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
+         1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
+         2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
+         2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
+         3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
+         3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
+         4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
+         8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
+         11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
+         43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
+    var i, j, start, end;
+    for (i = 0; i < singles.length; i++) {
+        result[singles[i]] = true;
+    }
+    var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
+         [722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
+         [1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
+         [1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
+         [1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
+         [2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
+         [2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
+         [2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
+         [2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
+         [2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
+         [2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
+         [2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
+         [3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
+         [3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
+         [3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
+         [3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
+         [3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
+         [3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
+         [4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
+         [4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
+         [4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
+         [4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
+         [5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
+         [6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
+         [6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
+         [6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
+         [6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
+         [7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
+         [7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
+         [8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
+         [8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
+         [8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
+         [10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
+         [11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
+         [12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
+         [12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
+         [12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
+         [19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
+         [42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
+         [42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
+         [43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
+         [43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
+         [43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
+         [43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
+         [44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
+         [57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
+         [64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
+         [65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
+         [65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
+    for (i = 0; i < ranges.length; i++) {
+        start = ranges[i][0];
+        end = ranges[i][1];
+        for (j = start; j <= end; j++) {
+            result[j] = true;
+        }
+    }
+    return result;
+})();
+
+function splitQuery(query) {
+    var result = [];
+    var start = -1;
+    for (var i = 0; i < query.length; i++) {
+        if (splitChars[query.charCodeAt(i)]) {
+            if (start !== -1) {
+                result.push(query.slice(start, i));
+                start = -1;
+            }
+        } else if (start === -1) {
+            start = i;
+        }
+    }
+    if (start !== -1) {
+        result.push(query.slice(start));
+    }
+    return result;
+}
+
+
diff --git a/docs/changes.html b/docs/changes.html
index 068e653..32f1eea 100644
--- a/docs/changes.html
+++ b/docs/changes.html
@@ -4,6 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Changes &#8212; ST Pipeline 1.8.0 documentation</title>
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -31,7 +32,8 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="example.html" title="Examples"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Changes</a></li> 
       </ul>
     </div>  
 
@@ -42,6 +44,11 @@ <h3>Navigation</h3>
             
   <div class="section" id="changes">
 <h1>Changes<a class="headerlink" href="#changes" title="Permalink to this headline">¶</a></h1>
+<p><strong>Version 1.8.1</strong></p>
+<ul class="simple">
+<li><p>Fixed a bug when having barcodes after the UMI</p></li>
+<li><p>Improved descriptions for parameters</p></li>
+</ul>
 <p><strong>Version 1.8.0</strong></p>
 <ul class="simple">
 <li><p>Improved the unit-tests</p></li>
@@ -636,6 +643,7 @@ <h1>Changes<a class="headerlink" href="#changes" title="Permalink to this headli
 </div>
 
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
@@ -680,12 +688,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="example.html" title="Examples"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Changes</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2020, Jose Fernandez Navarro.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.3.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/docs/contact.html b/docs/contact.html
index 2f0ae33..c9df688 100644
--- a/docs/contact.html
+++ b/docs/contact.html
@@ -4,6 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Contact &#8212; ST Pipeline 1.8.0 documentation</title>
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -27,7 +28,8 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="license.html" title="License"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Contact</a></li> 
       </ul>
     </div>  
 
@@ -42,6 +44,7 @@ <h1>Contact<a class="headerlink" href="#contact" title="Permalink to this headli
 </div>
 
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
@@ -80,12 +83,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="license.html" title="License"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Contact</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2020, Jose Fernandez Navarro.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.3.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/docs/example.html b/docs/example.html
index 8a0e5c8..0d5be1e 100644
--- a/docs/example.html
+++ b/docs/example.html
@@ -4,6 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Examples &#8212; ST Pipeline 1.8.0 documentation</title>
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -31,7 +32,8 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="manual.html" title="Manual"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Examples</a></li> 
       </ul>
     </div>  
 
@@ -78,7 +80,7 @@ <h1>Examples<a class="headerlink" href="#examples" title="Permalink to this head
 </div>
 <p>If you want to process Visium datasets it is recommended to use these settings</p>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>--allowed-missed <span class="m">1</span> <span class="se">\</span>
-    --allowed-kmer <span class="m">4</span> <span class="se">\</span>
+--allowed-kmer <span class="m">4</span> <span class="se">\</span>
     --umi-allowed-mismatches <span class="m">2</span> <span class="se">\</span>
     --umi-start-position <span class="m">16</span> <span class="se">\</span>
     --umi-end-position <span class="m">28</span> <span class="se">\</span>
@@ -87,6 +89,7 @@ <h1>Examples<a class="headerlink" href="#examples" title="Permalink to this head
 </div>
 
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
@@ -131,12 +134,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="manual.html" title="Manual"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Examples</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2020, Jose Fernandez Navarro.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.3.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/docs/genindex.html b/docs/genindex.html
index aeeb237..82232df 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -1,10 +1,10 @@
 
-
 <!DOCTYPE html>
 
 <html>
   <head>
     <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Index &#8212; ST Pipeline 1.8.0 documentation</title>
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -24,7 +24,8 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="#" title="General Index"
              accesskey="I">index</a></li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Index</a></li> 
       </ul>
     </div>  
 
@@ -41,6 +42,7 @@ <h1 id="index">Index</h1>
 </div>
 
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
@@ -66,12 +68,13 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="#" title="General Index"
              >index</a></li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Index</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2020, Jose Fernandez Navarro.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.3.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/docs/index.html b/docs/index.html
index 81a64cd..f76b726 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -4,6 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Welcome to ST Pipeline’s documentation! &#8212; ST Pipeline 1.8.0 documentation</title>
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -27,7 +28,8 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="intro.html" title="Introduction"
              accesskey="N">next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="#">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Welcome to ST Pipeline’s documentation!</a></li> 
       </ul>
     </div>  
 
@@ -61,6 +63,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Pe
 </div>
 
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
@@ -105,12 +108,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="intro.html" title="Introduction"
              >next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="#">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Welcome to ST Pipeline’s documentation!</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2020, Jose Fernandez Navarro.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.3.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/docs/installation.html b/docs/installation.html
index 9ae24bf..094060e 100644
--- a/docs/installation.html
+++ b/docs/installation.html
@@ -4,6 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Installing the Spatial Transcriptomics pipeline &#8212; ST Pipeline 1.8.0 documentation</title>
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -31,7 +32,8 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="intro.html" title="Introduction"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Installing the Spatial Transcriptomics pipeline</a></li> 
       </ul>
     </div>  
 
@@ -95,6 +97,7 @@ <h1>Installing the Spatial Transcriptomics pipeline<a class="headerlink" href="#
 </div>
 
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
@@ -139,12 +142,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="intro.html" title="Introduction"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Installing the Spatial Transcriptomics pipeline</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2020, Jose Fernandez Navarro.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.3.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/docs/intro.html b/docs/intro.html
index d14e77e..880b2e8 100644
--- a/docs/intro.html
+++ b/docs/intro.html
@@ -4,6 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Introduction &#8212; ST Pipeline 1.8.0 documentation</title>
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -31,7 +32,8 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="Welcome to ST Pipeline’s documentation!"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Introduction</a></li> 
       </ul>
     </div>  
 
@@ -99,13 +101,12 @@ <h1>Introduction<a class="headerlink" href="#introduction" title="Permalink to t
 <li><p>In the grouping/counting only unique molecules (UMIs) are kept.</p></li>
 </ul>
 <p>You can see a graphical more detailed description of the workflow in the documents workflow.pdf and workflow_extended.pdf</p>
-<p>The output will be a matrix of counts (genes as columns, spots as rows),
-a BED file containing the transcripts (Read name, coordinate, gene, etc..), and a JSON
-file with useful stats.
-The ST pipeline will also output a log file with useful information.</p>
+<p>The output will be a matrix of counts (genes as columns, spots as rows)
+and a log file with useful information and stats.</p>
 </div>
 
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
@@ -150,12 +151,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="index.html" title="Welcome to ST Pipeline’s documentation!"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Introduction</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2020, Jose Fernandez Navarro.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.3.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/docs/license.html b/docs/license.html
index f1b4060..5f6c712 100644
--- a/docs/license.html
+++ b/docs/license.html
@@ -4,6 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>License &#8212; ST Pipeline 1.8.0 documentation</title>
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -31,7 +32,8 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="changes.html" title="Changes"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">License</a></li> 
       </ul>
     </div>  
 
@@ -65,6 +67,7 @@ <h1>License<a class="headerlink" href="#license" title="Permalink to this headli
 </div>
 
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
@@ -109,12 +112,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="changes.html" title="Changes"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">License</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2020, Jose Fernandez Navarro.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.3.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/docs/manual.html b/docs/manual.html
index 72d15b0..5eff233 100644
--- a/docs/manual.html
+++ b/docs/manual.html
@@ -4,6 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Manual &#8212; ST Pipeline 1.8.0 documentation</title>
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -31,7 +32,8 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="installation.html" title="Installing the Spatial Transcriptomics pipeline"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Manual</a></li> 
       </ul>
     </div>  
 
@@ -42,14 +44,13 @@ <h3>Navigation</h3>
             
   <div class="section" id="manual">
 <h1>Manual<a class="headerlink" href="#manual" title="Permalink to this headline">¶</a></h1>
-<p>ST Pipeline is a tool to process the Spatial Transcriptomics raw data
-or single cell data.
+<p>ST Pipeline is a tool to process the Spatial Transcriptomics and Visium data.
 The data is filtered, aligned to a genome, annotated to a reference,
 demultiplexed by array coordinates and then aggregated by counts
 that are not duplicates using the Unique Molecular Indentifiers.
-The output contains the counts matrix, a stats file, a log file
-and a BED file with all the transcripts.</p>
-<p>The ST Pipeline requires two fastq files, an IDs files (BARCODE, X, Y),
+The output contains the counts matrix and a log file with useful
+stats in information.</p>
+<p>The ST Pipeline requires two FASTQ files, an IDs files (BARCODE, X, Y),
 the path to a STAR genome index, the path to a annotation file in GTF
 format and a dataset name.</p>
 <p>The ST Pipeline has many parameters, you can see a description of them
@@ -60,7 +61,7 @@ <h1>Manual<a class="headerlink" href="#manual" title="Permalink to this headline
 <p>Soft clipping is also not recommended when using the 75bp kit, due to the
 shorter length.</p>
 <p>The UMI filter can be used for array batches 1000L6 and earlier. It is
-unable to be used for array batches 1000L7 and newer as the UMI in
+not recommended to use it for array batches 1000L7 and newer as the UMI in
 these arrays is fully randomised.</p>
 <p>Author Jose Fernandez Navarro &lt;<a class="reference external" href="mailto:jc&#46;fernandez&#46;navaro&#37;&#52;&#48;gmail&#46;com">jc<span>&#46;</span>fernandez<span>&#46;</span>navaro<span>&#64;</span>gmail<span>&#46;</span>com</a>&gt;</p>
 <p><code class="docutils literal notranslate"><span class="pre">st_pipeline_run.py</span> <span class="pre">[options]</span> <span class="pre">fastq_files</span> <span class="pre">fastq_files</span></code></p>
@@ -78,47 +79,22 @@ <h1>Manual<a class="headerlink" href="#manual" title="Permalink to this headline
 --ids [FILE]          Path to the file containing the map of barcodes to the
                       array coordinates
 --ref-map [FOLDER]    Path to the folder with the STAR index for the genome
-                      that you want to use to align the reads
+                      that you want to use as reference
 --ref-annotation [FILE]
                       Path to the reference annotation file (GTF or GFF
-                      format is required) to be used to annotated the reads
---expName [STRING]    Name of the experiment/dataset (The output files will
-                      prepend this name)
---allowed-missed [INT]
-                      Number of allowed mismatches when demultiplexing
-                      against the barcodes with TaggD (default: 2)
---allowed-kmer [INT]  KMer length when demultiplexing against the barcodes
-                      with TaggD (default: 6)
---overhang [INT]      Extra flanking bases added when demultiplexing against
-                      the barcodes with TaggD (default: 2)
---min-length-qual-trimming [INT]
-                      Minimum length of the reads after trimming, shorter
-                      reads will be discarded (default: 20)
---mapping-rv-trimming [INT]
-                      Number of bases to trim in the reverse reads for the
-                      mapping step (5\&#39; end) (default: 0)
+                      format is required) to be used to annotated the mapped
+                      reads
+--expName [STRING]    Name of the dataset (The output files will prepend
+                      this name)
 --contaminant-index [FOLDER]
                       Path to the folder with a STAR index with a
-                      contaminant genome. Reads will be filtered against the
-                      specified genome and mapping reads will be descarded
---qual-64             Use phred-64 quality instead of phred-33(default)
---htseq-mode [STRING]
-                      Mode of Annotation when using HTSeq. Modes =
-                      {union,intersection-nonempty(default),intersection-
-                      strict}
---htseq-no-ambiguous  When using htseq discard reads annotating ambiguous
-                      genes (default False)
---start-id [INT]      Start position of the IDs (Barcodes) in the R1
-                      (counting from 0) (default: 0)
+                      contaminant genome reference. Reads will be filtered
+                      using the specified genome and mapping reads will be
+                      discarded
 --no-clean-up         Do not remove temporary/intermediary files (useful for
                       debugging)
 --verbose             Show extra information on the log file
---mapping-threads [INT]
-                      Number of threads to use in the mapping step (default:
-                      4)
---min-quality-trimming [INT]
-                      Minimum phred quality a base must have in the trimming
-                      step (default: 20)
+--threads [INT]       Number of threads to use (default: 4)
 --bin-path [FOLDER]   Path to folder where binary executables are present
                       (system path by default)
 --log-file [STR]      Name of the file that we want to use to store the logs
@@ -127,19 +103,16 @@ <h1>Manual<a class="headerlink" href="#manual" title="Permalink to this headline
                       Path of the output folder
 --temp-folder [FOLDER]
                       Path of the location for temporary files
---umi-allowed-mismatches [INT]
-                      Number of allowed mismatches (hamming distance) that
-                      UMIs of the same gene-spot must have in order to
-                      cluster together (default: 1)
---umi-start-position [INT]
-                      Position in R1 (base wise) of the first base of the
-                      UMI (starting by 0) (default: 18)
---umi-end-position [INT]
-                      Position in R1 (base wise) of the last base of the UMI
-                      (starting by 1) (default: 27)
 --keep-discarded-files
-                      Writes down unaligned, un-annotated and un-
-                      demultiplexed reads to files
+                      Keep files with discarded reads in every step
+--qual-64             Use phred-64 quality instead of phred-33(default) in
+                      the quality trimming step
+--min-length-qual-trimming [INT]
+                      Minimum length of the reads after trimming, shorter
+                      reads will be discarded (default: 20)
+--min-quality-trimming [INT]
+                      Minimum phred quality a base must have in order to be
+                      kept in the quality trimming step (default: 20)
 --remove-polyA [INT]  Remove PolyA stretches of the given length from R2
                       (Use 0 to disable it) (default: 10)
 --remove-polyT [INT]  Remove PolyT stretches of the given length from R2
@@ -150,25 +123,28 @@ <h1>Manual<a class="headerlink" href="#manual" title="Permalink to this headline
                       (Use 0 to disable it) (default: 10)
 --remove-polyN [INT]  Remove PolyN stretches of the given length from R2
                       (Use 0 to disable it) (default: 10)
+--homopolymer-mismatches [INT]
+                      Number of mismatches allowed when removing
+                      homopolymers (A, T, G, C or N) (default: 0)
 --filter-AT-content [INT%]
                       Discards reads whose number of A and T bases in total
-                      are more or equal than the number given in percentage
-                      (default: 90)
+                      are more or equal than the percentage given as input
+                      (0-100) (default: 90)
 --filter-GC-content [INT%]
                       Discards reads whose number of G and C bases in total
-                      are more or equal than the number given in percentage
-                      (default: 90)
+                      are more or equal the percentage given as input
+                      (0-100) (default: 90)
+--mapping-rv-trimming [INT]
+                      Number of bases to trim in the reverse reads (R2) for
+                      the mapping step (5&#39; end) (default: 0)
+--inverse-mapping-rv-trimming [INT]
+                      Number of bases to trim in the reverse reads (R2) for
+                      the mapping step (3&#39; end) (default: 0)
 --disable-multimap    If activated, multiple aligned reads obtained during
                       mapping will be all discarded. Otherwise the highest
                       scored one will be kept
 --disable-clipping    If activated, disable soft-clipping (local alignment)
                       in the mapping step
---umi-cluster-algorithm [STRING]
-                      Type of clustering algorithm to use when performing
-                      UMIs duplicates removal. Options = {naive,
-                      hierarchical(default), Affinity, Adjacent and
-                      AdjacentBi} Note that for the affinity method the umi
-                      allowed mismatches parameter will be ignored.
 --min-intron-size [INT]
                       Minimum allowed intron size when searching for splice
                       variants with STAR Splices alignments are disabled by
@@ -179,68 +155,103 @@ <h1>Manual<a class="headerlink" href="#manual" title="Permalink to this headline
                       variants with STAR Splices alignments are disabled by
                       default (=1) but to turn it on set this parameter to a
                       big number, for example 10000 or 100000. (default: 1)
+--star-two-pass-mode  Activates the 2-pass mode in STAR to improve mapping
+                      accuracy
+--star-genome-loading [STRING]
+                      Similar to the STAR option --genomeLoad. It allows to
+                      load the genome index into memory so it can easily be
+                      shared by other jobs to save loading time. Read the
+                      STAR manual for more info on this. (default:
+                      NoSharedMemory)
+--star-sort-mem-limit STAR_SORT_MEM_LIMIT
+                      The maximum available RAM for sorting BAM during
+                      mapping with STAR. Default is 0 which means that it
+                      will be set to the genome index size
+--demultiplexing-mismatches [INT]
+                      Number of allowed mismatches when demultiplexing the
+                      reads against the barcodes with TaggD (default: 2)
+--demultiplexing-kmer [INT]
+                      KMer size to use when demultiplexing against the
+                      barcodes with TaggD (default: 6)
+--demultiplexing-overhang [INT]
+                      Extra flanking bases added on each side of the barcode
+                      when demultiplexing against the barcodes with TaggD
+                      (default: 0)
+--demultiplexing-start [INT]
+                      Start position of the IDs (Barcodes) in R1 (counting
+                      from 0) (default: 0)
+--demultiplexing-metric [STRING]
+                      Distance metric to use for TaggD demultiplexing:
+                      Options: Subglobal, Levenshtein or Hamming (default:
+                      Subglobal)
+--demultiplexing-multiple-hits-keep-one
+                      When multiple ambiguous hits with same score are found
+                      in the demultiplexing step, keep only one (random).
+--demultiplexing-trim-sequences DEMULTIPLEXING_TRIM_SEQUENCES
+                      Trim the barcodes in the input file when doing
+                      demultiplexing. The input given is a list of tuples
+                      START END START END where START is the integer
+                      position of the first base (0 based) and END is the
+                      integer position of the last base (1 based). The final
+                      barcode will be obtained by combining all the
+                      sequences given in the input. This is useful when
+                      having a barcode composed of multiple sequences in the
+                      reador when the barcode needs to be trimmed out.
+                      Trimmng sequences can be given several times.
+--htseq-mode [STRING]
+                      Mode of annotation when using htseq-count. Modes =
+                      {union, intersection-nonempty(default), intersection-
+                      strict}
+--htseq-no-ambiguous  When using htseq-count discard reads annotating
+                      ambiguous genes (default False)
+--strandness [STRING]
+                      What strandness mode to use when annotating with
+                      htseq-count [no, yes(default), reverse]
+--include-non-annotated
+                      Do not discard un-annotated reads (they will be
+                      labeled __no_feature)
+--umi-cluster-algorithm [STRING]
+                      Type of clustering algorithm to use when performing
+                      UMIs duplicates removal. Options = {naive,
+                      hierarchical, Affinity, Adjacent and
+                      AdjacentBi(default)} Note that for the affinity method
+                      the umi allowed mismatches parameter will be ignored.
+--umi-allowed-mismatches [INT]
+                      Number of allowed mismatches (hamming distance) that
+                      UMIs of the same gene-spot must have in order to
+                      cluster together (default: 1)
+--umi-start-position [INT]
+                      Position in R1 (base wise) of the first base of the
+                      UMI (starting by 0) (default: 18)
+--umi-end-position [INT]
+                      Position in R1 (base wise) of the last base of the UMI
+                      (starting by 1) (default: 27)
 --umi-filter          Enables the UMI quality filter based on the template
                       given in --umi-filter-template
 --umi-filter-template [STRING]
                       UMI template (IUPAC nucleotide code) for the UMI
                       filter, default = WSNNWSNNV
---compute-saturation  Performs a saturation curve computation by sub-
-                      sampling the annotated reads, computing unique
-                      molecules and then a saturation curve (included in the
-                      log file)
---saturation-points SATURATION_POINTS [SATURATION_POINTS ...]
-                      Saturation points can be provided instead of using
-                      default values. Provide separate values like this for
-                      example: 10000 20000 50000 100000
---include-non-annotated
-                      Do not discard un-annotated reads (they will be
-                      labeled __no_feature)
---inverse-mapping-rv-trimming [INT]
-                      Number of bases to trim in the reverse reads for the
-                      mapping step on the 3\&#39; end
---two-pass-mode       Activates the 2-pass mode in STAR to improve mapping
-                      accuracy
---strandness [STRING]
-                      What strandness mode to use when annotating with
-                      htseq-count [no, yes(default), reverse]
 --umi-quality-bases [INT]
                       Maximum number of low quality bases allowed in an UMI
                       (default: 6)
 --umi-counting-offset [INT]
-                      Expression count for each gene-spot combination is
-                      expressed as the number of unique UMIs in each
-                      strand/start position. However some reads might have
-                      slightly different start positions due to
-                      amplification artifacts. This parameters allows to
-                      define an offset window from where to count unique
-                      UMIs. You can set it to a veryhigh value +9999 to
-                      count unique UMIs for the whole gene (default: 250)
---demultiplexing-metric [STRING]
-                      Distance metric for TaggD demultiplexing: Subglobal,
-                      Levenshtein or Hamming (default: Subglobal)
---demultiplexing-multiple-hits-keep-one
-                      When multiple ambiguous hits with same score are found
-                      in the demultiplexing, keep one (random).
---demultiplexing-trim-sequences DEMULTIPLEXING_TRIM_SEQUENCES [DEMULTIPLEXING_TRIM_SEQUENCES ...]
-                      Trims from the barcodes in the input file when doing
-                      demultiplexing. The bases given in the list of tuples
-                      as START END START END .. where START is the integer
-                      position of the first base (0 based) and END is the
-                      integer position of the last base (1 based). Trimmng
-                      sequences can be given several times.
---homopolymer-mismatches [INT]
-                      Number of mismatches allowed when removing
-                      homopolymers (default: 0)
---star-genome-loading [STRING]
-                      Similar to the STAR option --genomeLoad. It allows to
-                      load the genome index into memory so it can easily be
-                      shared by other jobs so to save loading time. Read the
-                      STAR manual for more info on this. (default:
-                      NoSharedMemory)
---star-sort-mem-limit STAR_SORT_MEM_LIMIT
-                      The maximum available RAM for sorting BAM during
-                      mapping. Default is 0 which means that it will be set
-                      to the genome index size
+                      UMI count for each gene-spot combination is computed
+                      as the number of unique UMIs in each strand/start
+                      position. However some reads might have slightly
+                      different start positions due to amplification
+                      artifacts. This parameters allows to define an offset
+                      window from where to count unique UMIs. You can set it
+                      to a very high value +9999 to count unique UMIs for
+                      the whole gene (default: 250)
+--compute-saturation  Performs a saturation curve computation by sub-
+                      sampling the annotated reads, computing unique UMIs
+                      and adding the stats to the log file (this can be used
+                      to plot saturation curves)
+--saturation-points SATURATION_POINTS [SATURATION_POINTS ...]
+                      Saturation points for the saturation curve computation
+                      can be provided instead of using default values.
+                      Provide a list of values like this for example: 10000
+                      20000 50000 100000
 --disable-trimming    Use this flag if you want to skip the trimming step
 --disable-mapping     Use this flag if you want to skip the mapping step
 --disable-annotation  Use this flag if you want to skip the annotation
@@ -248,14 +259,16 @@ <h1>Manual<a class="headerlink" href="#manual" title="Permalink to this headline
                       demultiplexing step
 --disable-umi         Use this flag if you want to skip the UMI filtering
                       step
---transcriptome       Use a transcriptome instead of a genome, the gene tag
-                      will be obtained from the transcriptome file
+--transcriptome       Use this flag if you want to use transcriptome instead
+                      of a genome, the gene tag will be obtained from the
+                      transcriptome file
 --version             show program&#39;s version number and exit
 </pre></div>
 </div>
 </div>
 
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
@@ -300,12 +313,13 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="installation.html" title="Installing the Spatial Transcriptomics pipeline"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Manual</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2020, Jose Fernandez Navarro.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.3.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/docs/search.html b/docs/search.html
index aa6cff7..a9e110e 100644
--- a/docs/search.html
+++ b/docs/search.html
@@ -4,6 +4,7 @@
 <html>
   <head>
     <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Search &#8212; ST Pipeline 1.8.0 documentation</title>
     <link rel="stylesheet" href="_static/classic.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -28,7 +29,8 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="genindex.html" title="General Index"
              accesskey="I">index</a></li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Search</a></li> 
       </ul>
     </div>  
 
@@ -59,6 +61,7 @@ <h1 id="search-documentation">Search</h1>
   
   </div>
 
+            <div class="clearer"></div>
           </div>
         </div>
       </div>
@@ -74,12 +77,13 @@ <h3>Navigation</h3>
         <li class="right" style="margin-right: 10px">
           <a href="genindex.html" title="General Index"
              >index</a></li>
-        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">ST Pipeline 1.8.0 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-this"><a href="">Search</a></li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">
         &#169; Copyright 2020, Jose Fernandez Navarro.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 3.0.3.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
   </body>
 </html>
\ No newline at end of file
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 00f3b09..a4efd91 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1,1 +1,1 @@
-Search.setIndex({docnames:["changes","contact","example","index","installation","intro","license","manual"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":2,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":2,"sphinx.domains.rst":2,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.todo":2,"sphinx.ext.viewcode":1,sphinx:56},filenames:["changes.rst","contact.rst","example.rst","index.rst","installation.rst","intro.rst","license.rst","manual.rst"],objects:{},objnames:{},objtypes:{},terms:{"1000l6":7,"1000l7":7,"150bp":7,"75bp":7,"default":[0,5,7],"function":0,"import":0,"int":[0,7],"long":5,"new":0,AND:6,Added:0,BUT:6,FOR:6,IDs:[0,7],NOT:6,THE:6,The:[0,2,4,5,6,7],These:4,USE:6,Use:7,Using:0,WITH:6,__no_featur:7,_log:2,abov:[5,6],accordingli:7,account:0,accuraci:7,action:6,activ:[4,7],adaptor:0,add:0,added:[0,7],adjac:7,adjacentbi:[0,7],adjust:[0,5,7],adjust_matrix_coordiant:0,adjust_matrix_coordin:0,affin:[0,7],after:[0,5,7],again:0,against:7,aggreg:7,algorithm:[0,7],align:[0,7],all:[4,5,6,7],allow:[0,2,5,7],alreadi:4,also:[0,5,7],altern:4,amazon:0,ambigu:[0,2,7],amplif:7,anaconda:4,analysi:[0,5],analyz:5,ani:[5,6],ann:2,annot:[0,2,5,7],anti:0,anyth:4,api:0,append:0,argpars:0,argument:[0,7],aris:6,arrai:[5,7],artifact:[5,7],associ:6,attach:0,author:[1,6,7],avail:7,awar:0,back:0,bam:[0,7],barcod:[0,2,5,7],base:[0,5,7],bash:2,basic:[0,5],batch:7,bcl:0,bed:[0,5,7],been:5,befor:0,better:0,big:7,bigger:7,bin:[2,7],binari:[0,7],bit:0,bowti:0,bug:0,build:[0,4],bump:0,bzip:[0,5],call:[0,4],can:[0,4,5,7],captur:0,caus:0,cell:[5,7],chang:[3,4],charg:6,check:[0,5],chose:5,claim:6,clean:[0,7],clip:[0,7],clone:4,cluster:[0,7],code:[0,7],color:0,column:[0,5],com:[1,4,5,6,7],combin:7,command:[0,4],comment:0,comput:[0,4,7],conda:4,condit:6,configur:0,connect:6,constant:[0,5],cont:2,contact:3,contain:[0,5,7],contamim:5,contamin:[2,7],content:[0,3,5,7],contract:6,convent:0,convert:0,convertensembltonam:0,coordin:[0,5,7],copi:6,copyright:6,correct:5,correctli:5,correspond:[0,7],count:[0,5,7],counttri:0,creat:[0,4],createdataset:0,ctt:0,curv:[0,7],cutadapt:0,damag:6,data:[0,5,7],dataset:[0,2,5,7],datfa:0,deactiv:4,deal:[0,6],debug:[0,7],defin:[5,7],delet:0,demultiplex:[0,5,7],demultiplexing_trim_sequ:7,depend:[0,7],deprec:0,descard:7,descript:[0,5,7],detail:5,detector:0,dict:0,differ:[0,7],directori:4,disabl:[0,7],disable_map:0,discard:[0,5,7],distanc:7,distribut:6,distributiosn:0,doc:0,document:[0,5,6],doe:[0,5],doing:7,down:[5,7],download:4,due:[0,7],duplic:[0,7],dure:7,each:[5,7],earlier:7,easi:5,easili:7,elev:4,emr:0,enabl:[0,7],end:[0,2,7],enough:5,ensembl:0,ensur:0,enter:4,environ:4,equal:7,error:0,etc:5,even:0,event:6,exampl:[3,5,7],exchang:0,execut:[0,7],exit:7,exp:[0,2],experi:[0,2,7],expnam:[2,7],express:[0,6,7],extra:[0,7],fail:[0,5],fals:7,faster:0,fastq:[0,2,5,7],fastq_fil:7,fastq_file_fw:7,fastq_file_rv:7,fernandez:[1,6,7],few:0,file:[0,2,5,6,7],filenam:0,filter:[0,2,5,7],filter_gene_type_matrix:0,find:0,findindex:0,first:[0,7],fit:6,fix:0,flag:[0,4,7],flank:7,folder:[0,2,5,7],follow:[2,4,5,6],format:[0,5,7],forward:0,found:7,frame:0,free:6,from:[0,4,6,7],full:5,fulli:[5,7],furnish:6,gap:0,gene:[0,5,7],gene_id:0,gene_nam:0,gener:[0,4,5],genom:[0,5,7],genomeload:7,get:5,gff:[5,7],git:4,github:[4,5],given:[0,5,7],gmai:6,gmail:[1,7],good:5,grant:6,graphic:5,grcm38_86v2:2,group:5,grow:0,gtf:[2,5,7],gzip:[0,5],gzipe:0,hadoop:0,ham:7,handl:0,happen:0,has:[0,5,7],hash:0,have:[4,5,7],heatmap:0,help:[5,7],here:4,herebi:6,hiearach:0,hierarch:[0,7],highest:7,hit:7,holder:6,home:4,homopolym:[0,7],how:[0,4],howev:7,htseq:[0,2,5,7],http:[4,5],identifi:5,identinfi:5,ids:[0,2,5,7],ignor:7,imag:0,impli:6,improv:[0,7],includ:[6,7],incorrect:0,increas:0,indentifi:7,index:[2,3,5,7],individu:4,info:[0,7],inform:[5,7],input:[0,5,7],instal:[0,3,5],instead:[0,7],instruct:4,integ:7,integr:0,intermediari:7,intern:0,intersect:7,introduct:3,intron:[0,7],invers:[0,7],invert:0,invok:0,issu:0,its:0,iupac:7,job:7,jose:[1,6,7],json2scatt:0,json:[0,5],just:4,keep:[0,5,7],kei:0,kept:[5,7],kimera:0,kind:6,kit:7,kmer:[0,2,7],label:7,last:7,latest:0,leav:0,length:[0,5,7],levenshtein:7,liabil:6,liabl:6,librari:0,licens:[0,3],like:7,limit:[0,6,7],line:0,list:[0,7],load:[0,7],local:7,locat:[0,7],log:[0,2,5,7],logic:0,look:5,low:[5,7],low_memori:0,made:0,make:0,mani:[0,5,7],manual:[0,3],map:[0,2,5,7],mapper:0,match:0,matrix:[0,5,7],max:[0,7],maximum:7,mean:7,mem:7,memori:[0,5,7],merchant:6,merg:[0,6],merge_bcl:0,merge_fastq:0,messag:[0,7],method:[0,7],metric:7,might:7,min:[0,7],minimum:[5,7],minor:0,mis:0,mismatch:[2,7],miss:[0,2,7],missmatch:0,mit:6,mode:[0,7],modifi:6,modul:3,modular:0,molecul:[0,5,7],molecular:[0,7],more:[0,5,7],mostli:5,mous:2,multimap:[0,7],multipl:[0,5,7],must:[4,7],naiv:[0,7],name:[0,2,4,5,7],navaro:7,navarro:[1,6,7],ncrna:2,neccessari:0,necessari:0,need:[0,4,5],newer:7,no_featur:0,non:[0,7],nonempti:7,noninfring:6,nonrna:2,normal:0,nosharedmemori:7,note:7,notic:6,now:[0,4],nucleotid:7,number:[0,5,7],obtain:[4,6,7],offset:[0,7],old:0,one:[0,5,7],onli:[0,5],optim:[0,5],option:[0,5,7],order:[5,7],origin:0,other:[0,6,7],otherwis:[6,7],out:[0,6],output:[0,2,5,7],overhang:7,page:3,pair:0,parallel:[0,5],paramet:[0,5,7],pars:0,part:0,particular:6,pass:[0,7],path:7,pattern:0,pdf:5,percentag:7,percentil:0,perform:[0,4,7],permiss:[4,6],permit:6,person:6,phred:7,pip:[0,4],pipelin:[0,2,5,7],plot:0,plotter:0,point:[0,7],polya:[0,5,7],polyc:[0,5,7],polyg:[0,5,7],polyn:[0,5,7],polyt:[0,5,7],port:0,portion:[0,6],pos:0,posit:[0,2,5,7],post:0,prefix:0,prepend:7,present:[0,7],primari:0,print:0,prior:0,process:[0,2,5,7],product:4,program:7,proper:0,provid:[0,5,6,7],publish:6,purpos:6,pypi:4,pysam:0,python:[0,4],qa_stat:0,qual:7,qualiti:[0,5,7],ram:7,random:7,randomis:7,rang:0,raw:[5,7],read:[0,2,5,7],read_1:7,read_2:7,readi:4,recommend:[2,4,7],reduc:0,ref:[0,2,7],refactor:0,refer:[2,5,7],relat:[0,5],relax:0,releas:0,remov:[0,5,7],renam:0,replac:0,repositori:[0,4],requir:[0,5,7],reserv:6,restor:0,restrict:[0,6],retriev:0,revers:[0,7],rewrit:0,right:6,rna:[0,5],robust:[0,5],row:5,rrna:[0,5],run:[0,2,4],sam:0,same:[0,5,7],sampl:7,saniti:5,satur:[0,7],saturation_point:7,save:7,score:7,scratch:4,screen:7,script:[0,5],search:[3,7],see:[5,7],sell:6,sens:0,separ:7,seq:5,sequenc:[5,7],set:[0,2,5,7],setup:4,sever:7,shall:6,share:7,shelv:0,shorter:7,should:7,show:7,similar:7,simpli:4,simplifi:0,singl:[5,7],size:[0,7],skip:[0,5,7],slide:0,slightli:7,small:0,soft:[0,7],softclip:0,softwar:[0,6],some:[0,7],sore:0,sort:[0,7],sourc:4,spatial:[3,5,7],spatialtranscriptomicsresearch:[4,5],specifi:[4,7],speed:[0,5],splice:[0,7],spot:[0,5,7],sqldict:0,st_pipelin:4,st_pipeline_run:[2,5,7],st_qa:0,stamp:0,star:[0,5,7],star_sort_mem_limit:7,starindex:2,start:[0,2,7],stat:[0,5,7],stdata:0,stdataplott:0,step:[0,4,5,7],store:[0,7],stpipelin:[2,4],str:7,strand:[0,7],strategi:0,stream:5,strech:0,stretch:7,strict:7,string:7,stringdoc:0,structur:0,stuff:0,stupid:0,sub:7,subglob:7,subject:6,sublicens:6,substanti:6,support:0,sure:0,system:[0,7],tag:7,taggd:[0,5,7],take:0,tell:4,temp:[0,7],templat:[0,7],temporari:7,termin:0,test:0,than:7,thei:7,them:7,thi:[4,5,6,7],thread:7,time:[0,7],tmp:0,togeth:7,too:5,tool:[0,5,7],top:0,tort:6,total:7,transcript:[5,7],transcriptom:[3,5,7],tree:0,trim:[0,5,7],trimmng:7,tupl:7,turn:7,two:[0,7],txt:2,type:[0,4,5,7],typo:0,umi:[0,2,5,7],unabl:7,unalign:7,union:7,uniqu:[0,5,7],unit:0,unittest:0,updat:0,upgrad:0,use:[0,2,4,5,6,7],used:[0,5,7],useful:[5,7],user:[0,4,5],using:[0,4,7],valid:5,valu:[0,5,7],variant:7,verbos:[2,7],veri:5,version:[0,7],veryhigh:7,virtual:4,visium:[2,5],want:[2,4,7],warranti:6,well:[0,5],what:[5,7],when:[0,7],where:[4,7],whether:6,which:[4,7],whole:[0,7],whom:6,whose:7,window:[0,7],wise:7,without:[0,5,6],work:0,workflow:[0,5],workflow_extend:5,would:0,write:7,wsnnwsnnv:7,www:4,yes:[0,7],you:[2,4,5,7],your:4,your_exp_nam:2,your_experiment_fold:2,your_id:2,your_run:2},titles:["Changes","Contact","Examples","Welcome to ST Pipeline\u2019s documentation!","Installing the Spatial Transcriptomics pipeline","Introduction","License","Manual"],titleterms:{chang:0,contact:1,document:3,exampl:2,indic:3,instal:4,introduct:5,licens:6,manual:7,pipelin:[3,4],spatial:4,tabl:3,transcriptom:4,welcom:3}})
\ No newline at end of file
+Search.setIndex({docnames:["changes","contact","example","index","installation","intro","license","manual"],envversion:{"sphinx.domains.c":2,"sphinx.domains.changeset":1,"sphinx.domains.citation":1,"sphinx.domains.cpp":3,"sphinx.domains.index":1,"sphinx.domains.javascript":2,"sphinx.domains.math":2,"sphinx.domains.python":2,"sphinx.domains.rst":2,"sphinx.domains.std":1,"sphinx.ext.intersphinx":1,"sphinx.ext.todo":2,"sphinx.ext.viewcode":1,sphinx:56},filenames:["changes.rst","contact.rst","example.rst","index.rst","installation.rst","intro.rst","license.rst","manual.rst"],objects:{},objnames:{},objtypes:{},terms:{"100":7,"10000":7,"100000":7,"1000l6":7,"1000l7":7,"150bp":7,"20000":7,"2020":6,"250":7,"50000":7,"75bp":7,"9999":7,"default":[0,5,7],"final":7,"function":0,"import":0,"int":[0,7],"long":5,"new":0,AND:6,Added:0,BUT:6,FOR:6,IDs:[0,7],NOT:6,THE:6,The:[0,2,4,5,6,7],These:4,USE:6,Use:7,Using:0,WITH:6,__no_featur:7,_log:2,abov:[5,6],accordingli:7,account:0,accuraci:7,action:6,activ:[4,7],adaptor:0,add:0,added:[0,7],adding:7,adjac:7,adjacentbi:[0,7],adjust:[0,5,7],adjust_matrix_coordiant:0,adjust_matrix_coordin:0,affin:[0,7],after:[0,5,7],again:0,against:7,aggreg:7,algorithm:[0,7],align:[0,7],all:[4,5,6,7],allow:[0,2,5,7],alreadi:4,also:[0,5,7],altern:4,amazon:0,ambigu:[0,2,7],amplif:7,anaconda:4,analysi:[0,5],analyz:5,ani:[5,6],ann:2,annot:[0,2,5,7],anti:0,anyth:4,api:0,append:0,argpars:0,argument:[0,7],aris:6,arrai:[5,7],artifact:[5,7],associ:6,attach:0,author:[1,6,7],avail:7,awar:0,back:0,bam:[0,7],barcod:[0,2,5,7],base:[0,5,7],bash:2,basic:[0,5],batch:7,bcl:0,bed:0,been:5,befor:0,better:0,big:7,bigger:7,bin:[2,7],binari:[0,7],bit:0,bowti:0,bug:0,build:[0,4],bump:0,bzip:[0,5],call:[0,4],can:[0,4,5,7],captur:0,caus:0,cell:5,chang:[3,4],charg:6,check:[0,5],chose:5,claim:6,clean:[0,7],clip:[0,7],clone:4,cluster:[0,7],code:[0,7],color:0,column:[0,5],com:[1,4,5,6,7],combin:7,command:[0,4],comment:0,compos:7,comput:[0,4,7],conda:4,condit:6,configur:0,connect:6,constant:[0,5],cont:2,contact:3,contain:[0,5,7],contamim:5,contamin:[2,7],content:[0,3,5,7],contract:6,convent:0,convert:0,convertensembltonam:0,coordin:[0,5,7],copi:6,copyright:6,correct:5,correctli:5,correspond:[0,7],count:[0,5,7],counttri:0,creat:[0,4],createdataset:0,ctt:0,curv:[0,7],cutadapt:0,damag:6,data:[0,5,7],dataset:[0,2,5,7],datfa:0,deactiv:4,deal:[0,6],debug:[0,7],defin:[5,7],delet:0,demultiplex:[0,5,7],demultiplexing_trim_sequ:7,depend:[0,7],deprec:0,descript:[0,5,7],detail:5,detector:0,dict:0,differ:[0,7],directori:4,disabl:[0,7],disable_map:0,discard:[0,5,7],distanc:7,distribut:6,distributiosn:0,doc:0,document:[0,5,6],doe:[0,5],doing:7,down:5,download:4,due:[0,7],duplic:[0,7],dure:7,each:[5,7],earlier:7,easi:5,easili:7,elev:4,emr:0,enabl:[0,7],end:[0,2,7],enough:5,ensembl:0,ensur:0,enter:4,environ:4,equal:7,error:0,etc:5,even:0,event:6,everi:7,exampl:[3,5,7],exchang:0,execut:[0,7],exit:7,exp:[0,2],experi:[0,2],expnam:[2,7],express:[0,6],extra:[0,7],fail:[0,5],fals:7,faster:0,fastq:[0,2,5,7],fastq_fil:7,fastq_file_fw:7,fastq_file_rv:7,fernandez:[1,6,7],few:0,file:[0,2,5,6,7],filenam:0,filter:[0,2,5,7],filter_gene_type_matrix:0,find:0,findindex:0,first:[0,7],fit:6,fix:0,flag:[0,4,7],flank:7,folder:[0,2,5,7],follow:[2,4,5,6],format:[0,5,7],forward:0,found:7,frame:0,free:6,from:[0,4,6,7],full:5,fulli:[5,7],furnish:6,gap:0,gene:[0,5,7],gene_id:0,gene_nam:0,gener:[0,4,5],genom:[0,5,7],genomeload:7,get:5,gff:[5,7],git:4,github:[4,5],given:[0,5,7],gmai:6,gmail:[1,7],good:5,grant:6,graphic:5,grcm38_86v2:2,group:5,grow:0,gtf:[2,5,7],gzip:[0,5],gzipe:0,hadoop:0,ham:7,handl:0,happen:0,has:[0,5,7],hash:0,have:[0,4,5,7],heatmap:0,help:[5,7],here:4,herebi:6,hiearach:0,hierarch:[0,7],high:7,highest:7,hit:7,holder:6,home:4,homopolym:[0,7],how:[0,4],howev:7,htseq:[0,2,5,7],http:[4,5],identifi:5,identinfi:5,ids:[0,2,5,7],ignor:7,imag:0,impli:6,improv:[0,7],includ:[6,7],incorrect:0,increas:0,indentifi:7,index:[2,3,5,7],individu:4,info:[0,7],inform:[5,7],input:[0,5,7],instal:[0,3,5],instead:[0,7],instruct:4,integ:7,integr:0,intermediari:7,intern:0,intersect:7,introduct:3,intron:[0,7],invers:[0,7],invert:0,invok:0,issu:0,its:0,iupac:7,job:7,jose:[1,6,7],json2scatt:0,json:0,just:4,keep:[0,5,7],kei:0,kept:[5,7],kimera:0,kind:6,kit:7,kmer:[0,2,7],label:7,last:7,latest:0,leav:0,length:[0,5,7],levenshtein:7,liabil:6,liabl:6,librari:0,licens:[0,3],like:7,limit:[0,6,7],line:0,list:[0,7],load:[0,7],local:7,locat:[0,7],log:[0,2,5,7],logic:0,look:5,low:[5,7],low_memori:0,made:0,make:0,mani:[0,5,7],manual:[0,3],map:[0,2,5,7],mapper:0,match:0,matrix:[0,5,7],max:[0,7],maximum:7,mean:7,mem:7,memori:[0,5,7],merchant:6,merg:[0,6],merge_bcl:0,merge_fastq:0,messag:[0,7],method:[0,7],metric:7,might:7,min:[0,7],minimum:[5,7],minor:0,mis:0,mismatch:[2,7],miss:[0,2],missmatch:0,mit:6,mode:[0,7],modifi:6,modul:3,modular:0,molecul:[0,5],molecular:[0,7],more:[0,5,7],mostli:5,mous:2,multimap:[0,7],multipl:[0,5,7],must:[4,7],naiv:[0,7],name:[0,2,4,5,7],navaro:7,navarro:[1,6,7],ncrna:2,neccessari:0,necessari:0,need:[0,4,5,7],newer:7,no_featur:0,non:[0,7],nonempti:7,noninfring:6,nonrna:2,normal:0,nosharedmemori:7,note:7,notic:6,now:[0,4],nucleotid:7,number:[0,5,7],obtain:[4,6,7],offset:[0,7],old:0,one:[0,5,7],onli:[0,5,7],optim:[0,5],option:[0,5,7],order:[5,7],origin:0,other:[0,6,7],otherwis:[6,7],out:[0,6,7],output:[0,2,5,7],overhang:7,page:3,pair:0,parallel:[0,5],paramet:[0,5,7],pars:0,part:0,particular:6,pass:[0,7],path:7,pattern:0,pdf:5,percentag:7,percentil:0,perform:[0,4,7],permiss:[4,6],permit:6,person:6,phred:7,pip:[0,4],pipelin:[0,2,5,7],plot:[0,7],plotter:0,point:[0,7],polya:[0,5,7],polyc:[0,5,7],polyg:[0,5,7],polyn:[0,5,7],polyt:[0,5,7],port:0,portion:[0,6],pos:0,posit:[0,2,5,7],post:0,prefix:0,prepend:7,present:[0,7],primari:0,print:0,prior:0,process:[0,2,5,7],product:4,program:7,proper:0,provid:[0,5,6,7],publish:6,purpos:6,pypi:4,pysam:0,python:[0,4],qa_stat:0,qual:7,qualiti:[0,5,7],ram:7,random:7,randomis:7,rang:0,raw:5,read:[0,2,5,7],read_1:7,read_2:7,readi:4,reador:7,recommend:[2,4,7],reduc:0,ref:[0,2,7],refactor:0,refer:[2,5,7],relat:[0,5],relax:0,releas:0,remov:[0,5,7],renam:0,replac:0,repositori:[0,4],requir:[0,5,7],reserv:6,restor:0,restrict:[0,6],retriev:0,revers:[0,7],rewrit:0,right:6,rna:[0,5],robust:[0,5],row:5,rrna:[0,5],run:[0,2,4],sam:0,same:[0,5,7],sampl:7,saniti:5,satur:[0,7],saturation_point:7,save:7,score:7,scratch:4,screen:7,script:[0,5],search:[3,7],see:[5,7],sell:6,sens:0,seq:5,sequenc:[5,7],set:[0,2,5,7],setup:4,sever:7,shall:6,share:7,shelv:0,shorter:7,should:7,show:7,side:7,similar:7,simpli:4,simplifi:0,singl:5,size:[0,7],skip:[0,5,7],slide:0,slightli:7,small:0,soft:[0,7],softclip:0,softwar:[0,6],some:[0,7],sore:0,sort:[0,7],sourc:4,spatial:[3,5,7],spatialtranscriptomicsresearch:[4,5],specifi:[4,7],speed:[0,5],splice:[0,7],spot:[0,5,7],sqldict:0,st_pipelin:4,st_pipeline_run:[2,5,7],st_qa:0,stamp:0,star:[0,5,7],star_sort_mem_limit:7,starindex:2,start:[0,2,7],stat:[0,5,7],stdata:0,stdataplott:0,step:[0,4,5,7],store:[0,7],stpipelin:[2,4],str:7,strand:[0,7],strategi:0,stream:5,strech:0,stretch:7,strict:7,string:7,stringdoc:0,structur:0,stuff:0,stupid:0,sub:7,subglob:7,subject:6,sublicens:6,substanti:6,support:0,sure:0,system:[0,7],tag:7,taggd:[0,5,7],take:0,tell:4,temp:[0,7],templat:[0,7],temporari:7,termin:0,test:0,than:7,thei:7,them:7,thi:[4,5,6,7],thread:7,time:[0,7],tmp:0,togeth:7,too:5,tool:[0,5,7],top:0,tort:6,total:7,transcriptom:[3,5,7],tree:0,trim:[0,5,7],trimmng:7,tupl:7,turn:7,two:[0,7],txt:2,type:[0,4,5,7],typo:0,umi:[0,2,5,7],union:7,uniqu:[0,5,7],unit:0,unittest:0,updat:0,upgrad:0,use:[0,2,4,5,6,7],used:[0,5,7],useful:[5,7],user:[0,4,5],using:[0,4,7],valid:5,valu:[0,5,7],variant:7,verbos:[2,7],veri:[5,7],version:[0,7],virtual:4,visium:[2,5,7],want:[2,4,7],warranti:6,well:[0,5],what:[5,7],when:[0,7],where:[4,7],whether:6,which:[4,7],whole:[0,7],whom:6,whose:7,window:[0,7],wise:7,without:[0,5,6],work:0,workflow:[0,5],workflow_extend:5,would:0,wsnnwsnnv:7,www:4,yes:[0,7],you:[2,4,5,7],your:4,your_exp_nam:2,your_experiment_fold:2,your_id:2,your_run:2},titles:["Changes","Contact","Examples","Welcome to ST Pipeline\u2019s documentation!","Installing the Spatial Transcriptomics pipeline","Introduction","License","Manual"],titleterms:{chang:0,contact:1,document:3,exampl:2,indic:3,instal:4,introduct:5,licens:6,manual:7,pipelin:[3,4],spatial:4,tabl:3,transcriptom:4,welcom:3}})
\ No newline at end of file
diff --git a/docsrc/changes.rst b/docsrc/changes.rst
index 36310df..b4734a7 100644
--- a/docsrc/changes.rst
+++ b/docsrc/changes.rst
@@ -1,6 +1,11 @@
 Changes
 -------
 
+**Version 1.8.1**
+
+* Fixed a bug when having barcodes after the UMI
+* Improved descriptions for parameters
+
 **Version 1.8.0**
 
 * Improved the unit-tests
diff --git a/docsrc/example.rst b/docsrc/example.rst
index 98e05e2..112fda8 100644
--- a/docsrc/example.rst
+++ b/docsrc/example.rst
@@ -43,7 +43,7 @@ If you want to process Visium datasets it is recommended to use these settings
 .. code-block:: bash
 
     --allowed-missed 1 \
-  	--allowed-kmer 4 \
+    --allowed-kmer 4 \
   	--umi-allowed-mismatches 2 \
   	--umi-start-position 16 \
   	--umi-end-position 28 \
diff --git a/docsrc/intro.rst b/docsrc/intro.rst
index d6e2c93..4e04c0f 100644
--- a/docsrc/intro.rst
+++ b/docsrc/intro.rst
@@ -39,12 +39,12 @@ The input FASTQ files can be given in gzip/bzip format as well.
 Basically what the ST pipeline does is:
 
 - Quality trimming (read 1 and read 2):
-	- Remove low quality bases
-	- Sanity check (reads same length, reads order, etc..)
-	- Check quality UMI (if provided)
-	- Remove artifacts (PolyT, PolyA, PolyG, PolyN and PolyC) of user defined length
-	- Check for AT and GC content
-	- Discard reads with a minimum number of bases of that failed any of the checks above
+    - Remove low quality bases
+    - Sanity check (reads same length, reads order, etc..)
+    - Check quality UMI (if provided)
+    - Remove artifacts (PolyT, PolyA, PolyG, PolyN and PolyC) of user defined length
+    - Check for AT and GC content
+    - Discard reads with a minimum number of bases of that failed any of the checks above
 - Contamimant filter e.x. rRNA genome (Optional)
 - Mapping with STAR (only read 2)
 - Demultiplexing with [Taggd](https://github.com/SpatialTranscriptomicsResearch/taggd) (only read 1)
@@ -55,7 +55,5 @@ Basically what the ST pipeline does is:
 
 You can see a graphical more detailed description of the workflow in the documents workflow.pdf and workflow_extended.pdf
 
-The output will be a matrix of counts (genes as columns, spots as rows),
-a BED file containing the transcripts (Read name, coordinate, gene, etc..), and a JSON
-file with useful stats.
-The ST pipeline will also output a log file with useful information.
\ No newline at end of file
+The output will be a matrix of counts (genes as columns, spots as rows)
+and a log file with useful information and stats.
\ No newline at end of file
diff --git a/docsrc/manual.rst b/docsrc/manual.rst
index 9f9cc8a..07322c9 100644
--- a/docsrc/manual.rst
+++ b/docsrc/manual.rst
@@ -1,15 +1,14 @@
 Manual
 ------
 
-ST Pipeline is a tool to process the Spatial Transcriptomics raw data
-or single cell data.
+ST Pipeline is a tool to process the Spatial Transcriptomics and Visium data.
 The data is filtered, aligned to a genome, annotated to a reference,
 demultiplexed by array coordinates and then aggregated by counts
 that are not duplicates using the Unique Molecular Indentifiers.
-The output contains the counts matrix, a stats file, a log file
-and a BED file with all the transcripts.
+The output contains the counts matrix and a log file with useful
+stats in information.
 
-The ST Pipeline requires two fastq files, an IDs files (BARCODE, X, Y),
+The ST Pipeline requires two FASTQ files, an IDs files (BARCODE, X, Y),
 the path to a STAR genome index, the path to a annotation file in GTF
 format and a dataset name.
 
@@ -24,7 +23,7 @@ Soft clipping is also not recommended when using the 75bp kit, due to the
 shorter length.
 
 The UMI filter can be used for array batches 1000L6 and earlier. It is
-unable to be used for array batches 1000L7 and newer as the UMI in
+not recommended to use it for array batches 1000L7 and newer as the UMI in
 these arrays is fully randomised.
 
 Author Jose Fernandez Navarro <jc.fernandez.navaro@gmail.com>
@@ -51,47 +50,22 @@ Author Jose Fernandez Navarro <jc.fernandez.navaro@gmail.com>
   --ids [FILE]          Path to the file containing the map of barcodes to the
                         array coordinates
   --ref-map [FOLDER]    Path to the folder with the STAR index for the genome
-                        that you want to use to align the reads
+                        that you want to use as reference
   --ref-annotation [FILE]
                         Path to the reference annotation file (GTF or GFF
-                        format is required) to be used to annotated the reads
-  --expName [STRING]    Name of the experiment/dataset (The output files will
-                        prepend this name)
-  --allowed-missed [INT]
-                        Number of allowed mismatches when demultiplexing
-                        against the barcodes with TaggD (default: 2)
-  --allowed-kmer [INT]  KMer length when demultiplexing against the barcodes
-                        with TaggD (default: 6)
-  --overhang [INT]      Extra flanking bases added when demultiplexing against
-                        the barcodes with TaggD (default: 2)
-  --min-length-qual-trimming [INT]
-                        Minimum length of the reads after trimming, shorter
-                        reads will be discarded (default: 20)
-  --mapping-rv-trimming [INT]
-                        Number of bases to trim in the reverse reads for the
-                        mapping step (5\' end) (default: 0)
+                        format is required) to be used to annotated the mapped
+                        reads
+  --expName [STRING]    Name of the dataset (The output files will prepend
+                        this name)
   --contaminant-index [FOLDER]
                         Path to the folder with a STAR index with a
-                        contaminant genome. Reads will be filtered against the
-                        specified genome and mapping reads will be descarded
-  --qual-64             Use phred-64 quality instead of phred-33(default)
-  --htseq-mode [STRING]
-                        Mode of Annotation when using HTSeq. Modes =
-                        {union,intersection-nonempty(default),intersection-
-                        strict}
-  --htseq-no-ambiguous  When using htseq discard reads annotating ambiguous
-                        genes (default False)
-  --start-id [INT]      Start position of the IDs (Barcodes) in the R1
-                        (counting from 0) (default: 0)
+                        contaminant genome reference. Reads will be filtered
+                        using the specified genome and mapping reads will be
+                        discarded
   --no-clean-up         Do not remove temporary/intermediary files (useful for
                         debugging)
   --verbose             Show extra information on the log file
-  --mapping-threads [INT]
-                        Number of threads to use in the mapping step (default:
-                        4)
-  --min-quality-trimming [INT]
-                        Minimum phred quality a base must have in the trimming
-                        step (default: 20)
+  --threads [INT]       Number of threads to use (default: 4)
   --bin-path [FOLDER]   Path to folder where binary executables are present
                         (system path by default)
   --log-file [STR]      Name of the file that we want to use to store the logs
@@ -100,19 +74,16 @@ Author Jose Fernandez Navarro <jc.fernandez.navaro@gmail.com>
                         Path of the output folder
   --temp-folder [FOLDER]
                         Path of the location for temporary files
-  --umi-allowed-mismatches [INT]
-                        Number of allowed mismatches (hamming distance) that
-                        UMIs of the same gene-spot must have in order to
-                        cluster together (default: 1)
-  --umi-start-position [INT]
-                        Position in R1 (base wise) of the first base of the
-                        UMI (starting by 0) (default: 18)
-  --umi-end-position [INT]
-                        Position in R1 (base wise) of the last base of the UMI
-                        (starting by 1) (default: 27)
   --keep-discarded-files
-                        Writes down unaligned, un-annotated and un-
-                        demultiplexed reads to files
+                        Keep files with discarded reads in every step
+  --qual-64             Use phred-64 quality instead of phred-33(default) in
+                        the quality trimming step
+  --min-length-qual-trimming [INT]
+                        Minimum length of the reads after trimming, shorter
+                        reads will be discarded (default: 20)
+  --min-quality-trimming [INT]
+                        Minimum phred quality a base must have in order to be
+                        kept in the quality trimming step (default: 20)
   --remove-polyA [INT]  Remove PolyA stretches of the given length from R2
                         (Use 0 to disable it) (default: 10)
   --remove-polyT [INT]  Remove PolyT stretches of the given length from R2
@@ -123,25 +94,28 @@ Author Jose Fernandez Navarro <jc.fernandez.navaro@gmail.com>
                         (Use 0 to disable it) (default: 10)
   --remove-polyN [INT]  Remove PolyN stretches of the given length from R2
                         (Use 0 to disable it) (default: 10)
+  --homopolymer-mismatches [INT]
+                        Number of mismatches allowed when removing
+                        homopolymers (A, T, G, C or N) (default: 0)
   --filter-AT-content [INT%]
                         Discards reads whose number of A and T bases in total
-                        are more or equal than the number given in percentage
-                        (default: 90)
+                        are more or equal than the percentage given as input
+                        (0-100) (default: 90)
   --filter-GC-content [INT%]
                         Discards reads whose number of G and C bases in total
-                        are more or equal than the number given in percentage
-                        (default: 90)
+                        are more or equal the percentage given as input
+                        (0-100) (default: 90)
+  --mapping-rv-trimming [INT]
+                        Number of bases to trim in the reverse reads (R2) for
+                        the mapping step (5' end) (default: 0)
+  --inverse-mapping-rv-trimming [INT]
+                        Number of bases to trim in the reverse reads (R2) for
+                        the mapping step (3' end) (default: 0)
   --disable-multimap    If activated, multiple aligned reads obtained during
                         mapping will be all discarded. Otherwise the highest
                         scored one will be kept
   --disable-clipping    If activated, disable soft-clipping (local alignment)
                         in the mapping step
-  --umi-cluster-algorithm [STRING]
-                        Type of clustering algorithm to use when performing
-                        UMIs duplicates removal. Options = {naive,
-                        hierarchical(default), Affinity, Adjacent and
-                        AdjacentBi} Note that for the affinity method the umi
-                        allowed mismatches parameter will be ignored.
   --min-intron-size [INT]
                         Minimum allowed intron size when searching for splice
                         variants with STAR Splices alignments are disabled by
@@ -152,68 +126,103 @@ Author Jose Fernandez Navarro <jc.fernandez.navaro@gmail.com>
                         variants with STAR Splices alignments are disabled by
                         default (=1) but to turn it on set this parameter to a
                         big number, for example 10000 or 100000. (default: 1)
+  --star-two-pass-mode  Activates the 2-pass mode in STAR to improve mapping
+                        accuracy
+  --star-genome-loading [STRING]
+                        Similar to the STAR option --genomeLoad. It allows to
+                        load the genome index into memory so it can easily be
+                        shared by other jobs to save loading time. Read the
+                        STAR manual for more info on this. (default:
+                        NoSharedMemory)
+  --star-sort-mem-limit STAR_SORT_MEM_LIMIT
+                        The maximum available RAM for sorting BAM during
+                        mapping with STAR. Default is 0 which means that it
+                        will be set to the genome index size
+  --demultiplexing-mismatches [INT]
+                        Number of allowed mismatches when demultiplexing the
+                        reads against the barcodes with TaggD (default: 2)
+  --demultiplexing-kmer [INT]
+                        KMer size to use when demultiplexing against the
+                        barcodes with TaggD (default: 6)
+  --demultiplexing-overhang [INT]
+                        Extra flanking bases added on each side of the barcode
+                        when demultiplexing against the barcodes with TaggD
+                        (default: 0)
+  --demultiplexing-start [INT]
+                        Start position of the IDs (Barcodes) in R1 (counting
+                        from 0) (default: 0)
+  --demultiplexing-metric [STRING]
+                        Distance metric to use for TaggD demultiplexing:
+                        Options: Subglobal, Levenshtein or Hamming (default:
+                        Subglobal)
+  --demultiplexing-multiple-hits-keep-one
+                        When multiple ambiguous hits with same score are found
+                        in the demultiplexing step, keep only one (random).
+  --demultiplexing-trim-sequences DEMULTIPLEXING_TRIM_SEQUENCES
+                        Trim the barcodes in the input file when doing
+                        demultiplexing. The input given is a list of tuples
+                        START END START END where START is the integer
+                        position of the first base (0 based) and END is the
+                        integer position of the last base (1 based). The final
+                        barcode will be obtained by combining all the
+                        sequences given in the input. This is useful when
+                        having a barcode composed of multiple sequences in the
+                        reador when the barcode needs to be trimmed out.
+                        Trimmng sequences can be given several times.
+  --htseq-mode [STRING]
+                        Mode of annotation when using htseq-count. Modes =
+                        {union, intersection-nonempty(default), intersection-
+                        strict}
+  --htseq-no-ambiguous  When using htseq-count discard reads annotating
+                        ambiguous genes (default False)
+  --strandness [STRING]
+                        What strandness mode to use when annotating with
+                        htseq-count [no, yes(default), reverse]
+  --include-non-annotated
+                        Do not discard un-annotated reads (they will be
+                        labeled __no_feature)
+  --umi-cluster-algorithm [STRING]
+                        Type of clustering algorithm to use when performing
+                        UMIs duplicates removal. Options = {naive,
+                        hierarchical, Affinity, Adjacent and
+                        AdjacentBi(default)} Note that for the affinity method
+                        the umi allowed mismatches parameter will be ignored.
+  --umi-allowed-mismatches [INT]
+                        Number of allowed mismatches (hamming distance) that
+                        UMIs of the same gene-spot must have in order to
+                        cluster together (default: 1)
+  --umi-start-position [INT]
+                        Position in R1 (base wise) of the first base of the
+                        UMI (starting by 0) (default: 18)
+  --umi-end-position [INT]
+                        Position in R1 (base wise) of the last base of the UMI
+                        (starting by 1) (default: 27)
   --umi-filter          Enables the UMI quality filter based on the template
                         given in --umi-filter-template
   --umi-filter-template [STRING]
                         UMI template (IUPAC nucleotide code) for the UMI
                         filter, default = WSNNWSNNV
-  --compute-saturation  Performs a saturation curve computation by sub-
-                        sampling the annotated reads, computing unique
-                        molecules and then a saturation curve (included in the
-                        log file)
-  --saturation-points SATURATION_POINTS [SATURATION_POINTS ...]
-                        Saturation points can be provided instead of using
-                        default values. Provide separate values like this for
-                        example: 10000 20000 50000 100000
-  --include-non-annotated
-                        Do not discard un-annotated reads (they will be
-                        labeled __no_feature)
-  --inverse-mapping-rv-trimming [INT]
-                        Number of bases to trim in the reverse reads for the
-                        mapping step on the 3\' end
-  --two-pass-mode       Activates the 2-pass mode in STAR to improve mapping
-                        accuracy
-  --strandness [STRING]
-                        What strandness mode to use when annotating with
-                        htseq-count [no, yes(default), reverse]
   --umi-quality-bases [INT]
                         Maximum number of low quality bases allowed in an UMI
                         (default: 6)
   --umi-counting-offset [INT]
-                        Expression count for each gene-spot combination is
-                        expressed as the number of unique UMIs in each
-                        strand/start position. However some reads might have
-                        slightly different start positions due to
-                        amplification artifacts. This parameters allows to
-                        define an offset window from where to count unique
-                        UMIs. You can set it to a veryhigh value +9999 to
-                        count unique UMIs for the whole gene (default: 250)
-  --demultiplexing-metric [STRING]
-                        Distance metric for TaggD demultiplexing: Subglobal,
-                        Levenshtein or Hamming (default: Subglobal)
-  --demultiplexing-multiple-hits-keep-one
-                        When multiple ambiguous hits with same score are found
-                        in the demultiplexing, keep one (random).
-  --demultiplexing-trim-sequences DEMULTIPLEXING_TRIM_SEQUENCES [DEMULTIPLEXING_TRIM_SEQUENCES ...]
-                        Trims from the barcodes in the input file when doing
-                        demultiplexing. The bases given in the list of tuples
-                        as START END START END .. where START is the integer
-                        position of the first base (0 based) and END is the
-                        integer position of the last base (1 based). Trimmng
-                        sequences can be given several times.
-  --homopolymer-mismatches [INT]
-                        Number of mismatches allowed when removing
-                        homopolymers (default: 0)
-  --star-genome-loading [STRING]
-                        Similar to the STAR option --genomeLoad. It allows to
-                        load the genome index into memory so it can easily be
-                        shared by other jobs so to save loading time. Read the
-                        STAR manual for more info on this. (default:
-                        NoSharedMemory)
-  --star-sort-mem-limit STAR_SORT_MEM_LIMIT
-                        The maximum available RAM for sorting BAM during
-                        mapping. Default is 0 which means that it will be set
-                        to the genome index size
+                        UMI count for each gene-spot combination is computed
+                        as the number of unique UMIs in each strand/start
+                        position. However some reads might have slightly
+                        different start positions due to amplification
+                        artifacts. This parameters allows to define an offset
+                        window from where to count unique UMIs. You can set it
+                        to a very high value +9999 to count unique UMIs for
+                        the whole gene (default: 250)
+  --compute-saturation  Performs a saturation curve computation by sub-
+                        sampling the annotated reads, computing unique UMIs
+                        and adding the stats to the log file (this can be used
+                        to plot saturation curves)
+  --saturation-points SATURATION_POINTS [SATURATION_POINTS ...]
+                        Saturation points for the saturation curve computation
+                        can be provided instead of using default values.
+                        Provide a list of values like this for example: 10000
+                        20000 50000 100000
   --disable-trimming    Use this flag if you want to skip the trimming step
   --disable-mapping     Use this flag if you want to skip the mapping step
   --disable-annotation  Use this flag if you want to skip the annotation
@@ -221,7 +230,7 @@ Author Jose Fernandez Navarro <jc.fernandez.navaro@gmail.com>
                         demultiplexing step
   --disable-umi         Use this flag if you want to skip the UMI filtering
                         step
-  --transcriptome       Use a transcriptome instead of a genome, the gene tag
-                        will be obtained from the transcriptome file
-  --version             show program's version number and exit
-
+  --transcriptome       Use this flag if you want to use transcriptome instead
+                        of a genome, the gene tag will be obtained from the
+                        transcriptome file
+  --version             show program's version number and exit
\ No newline at end of file
diff --git a/scripts/adjust_matrix_coordinates.py b/scripts/adjust_matrix_coordinates.py
index 654889e..d8b9820 100644
--- a/scripts/adjust_matrix_coordinates.py
+++ b/scripts/adjust_matrix_coordinates.py
@@ -33,21 +33,21 @@
 import os
 import pandas as pd
 
-def main(counts_matrix, coordinates_file, update_coordinates, outfile):
 
+def main(counts_matrix, coordinates_file, update_coordinates, outfile):
     if not os.path.isfile(counts_matrix) or not os.path.isfile(coordinates_file):
         sys.stderr.write("Error, input file not present or invalid format\n")
         sys.exit(1)
-     
+
     if not outfile:
         outfile = "adjusted_{}".format(os.path.basename(counts_matrix))
-           
+
     # Get a map of the new coordinates
     new_coordinates = dict()
     with open(coordinates_file, "r") as filehandler:
         for line in filehandler.readlines():
             tokens = line.split()
-            assert(len(tokens) == 6 or len(tokens) == 4 or len(tokens) == 7)
+            assert (len(tokens) == 6 or len(tokens) == 4 or len(tokens) == 7)
             if tokens[0] != "x":
                 old_x = int(tokens[0])
                 old_y = int(tokens[1])
@@ -68,20 +68,21 @@ def main(counts_matrix, coordinates_file, update_coordinates, outfile):
         try:
             new_x, new_y = new_coordinates[(x, y)]
             if not update_coordinates:
-                new_x, new_y = x,y
-            new_index_values.append("{0}x{1}".format(new_x,new_y))
+                new_x, new_y = x, y
+            new_index_values.append("{0}x{1}".format(new_x, new_y))
         except KeyError:
             counts_table.drop(index, inplace=True)
 
     # Assign the new indexes 
     counts_table.index = new_index_values
-    
+
     # Remove genes that have now a total count of zero
     counts_table = counts_table.transpose()[counts_table.sum(axis=0) > 0].transpose()
-    
+
     # Write table again
     counts_table.to_csv(outfile, sep='\t')
-               
+
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description=__doc__,
                                      formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -90,11 +91,9 @@ def main(counts_matrix, coordinates_file, update_coordinates, outfile):
     parser.add_argument("--outfile", help="Name of the output file")
     parser.add_argument("--update-coordinates", action="store_true", default=False,
                         help="Updates the spot coordinates in the output matrix with the\n"
-                        "new coordinates present in the coordinates file")
-    parser.add_argument("--coordinates-file",  required=True,
+                             "new coordinates present in the coordinates file")
+    parser.add_argument("--coordinates-file", required=True,
                         help="New coordinates in a tab delimited file")
     args = parser.parse_args()
 
     main(args.counts_matrix, args.coordinates_file, args.update_coordinates, args.outfile)
-
-
diff --git a/scripts/convertEnsemblToNames.py b/scripts/convertEnsemblToNames.py
index b6b6c32..19f4903 100755
--- a/scripts/convertEnsemblToNames.py
+++ b/scripts/convertEnsemblToNames.py
@@ -15,8 +15,8 @@
 from stpipeline.common.gff_reader import *
 from collections import Counter
 
-def main(st_data_file, annotation, output_file):
 
+def main(st_data_file, annotation, output_file):
     if not os.path.isfile(st_data_file) or not os.path.isfile(annotation):
         sys.stderr.write("Error, input file not present or invalid format\n")
         sys.exit(1)
@@ -25,7 +25,7 @@ def main(st_data_file, annotation, output_file):
     gene_map = dict()
     for line in gff_lines(annotation):
         gene_map[line["gene_id"]] = line["gene_name"]
-    
+
     # Load the ST dataset
     st_data = pd.read_table(st_data_file, sep="\t", header=0, index_col=0)
 
@@ -33,12 +33,12 @@ def main(st_data_file, annotation, output_file):
     if len(gene_map) < len(st_data.columns):
         sys.stdout.write("Error, the annotation file given is invalid\n")
         sys.exit(1)
-            
+
     # Checks that there are no duplicated genes
     gene_ids_counter = Counter(st_data.columns)
     for gene_id, count in gene_ids_counter.most_common():
         if count > 1:
-            sys.stdout.write("Error, Ensembl ID {} was found {} times in the input " \
+            sys.stdout.write("Error, Ensembl ID {} was found {} times in the input "
                              "matrix.\n".format(gene_id, count))
             sys.exit(1)
 
@@ -56,10 +56,10 @@ def main(st_data_file, annotation, output_file):
                 # so we keep the Ensmelb ID.
                 # We assume input Ensemgl ids are unique as we checked this before
                 gene_name = gene_id
-                sys.stdout.write("Warning, gene name {} was already matched so the original " \
+                sys.stdout.write("Warning, gene name {} was already matched so the original "
                                  "Ensembl ID {} will be kept\n".format(gene_name, gene_id))
         except KeyError:
-            sys.stdout.write("Warning, {} was not found in the annotation, " \
+            sys.stdout.write("Warning, {} was not found in the annotation, "
                              "so the original Ensembl ID will be kept\n".format(gene_id))
             gene_name = gene_id
         adjustedList.append(gene_name)
@@ -70,10 +70,11 @@ def main(st_data_file, annotation, output_file):
     # Write table to file
     st_data.to_csv(output_file, sep="\t")
 
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description=__doc__,
                                      formatter_class=argparse.RawDescriptionHelpFormatter)
-    parser.add_argument("counts_matrix", 
+    parser.add_argument("counts_matrix",
                         help="Matrix with gene counts (genes as columns) in TSV format")
     parser.add_argument("--output", default="output.tsv",
                         help="Name of the output file, default output.tsv")
@@ -81,4 +82,3 @@ def main(st_data_file, annotation, output_file):
                         help="Path to the annotation file used to generate the data")
     args = parser.parse_args()
     main(args.counts_matrix, args.annotation, args.output)
-
diff --git a/scripts/filter_gene_type_matrix.py b/scripts/filter_gene_type_matrix.py
index 83fc6d0..252080b 100644
--- a/scripts/filter_gene_type_matrix.py
+++ b/scripts/filter_gene_type_matrix.py
@@ -19,21 +19,21 @@
 import os
 import pandas as pd
 from stpipeline.common.gff_reader import *
-              
-def main(counts_matrix, gene_types_keep, outfile, annotation, ensembl_ids):
 
+
+def main(counts_matrix, gene_types_keep, outfile, annotation, ensembl_ids):
     if not os.path.isfile(counts_matrix) or not os.path.isfile(annotation):
         sys.stderr.write("Error, input file not present or invalid format\n")
         sys.exit(1)
-     
+
     if not outfile:
         outfile = "filtered_{}".format(os.path.basename(counts_matrix))
-    
+
     gene_types = dict()
     for line in gff_lines(annotation):
         gene_name = line["gene_id"] if ensembl_ids else line["gene_name"]
         gene_types[gene_name] = line["gene_type"] if "gene_type" in line else line["gene_biotype"]
-    assert(len(gene_types) > 0)
+    assert (len(gene_types) > 0)
 
     # Read the data frame (genes as columns)
     counts_table = pd.read_table(counts_matrix, sep="\t", header=0, index_col=0)
@@ -52,7 +52,8 @@ def main(counts_matrix, gene_types_keep, outfile, annotation, ensembl_ids):
         print("Not a single gene could be discarded...")
     # Write filtered table
     counts_table.to_csv(outfile, sep='\t')
-               
+
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description=__doc__,
                                      formatter_class=argparse.RawDescriptionHelpFormatter)
@@ -62,8 +63,8 @@ def main(counts_matrix, gene_types_keep, outfile, annotation, ensembl_ids):
     parser.add_argument("--gene-types-keep", required=True, nargs='+', type=str,
                         help="List of Ensembl gene types to keep (E.x protein_coding lincRNA")
     parser.add_argument("--annotation", help="The Ensembl annotation file", required=True, type=str)
-    parser.add_argument("--ensembl-ids", action="store_true", 
+    parser.add_argument("--ensembl-ids", action="store_true",
                         default=False, help="Pass this parameter if the genes in the matrix" \
-                        "are named with Ensembl Ids instead of gene names")
+                                            "are named with Ensembl Ids instead of gene names")
     args = parser.parse_args()
     main(args.counts_matrix, args.gene_types_keep, args.outfile, args.annotation, args.ensembl_ids)
diff --git a/scripts/merge_fastq.py b/scripts/merge_fastq.py
index b49f7f5..b053a46 100644
--- a/scripts/merge_fastq.py
+++ b/scripts/merge_fastq.py
@@ -14,6 +14,7 @@
 import shutil
 import subprocess
 
+
 def run_command(command, out=subprocess.PIPE):
     try:
         print("Running command: {}".format(" ".join(x for x in command).rstrip()))
@@ -25,13 +26,14 @@ def run_command(command, out=subprocess.PIPE):
         print(errmsg)
     except Exception as e:
         raise e
-               
+
+
 def main(run_path, indexes, out_path):
 
     if not os.path.isdir(run_path) or not os.path.isdir(out_path):
         sys.stderr.write("Error, run path or output path folders do not exist\n")
         sys.exit(1)
-                
+
     # First gunzip all the FASTQ files
     os.chdir(run_path)
     try:
@@ -40,7 +42,7 @@ def main(run_path, indexes, out_path):
     except Exception as e:
         sys.stderr.write("Error, gunziping FASTQ files\n" + str(e))
         sys.exit(1)
-       
+
     # Second merge the FASTQ files
     for index in indexes:
         r1_files = sorted(glob.glob("*{}*R1*.fastq".format(index)))
@@ -53,21 +55,22 @@ def main(run_path, indexes, out_path):
         except Exception as e:
             sys.stderr.write("Error, merging FASTQ files\n" + str(e))
             sys.exit(1)
-    
+
     # Third gzip everything again
     try:
-        for file in glob.glob("*.fastq"): 
+        for file in glob.glob("*.fastq"):
             run_command(["gzip", "-f", file])
     except Exception as e:
         sys.stderr.write("Error, gziping FASTQ files\n" + str(e))
         sys.exit(1)
-        
+
     # Move merged FASTQ files to output path
     if run_path != out_path:
         for index in indexes:
             for file in glob.glob("{}_R*".format(index)):
                 shutil.move(file, out_path)
-                   
+
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description=__doc__,
                                      formatter_class=argparse.RawDescriptionHelpFormatter)
diff --git a/scripts/multi_qa.py b/scripts/multi_qa.py
index e2257ce..88313ad 100644
--- a/scripts/multi_qa.py
+++ b/scripts/multi_qa.py
@@ -27,69 +27,71 @@
 import os
 import sys
 
-color_map = ["red", "green", "blue", "orange", "cyan", "yellow", "orchid", 
-             "saddlebrown", "darkcyan", "gray", "darkred", "darkgreen", "darkblue", 
+color_map = ["red", "green", "blue", "orange", "cyan", "yellow", "orchid",
+             "saddlebrown", "darkcyan", "gray", "darkred", "darkgreen", "darkblue",
              "antiquewhite", "bisque", "black", "slategray", "gold", "floralwhite",
              "aliceblue", "plum", "cadetblue", "coral", "olive", "khaki", "lightsalmon"]
 
+
 def create_violin_plot(data, pos, labels, title, fontsize, outfile):
     fig, ax = plt.subplots(figsize=(14, 10))
     fig.subplots_adjust(left=0.075, right=0.95, top=0.9, bottom=0.25)
     ax.violinplot(data, pos, showmeans=True, showextrema=True, showmedians=True)
-    #ax.set_xticklabels(labels, rotation=90, fontsize=6)
-    #ax.set_xlim(0.5, len(labels) + 0.5)
+    # ax.set_xticklabels(labels, rotation=90, fontsize=6)
+    # ax.set_xlim(0.5, len(labels) + 0.5)
     ax.set_axisbelow(True)
     ax.set_title(title)
-    #ax.get_xaxis().set_tick_params(direction='out')
-    #ax.xaxis.set_ticks_position('bottom')
+    # ax.get_xaxis().set_tick_params(direction='out')
+    # ax.xaxis.set_ticks_position('bottom')
     fig.savefig(outfile, format='pdf', dpi=90)
-        
+
+
 def create_pca_plot(data, labels, title, outfile):
     fig, ax = plt.subplots(figsize=(14, 10))
-    class_colours = [color_map[i] for i in range(0,len(data))]
-    ax.scatter(data[:,0], data[:,1], s=20, c=class_colours,
+    class_colours = [color_map[i] for i in range(0, len(data))]
+    ax.scatter(data[:, 0], data[:, 1], s=20, c=class_colours,
                edgecolor="none")
     ax.set_xlabel("PC1")
     ax.set_ylabel("PC2")
     ax.set_title("PCA scatter (sum. gene counts)")
     recs = list()
-    for i in range(0,len(class_colours)):
-        recs.append(mpatches.Rectangle((0,0),1,1,fc=class_colours[i]))
+    for i in range(0, len(class_colours)):
+        recs.append(mpatches.Rectangle((0, 0), 1, 1, fc=class_colours[i]))
     ax.legend(recs, labels, loc=4, prop={'size': 6})
-    fig.savefig(outfile, format='pdf', dpi=90)   
-      
-def main(counts_table_files, outdir, use_log):
+    fig.savefig(outfile, format='pdf', dpi=90)
+
 
+def main(counts_table_files, outdir, use_log):
     if len(counts_table_files) == 0 or \
-    any([not os.path.isfile(f) for f in counts_table_files]):
+            any([not os.path.isfile(f) for f in counts_table_files]):
         sys.stderr.write("Error, input file/s not present or invalid format\n")
         sys.exit(1)
-            
+
     if len(counts_table_files) < 2:
         sys.stderr.write("Error, minimum number of input matrices is 2\n")
         sys.exit(1)
-        
-    if outdir is None or not os.path.isdir(outdir): 
+
+    if outdir is None or not os.path.isdir(outdir):
         outdir = os.getcwd()
     outdir = os.path.abspath(outdir)
 
     print("Output directory {}".format(outdir))
-    print("Input datasets {}".format(" ".join(counts_table_files))) 
-    
+    print("Input datasets {}".format(" ".join(counts_table_files)))
+
     # Parse datasets and sort them by column
-    datasets = [(pd.read_table(x, 
-                               sep="\t", 
-                               header=0, 
-                               index_col=0).sort_index(axis=1), 
-                               os.path.splitext(os.path.basename(x))[0]) for x in counts_table_files]
-    
+    datasets = [(pd.read_table(x,
+                               sep="\t",
+                               header=0,
+                               index_col=0).sort_index(axis=1),
+                 os.path.splitext(os.path.basename(x))[0]) for x in counts_table_files]
+
     # Common genes
     common_genes = set(datasets[0][0].columns)
     all_genes = set(datasets[0][0].columns)
-    for (dataset,_) in datasets[1:]:
+    for (dataset, _) in datasets[1:]:
         common_genes = common_genes.intersection(set(dataset.columns))
         all_genes = all_genes.union(set(dataset.columns))
-        
+
     # Compute violin plots data
     violin_data_reads = list()
     violin_data_genes = list()
@@ -97,59 +99,60 @@ def main(counts_table_files, outdir, use_log):
     violin_data_pos = list()
     genes_counts = pd.DataFrame(index=[x[1] for x in datasets], columns=all_genes)
     genes_counts.fillna(0, inplace=True)
-    for i,(dataset, name) in enumerate(datasets):
+    for i, (dataset, name) in enumerate(datasets):
         violin_data_reads.append(dataset.sum(axis=1).values)
         violin_data_genes.append((dataset > 0).sum(axis=1).values)
         violin_data_names.append(name)
         violin_data_pos.append(i + 1)
-        genes_counts.loc[name,dataset.columns] = dataset.sum(axis=0)
+        genes_counts.loc[name, dataset.columns] = dataset.sum(axis=0)
     genes_counts.fillna(0, inplace=True)
     # Make the violin plots
-    create_violin_plot(violin_data_reads, violin_data_pos, violin_data_names, 
+    create_violin_plot(violin_data_reads, violin_data_pos, violin_data_names,
                        "Total reads", 6, os.path.join(outdir, "violin_plot_reads.pdf"))
-    create_violin_plot(violin_data_genes, violin_data_pos, violin_data_names, 
-                       "Total genes", 6, os.path.join(outdir, "violin_plot_genes.pdf"))   
-    
+    create_violin_plot(violin_data_genes, violin_data_pos, violin_data_names,
+                       "Total genes", 6, os.path.join(outdir, "violin_plot_genes.pdf"))
+
     # Compute and plot PCA (sum gene counts)
     decomp_model = PCA(n_components=2, whiten=True, copy=True)
     reduced_data = decomp_model.fit_transform(np.log1p(genes_counts))
-    create_pca_plot(reduced_data, genes_counts.index, 
+    create_pca_plot(reduced_data, genes_counts.index,
                     "PCA (sum gene counts", os.path.join(outdir, "pca.pdf"))
 
     # Measure percentage of genes and correlations
     genes_similarities = pd.DataFrame(index=counts_table_files, columns=counts_table_files)
     genes_similarities.fillna(0, inplace=True)
-    
+
     genes_correlations = pd.DataFrame(index=counts_table_files, columns=counts_table_files)
     genes_correlations.fillna(0, inplace=True)
 
     n_col = len(counts_table_files)
     n_row = len(counts_table_files)
     plt.rcParams.update({'font.size': 6})
-    fig, ax = plt.subplots(n_col, n_row, sharex='col', sharey='row', figsize=(3*n_col,3*n_row))
+    fig, ax = plt.subplots(n_col, n_row, sharex='col', sharey='row', figsize=(3 * n_col, 3 * n_row))
     fig.subplots_adjust(hspace=0.4, wspace=0.4)
-    for i,(d1,n1) in enumerate(datasets):
+    for i, (d1, n1) in enumerate(datasets):
         genes_1 = set(d1.columns)
         n_genes_1 = float(len(genes_1))
         common_to_all = (n_genes_1 - len(genes_1 - common_genes)) / n_genes_1
         print("{} shares {} genes with all the rest".format(n1, common_to_all))
-        for j,(d2,n2) in enumerate(datasets):
+        for j, (d2, n2) in enumerate(datasets):
             genes_2 = set(d2.columns)
             common_to_d2 = (n_genes_1 - len(genes_1 - genes_2)) / n_genes_1
             common_d1_d2 = genes_1.intersection(genes_2)
-            sum_counts_1 = d1.loc[:,common_d1_d2].sum(axis=0)
+            sum_counts_1 = d1.loc[:, common_d1_d2].sum(axis=0)
             sum_counts_1 = np.log(sum_counts_1) if use_log else sum_counts_1
-            sum_counts_2 = d2.loc[:,common_d1_d2].sum(axis=0)
+            sum_counts_2 = d2.loc[:, common_d1_d2].sum(axis=0)
             sum_counts_2 = np.log(sum_counts_2) if use_log else sum_counts_2
-            genes_similarities.loc[n1,n2] = common_to_d2
-            genes_correlations.loc[n1,n2] = pearsonr(sum_counts_1, sum_counts_2)[0]
-            ax[i,j].scatter(sum_counts_1, sum_counts_2, s=5, c="blue", edgecolor="none")
-            ax[i,j].set_xlabel(n1)
-            ax[i,j].set_ylabel(n2)
-    
-    fig.savefig(os.path.join(outdir,"gene_correlations.png"), format='png', dpi=180)
-    genes_similarities.to_csv(os.path.join(outdir,"gene_similarities.tsv"), sep='\t')
-    genes_correlations.to_csv(os.path.join(outdir,"gene_correlations.tsv"), sep='\t')
+            genes_similarities.loc[n1, n2] = common_to_d2
+            genes_correlations.loc[n1, n2] = pearsonr(sum_counts_1, sum_counts_2)[0]
+            ax[i, j].scatter(sum_counts_1, sum_counts_2, s=5, c="blue", edgecolor="none")
+            ax[i, j].set_xlabel(n1)
+            ax[i, j].set_ylabel(n2)
+
+    fig.savefig(os.path.join(outdir, "gene_correlations.png"), format='png', dpi=180)
+    genes_similarities.to_csv(os.path.join(outdir, "gene_similarities.tsv"), sep='\t')
+    genes_correlations.to_csv(os.path.join(outdir, "gene_correlations.tsv"), sep='\t')
+
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description=__doc__,
@@ -157,7 +160,7 @@ def main(counts_table_files, outdir, use_log):
     parser.add_argument("counts_matrix_files", nargs='+',
                         help="One or more matrices with gene counts (genes as columns) in TSV format")
     parser.add_argument("--outdir", default=None, help="Path to the output directory")
-    parser.add_argument("--use-log-scale", action="store_true", default=False, 
+    parser.add_argument("--use-log-scale", action="store_true", default=False,
                         help="Convert counts to log space for the correlation")
     args = parser.parse_args()
 
diff --git a/scripts/st_pipeline_run.py b/scripts/st_pipeline_run.py
index d083628..d8e2ea8 100755
--- a/scripts/st_pipeline_run.py
+++ b/scripts/st_pipeline_run.py
@@ -21,15 +21,15 @@
 import argparse
 from stpipeline.core.pipeline import Pipeline
 
+
 def main(argv):
-    
     # Create pipeline object
     pipeline = Pipeline()
-    
+
     # Create a parser
     parser = argparse.ArgumentParser(description=__doc__,
                                      formatter_class=argparse.RawDescriptionHelpFormatter)
-        
+
     # Parse parameters, sanity check and run the pipeline                  
     try:
         parser = pipeline.createParameters(parser)
@@ -49,8 +49,7 @@ def main(argv):
         sys.exit(1)
     finally:
         pipeline.clean_filenames()
-        
+
+
 if __name__ == "__main__":
     main(sys.argv[1:])
-    
-
diff --git a/scripts/st_qa.py b/scripts/st_qa.py
index 14c760c..9780fc1 100644
--- a/scripts/st_qa.py
+++ b/scripts/st_qa.py
@@ -10,6 +10,7 @@
 @Author Jose Fernandez Navarro <jc.fernandez.navarro@gmail.com>
 """
 import matplotlib
+
 matplotlib.use('Agg')
 import pandas as pd
 import numpy as np
@@ -18,6 +19,7 @@
 import matplotlib.pyplot as plt
 import seaborn as sns
 
+
 def scatter_plot(x_points, y_points, output, colors,
                  title="Scatter", xlabel="X", ylabel="Y"):
     """ 
@@ -35,12 +37,12 @@ def scatter_plot(x_points, y_points, output, colors,
     """
     # Plot spots with the color class in the tissue image
     fig = plt.figure()
-    plt.scatter(x_points, 
-              y_points,  
-              c=colors, 
-              cmap=plt.get_cmap("YlOrBr"), 
-              edgecolor="none", 
-              s=50)
+    plt.scatter(x_points,
+                y_points,
+                c=colors,
+                cmap=plt.get_cmap("YlOrBr"),
+                edgecolor="none",
+                s=50)
     plt.xlabel(xlabel)
     plt.ylabel(ylabel)
     plt.gca().invert_yaxis()
@@ -49,10 +51,10 @@ def scatter_plot(x_points, y_points, output, colors,
     # Tweak spacing to prevent clipping of ylabel
     plt.subplots_adjust(left=0.15)
     fig.savefig(output, format='pdf', dpi=300)
-    
+
+
 def histogram(x_points, output, title="Histogram", xlabel="X",
               ylabel="Y", nbins=50, color="blue"):
-
     """ This function generates a simple histogram
     with the points given as input.
     :param x_points: a list of x coordinates
@@ -73,6 +75,7 @@ def histogram(x_points, output, title="Histogram", xlabel="X",
     plt.subplots_adjust(left=0.15)
     fig.savefig(output, format='pdf', dpi=300)
 
+
 def main(input_data):
     # Parse the data
     counts_table = pd.read_table(input_data, sep="\t", header=0, index_col=0)
@@ -102,90 +105,91 @@ def main(input_data):
     # Generate heatmap plots
     histogram(aggregated_spot_counts, nbins=20, xlabel="#Reads", ylabel="#Spots",
               output=input_name + "_hist_reads_spot.pdf", title="Reads per spot")
-    histogram(aggregated_gene_counts, nbins=20, xlabel="#Genes", ylabel="#Spots", 
+    histogram(aggregated_gene_counts, nbins=20, xlabel="#Genes", ylabel="#Spots",
               output=input_name + "_hist_genes_spot.pdf", title="Genes per spot (>0)")
-    histogram(aggregated_gene_counts_1, nbins=20, xlabel="#Genes", ylabel="#Spots", 
+    histogram(aggregated_gene_counts_1, nbins=20, xlabel="#Genes", ylabel="#Spots",
               output=input_name + "_hist_genes_spots_1.pdf", title="Genes per spot (>1)")
-    histogram(aggregated_gene_counts_2, nbins=20, xlabel="#Genes", ylabel="#Spots", 
+    histogram(aggregated_gene_counts_2, nbins=20, xlabel="#Genes", ylabel="#Spots",
               output=input_name + "_hist_genes_spots_2.pdf", title="Genes per spot (>2)")
-    histogram(aggregated_gene_gene_counts, nbins=20, xlabel="#Spots", ylabel="#Genes", 
+    histogram(aggregated_gene_gene_counts, nbins=20, xlabel="#Spots", ylabel="#Genes",
               output=input_name + "_hist_spots_gene.pdf", title="Spots per gene (>0)")
-    histogram(aggregated_gene_gene_counts_1, nbins=20, xlabel="#Spots", ylabel="#Genes", 
+    histogram(aggregated_gene_gene_counts_1, nbins=20, xlabel="#Spots", ylabel="#Genes",
               output=input_name + "_hist_spots_gene_1.pdf", title="Spots per gene (>1)")
-    histogram(aggregated_gene_gene_counts_2, nbins=20, xlabel="#Spots", ylabel="#Genes", 
+    histogram(aggregated_gene_gene_counts_2, nbins=20, xlabel="#Spots", ylabel="#Genes",
               output=input_name + "_hist_spots_gene_2.pdf", title="Spots per gene (>2)")
-    plt.clf() 
-        
+    plt.clf()
+
     # Generate density plots
     sns.distplot(aggregated_gene_counts, hist=False, label="Counts > 0")
     sns.distplot(aggregated_gene_counts_1, hist=False, label="Counts > 1")
-    sns_plot = sns.distplot(aggregated_gene_counts_2, 
+    sns_plot = sns.distplot(aggregated_gene_counts_2,
                             axlabel="#Genes", hist=False, label="Counts > 2")
     fig = sns_plot.get_figure()
     fig.savefig(input_name + "_density_genes_by_spot.pdf")
     plt.clf()
-    
+
     sns.distplot(aggregated_gene_gene_counts, hist=False, label="Counts > 0")
     sns.distplot(aggregated_gene_gene_counts_1, hist=False, label="Counts > 1")
-    sns_plot = sns.distplot(aggregated_gene_gene_counts_2, 
+    sns_plot = sns.distplot(aggregated_gene_gene_counts_2,
                             axlabel="#Spots", hist=False, label="Counts > 2")
     fig = sns_plot.get_figure()
     fig.savefig(input_name + "_density_spots_by_gene.pdf")
-    plt.clf() 
-    
+    plt.clf()
+
     sns.scatterplot(x=aggregated_spot_counts, y=aggregated_gene_counts, label="Gene counts >0")
     sns.scatterplot(x=aggregated_spot_counts, y=aggregated_gene_counts_1, label="Gene counts >1")
     sns_plot = sns.scatterplot(x=aggregated_spot_counts, y=aggregated_gene_counts_2, label="Gene counts >2")
     fig = sns_plot.get_figure()
     fig.savefig(input_name + "_scatter_reads_vs_genes.pdf")
-    plt.clf() 
-    
-    #sns_plot = sns.jointplot(x=aggregated_spot_counts, 
+    plt.clf()
+
+    # sns_plot = sns.jointplot(x=aggregated_spot_counts,
     #                         y=aggregated_gene_counts, kind='kde', color="skyblue")
-    #fig = sns_plot.get_figure()
-    #fig.savefig(input_name + "_join_density_reads_vs_genes.pdf")
-    #plt.clf() 
-    
+    # fig = sns_plot.get_figure()
+    # fig.savefig(input_name + "_join_density_reads_vs_genes.pdf")
+    # plt.clf()
+
     qa_stats = [
-    ("Number of spots: {}".format(total_barcodes)+"\n"),
-    ("Number of reads present: {}".format(total_transcripts)+"\n"),
-    ("Number of unique genes present: {}".format(number_genes)+"\n"),
-    ("Max number of genes over all spots: {}".format(max_genes_feature)+"\n"),
-    ("Min number of genes over all spots: {}".format(min_genes_feature)+"\n"),
-    ("Max number of reads over all spots: {}".format(max_reads_feature)+"\n"),
-    ("Min number of reads over all spots: {}".format(min_reads_feature)+"\n"),
-    ("Average number genes per spots: {}".format(average_genes_feature)+"\n"),
-    ("Average number reads per spot: {}".format(average_reads_feature)+"\n"),
-    ("Std number genes per spot: {}".format(std_genes_feature)+"\n"),
-    ("Std number reads per spot: {}".format(std_reads_feature)+"\n"),
-    ("Max number of reads over all spots/genes: {}".format(max_count)+"\n"),
-    ("Min number of reads over all spots/genes: {}".format(min_count)+"\n")
+        ("Number of spots: {}".format(total_barcodes) + "\n"),
+        ("Number of reads present: {}".format(total_transcripts) + "\n"),
+        ("Number of unique genes present: {}".format(number_genes) + "\n"),
+        ("Max number of genes over all spots: {}".format(max_genes_feature) + "\n"),
+        ("Min number of genes over all spots: {}".format(min_genes_feature) + "\n"),
+        ("Max number of reads over all spots: {}".format(max_reads_feature) + "\n"),
+        ("Min number of reads over all spots: {}".format(min_reads_feature) + "\n"),
+        ("Average number genes per spots: {}".format(average_genes_feature) + "\n"),
+        ("Average number reads per spot: {}".format(average_reads_feature) + "\n"),
+        ("Std number genes per spot: {}".format(std_genes_feature) + "\n"),
+        ("Std number reads per spot: {}".format(std_reads_feature) + "\n"),
+        ("Max number of reads over all spots/genes: {}".format(max_count) + "\n"),
+        ("Min number of reads over all spots/genes: {}".format(min_count) + "\n")
     ]
     # Print stats to stdout and a file
     print("".join(qa_stats))
     with open("{}_qa_stats.txt".format(input_name), "a") as outfile:
         outfile.write("".join(qa_stats))
-        
+
     # Generate scatter plots
     # Get the spot coordinates
     x_points = list()
     y_points = list()
     for spot in counts_table.index:
         tokens = spot.split("x")
-        assert(len(tokens) == 2)
+        assert (len(tokens) == 2)
         y_points.append(float(tokens[1]))
         x_points.append(float(tokens[0]))
-    scatter_plot(x_points, y_points, colors=aggregated_spot_counts, 
-                 xlabel="X", ylabel="Y", output=input_name + "_heatmap_counts.pdf", 
+    scatter_plot(x_points, y_points, colors=aggregated_spot_counts,
+                 xlabel="X", ylabel="Y", output=input_name + "_heatmap_counts.pdf",
                  title="Heatmap expression")
-    scatter_plot(x_points, y_points, colors=aggregated_gene_counts, 
-                 xlabel="X", ylabel="Y", output=input_name + "_heatmap_genes.pdf", 
+    scatter_plot(x_points, y_points, colors=aggregated_gene_counts,
+                 xlabel="X", ylabel="Y", output=input_name + "_heatmap_genes.pdf",
                  title="Heatmap genes")
-        
+
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description=__doc__,
                                      formatter_class=argparse.RawDescriptionHelpFormatter)
-    parser.add_argument("counts_matrix", 
+    parser.add_argument("counts_matrix",
                         help="Matrix with gene counts (genes as columns) in TSV format")
     args = parser.parse_args()
     main(args.counts_matrix)
diff --git a/setup.py b/setup.py
index fe27049..4864479 100755
--- a/setup.py
+++ b/setup.py
@@ -20,60 +20,60 @@
 here = os.path.abspath(os.path.dirname(__file__))
 
 # Get the long description from the relevant file
-try:    
+try:
     with io.open(os.path.join(here, 'README_SHORT'), encoding='utf-8') as f:
         long_description = f.read()
 except IOError:
     long_description = ""
-    
+
 try:
-    with open(os.path.join(here,"requirements.txt"), "r") as f:
+    with open(os.path.join(here, "requirements.txt"), "r") as f:
         install_requires = [x.strip() for x in f.readlines()]
 except IOError:
     raise SystemExit("Could not find requirements.txt file")
-   
+
 major, minor1, minor2, s, tmp = sys.version_info
 if major != 3 or minor1 < 6:
     raise SystemExit("ST Pipeline requires Python 3.6 or bigger")
 
 # setuptools DWIM monkey-patch madness
 # http://mail.python.org/pipermail/distutils-sig/2007-September/thread.html#8204
-#if 'setuptools.extension' in sys.modules:
+# if 'setuptools.extension' in sys.modules:
 #    m = sys.modules['setuptools.extension']
 #    m.Extension.__dict__ = m._Extension.__dict__
-    
+
 setup(
-  name = 'stpipeline',
-  version = version_number,
-  description = "ST Pipeline: An automated pipeline for spatial mapping of unique transcripts",
-  long_description = long_description,
-  keywords = 'rna-seq analysis spatial transcriptomics toolkit',
-  author = 'Jose Fernandez Navarro',
-  author_email = 'jc.fernandez.navarro@gmail.com',
-  license = 'MIT',
-  url = 'https://github.com/SpatialTranscriptomicsResearch/st_pipeline',
-  packages = find_packages(exclude=('tests*', 'utils', '*.pyx')),
-  ext_modules=[
+    name='stpipeline',
+    version=version_number,
+    description="ST Pipeline: An automated pipeline for spatial mapping of unique transcripts",
+    long_description=long_description,
+    keywords='rna-seq analysis spatial transcriptomics toolkit',
+    author='Jose Fernandez Navarro',
+    author_email='jc.fernandez.navarro@gmail.com',
+    license='MIT',
+    url='https://github.com/SpatialTranscriptomicsResearch/st_pipeline',
+    packages=find_packages(exclude=('tests*', 'utils', '*.pyx')),
+    ext_modules=[
         Extension('stpipeline.common.cdistance', ['stpipeline/common/cdistance.pyx']),
         Extension('stpipeline.common.unique_events_parser', ['stpipeline/common/unique_events_parser.pyx']),
         Extension('stpipeline.common.filterInputReads', ['stpipeline/common/filterInputReads.pyx'])
     ],
-  include_package_data = True,
-  zip_safe = False,
-  setup_requires=['setuptools_cython'],
-  install_requires = install_requires,
-  test_suite = 'tests',
-  scripts = glob.glob('scripts/*.py'),
-  classifiers = [
-    'Development Status :: 5 - Production/Stable',
-    'Intended Audience :: Science/Research',
-    'Topic :: Software Development',
-    'Topic :: Scientific/Engineering :: Bio-Informatics',
-    'License :: OSI Approved :: MIT License',
-    'Programming Language :: Python :: 3.6',
-    'Programming Language :: Python :: 3.7',
-    'Operating System :: Unix',
-    'Operating System :: MacOS',
-    'Environment :: Console',
-  ],
+    include_package_data=True,
+    zip_safe=False,
+    setup_requires=['setuptools_cython'],
+    install_requires=install_requires,
+    test_suite='tests',
+    scripts=glob.glob('scripts/*.py'),
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Intended Audience :: Science/Research',
+        'Topic :: Software Development',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python :: 3.6',
+        'Programming Language :: Python :: 3.7',
+        'Operating System :: Unix',
+        'Operating System :: MacOS',
+        'Environment :: Console',
+    ],
 )
diff --git a/stpipeline/common/adaptors.py b/stpipeline/common/adaptors.py
index 9ce3a91..bc5b31c 100755
--- a/stpipeline/common/adaptors.py
+++ b/stpipeline/common/adaptors.py
@@ -3,6 +3,7 @@
 """
 import regex
 
+
 def removeAdaptor(sequence, quality, adaptor, missmatches=2):
     """
     Tries to find the given adaptor sequence in the given fastq read (sequence, quality)
@@ -27,7 +28,7 @@ def removeAdaptor(sequence, quality, adaptor, missmatches=2):
     if missmatches == 0:
         pos = sequence.find(adaptor)
     else:
-        candidates = regex.findall(r'(?:%s){s<=%s}' % (adaptor, missmatches), 
+        candidates = regex.findall(r'(?:%s){s<=%s}' % (adaptor, missmatches),
                                    sequence, overlapped=False)
         if len(candidates) > 0:
             local_seq = candidates[0]
@@ -44,9 +45,4 @@ def removeAdaptor(sequence, quality, adaptor, missmatches=2):
     if pos != -1:
         return sequence[:pos], quality[:pos]
     else:
-        return sequence, quality    
-
-            
-    
-    
-    
+        return sequence, quality
diff --git a/stpipeline/common/clustering.py b/stpipeline/common/clustering.py
index 9e7208e..f9e6ea8 100755
--- a/stpipeline/common/clustering.py
+++ b/stpipeline/common/clustering.py
@@ -4,16 +4,17 @@
 """
 
 import numpy as np
-from scipy.cluster.hierarchy import linkage,fcluster
+from scipy.cluster.hierarchy import linkage, fcluster
 from sklearn.cluster import AffinityPropagation
 from collections import defaultdict
 from stpipeline.common.cdistance import hamming_distance
 import random
 from collections import Counter
 
-def countUMIHierarchical(molecular_barcodes, 
-                         allowed_mismatches, 
-                         method = "single"):
+
+def countUMIHierarchical(molecular_barcodes,
+                         allowed_mismatches,
+                         method="single"):
     """
     Tries to finds clusters of similar UMIs using a hierarchical clustering
     with a minimum distance (allowed_mismatches). 
@@ -32,11 +33,13 @@ def countUMIHierarchical(molecular_barcodes,
     # we use the naive clustering
     if len(molecular_barcodes) <= 2:
         return countUMINaive(molecular_barcodes, allowed_mismatches)
+
     # Distance computation function
     def d(coord):
-        i,j = coord
-        return hamming_distance(molecular_barcodes[i].encode("UTF-8"), 
+        i, j = coord
+        return hamming_distance(molecular_barcodes[i].encode("UTF-8"),
                                 molecular_barcodes[j].encode("UTF-8"))
+
     # Create hierarchical clustering and obtain flat clusters at the distance given
     indices = np.triu_indices(len(molecular_barcodes), 1)
     distance_matrix = np.apply_along_axis(d, 0, indices)
@@ -47,7 +50,8 @@ def d(coord):
     for i, item in enumerate(flat_clusters):
         items[item].append(i)
     return [molecular_barcodes[random.choice(members)] for members in list(items.values())]
-  
+
+
 def countUMINaive(molecular_barcodes, allowed_mismatches):
     """
     Tries to finds clusters of similar UMIs using a naive proximity
@@ -74,7 +78,7 @@ def countUMINaive(molecular_barcodes, allowed_mismatches):
             # compare distant of previous molecular barcodes and new one
             # if distance is between threshold we add it to the cluster 
             # otherwise we create a new cluster
-            if hamming_distance(clusters_dict[nclusters][-1].encode("UTF-8"), 
+            if hamming_distance(clusters_dict[nclusters][-1].encode("UTF-8"),
                                 molecular_barcode.encode("UTF-8")) <= allowed_mismatches:
                 clusters_dict[nclusters].append(molecular_barcode)
             else:
@@ -83,8 +87,10 @@ def countUMINaive(molecular_barcodes, allowed_mismatches):
     # Return the non clustered UMIs
     return [random.choice(members) for members in list(clusters_dict.values())]
 
+
 def breadth_first_search(node, adj_list):
-    """ This function has been obtained from 
+    """
+    This function has been obtained from
     https://github.com/CGATOxford/UMI-tools
     The logic behind the algorithm to cluster UMIs using
     an adjacent distance matrix is described in 
@@ -103,24 +109,29 @@ def breadth_first_search(node, adj_list):
         queue.difference_update(searched)
     return found
 
+
 def remove_umis(adj_list, cluster, nodes):
-    """Removes the specified nodes from the cluster and returns
-    the remaining nodes"""
+    """
+    Removes the specified nodes from the cluster and returns
+    the remaining nodes
+    """
     # list incomprehension: for x in nodes: for node in adj_list[x]: yield node
     nodes_to_remove = set([node for x in nodes for node in adj_list[x]] + nodes)
     return cluster - nodes_to_remove
-    
+
+
 def dedup_adj(molecular_barcodes, allowed_mismatches):
-    """ This function has been obtained from 
+    """
+    This function has been obtained from
     https://github.com/CGATOxford/UMI-tools
     The logic behind the algorithm to cluster UMIs using
     an adjacent distance matrix is described in 
     http://genome.cshlp.org/content/early/2017/01/18/gr.209601.116.abstract
     """
     c = Counter(molecular_barcodes)
-        
+
     def get_adj_list_adjacency(umis):
-        return {umi: [umi2 for umi2 in umis if hamming_distance(umi.encode("UTF-8"), 
+        return {umi: [umi2 for umi2 in umis if hamming_distance(umi.encode("UTF-8"),
                                                                 umi2.encode("UTF-8")) \
                       <= allowed_mismatches] for umi in umis}
 
@@ -138,8 +149,8 @@ def get_best_adjacency(cluster, adj_list, counts):
         if len(cluster) == 1: return list(cluster)
         sorted_nodes = sorted(cluster, key=lambda x: counts[x], reverse=True)
         for i in range(len(sorted_nodes) - 1):
-            if len(remove_umis(adj_list, cluster, sorted_nodes[:i+1])) == 0:
-                return sorted_nodes[:i+1]
+            if len(remove_umis(adj_list, cluster, sorted_nodes[:i + 1])) == 0:
+                return sorted_nodes[:i + 1]
 
     def reduce_clusters_adjacency(adj_list, clusters, counts):
         # TS - the "adjacency" variant of this function requires an adjacency
@@ -149,27 +160,29 @@ def reduce_clusters_adjacency(adj_list, clusters, counts):
         for cluster in clusters:
             parent_umis = get_best_adjacency(cluster, adj_list, counts)
             unique_umis += parent_umis
-        return unique_umis 
+        return unique_umis
 
     adj_list = get_adj_list_adjacency(c.keys())
     clusters = get_connected_components_adjacency(adj_list, c)
     unique_umis = reduce_clusters_adjacency(adj_list, clusters, c)
     return unique_umis
 
+
 def dedup_dir_adj(molecular_barcodes, allowed_mismatches):
-    """ This function has been obtained from
+    """
+    This function has been obtained from
     https://github.com/CGATOxford/UMI-tools
     The logic behind the algorithm to cluster UMIs using
     an adjacent distance matrix is described in
     http://genome.cshlp.org/content/early/2017/01/18/gr.209601.116.abstract
     """
     c = Counter(molecular_barcodes)
-    
+
     def get_adj_list_directional_adjacency(umis, counts):
-        return {umi: [umi2 for umi2 in umis if hamming_distance(umi.encode("UTF-8"), 
+        return {umi: [umi2 for umi2 in umis if hamming_distance(umi.encode("UTF-8"),
                                                                 umi2.encode("UTF-8")) <= allowed_mismatches and
-                      counts[umi] >= (counts[umi2]*2)-1] for umi in umis}  
-    
+                      counts[umi] >= (counts[umi2] * 2) - 1] for umi in umis}
+
     def get_connected_components_adjacency(graph, Counter):
         found = list()
         components = list()
@@ -179,15 +192,16 @@ def get_connected_components_adjacency(graph, Counter):
                 found.extend(component)
                 components.append(component)
         return components
-       
-    def reduce_clusters_directional_adjacency(adj_list, clusters, counts):
+
+    def reduce_clusters_directional_adjacency(clusters):
         return [cluster.pop() for cluster in clusters]
-    
+
     adj_list = get_adj_list_directional_adjacency(c.keys(), c)
     clusters = get_connected_components_adjacency(adj_list, c)
-    unique_umis = reduce_clusters_directional_adjacency(adj_list, clusters, c)
+    unique_umis = reduce_clusters_directional_adjacency(clusters)
     return unique_umis
 
+
 def affinity_umi_removal(molecular_barcodes, _):
     """
     Tries to finds clusters of similar UMIs using an affinity based approach. 
@@ -198,7 +212,7 @@ def affinity_umi_removal(molecular_barcodes, _):
     :rtype: list
     """
     if len(molecular_barcodes) <= 2:
-        return countUMINaive(molecular_barcodes, allowed_mismatches)
+        return countUMINaive(molecular_barcodes, 0)
     words = np.asarray(molecular_barcodes)
     lev_similarity = -1 * np.array([[hamming_distance(w1.encode("UTF-8"),
                                                       w2.encode("UTF-8")) for w1 in words] for w2 in words])
@@ -207,6 +221,6 @@ def affinity_umi_removal(molecular_barcodes, _):
     unique_clusters = list()
     for cluster_id in np.unique(affprop.labels_):
         exemplar = words[affprop.cluster_centers_indices_[cluster_id]]
-        cluster = np.unique(words[np.nonzero(affprop.labels_==cluster_id)])
+        cluster = np.unique(words[np.nonzero(affprop.labels_ == cluster_id)])
         unique_clusters.append(random.choice(cluster))
-    return unique_clusters
\ No newline at end of file
+    return unique_clusters
diff --git a/stpipeline/common/dataset.py b/stpipeline/common/dataset.py
index 8996a2a..5bda37c 100644
--- a/stpipeline/common/dataset.py
+++ b/stpipeline/common/dataset.py
@@ -14,6 +14,7 @@
 import logging
 import sys
 
+
 def computeUniqueUMIs(transcripts, umi_counting_offset, umi_allowed_mismatches, group_umi_func):
     """ 
     Helper function to compute unique transcripts UMIs from
@@ -22,7 +23,7 @@ def computeUniqueUMIs(transcripts, umi_counting_offset, umi_allowed_mismatches,
     number of mismatches allowed (hamming distance)
     """
     # Sort transcripts by strand and start position
-    sorted_transcripts = sorted(transcripts, key = lambda x: (x[5], x[1]))
+    sorted_transcripts = sorted(transcripts, key=lambda x: (x[5], x[1]))
     # Group transcripts by strand and start-position allowing an offset
     # And then performs the UMI clustering in each group to finally
     # compute the gene count as the sum of the unique UMIs for each group (strand,start,offset)
@@ -51,6 +52,7 @@ def computeUniqueUMIs(transcripts, umi_counting_offset, umi_allowed_mismatches,
     unique_transcripts += [random.choice(grouped_transcripts[u_umi]) for u_umi in unique_umis]
     return unique_transcripts
 
+
 def createDataset(input_file,
                   qa_stats,
                   gff_filename=None,
@@ -70,6 +72,7 @@ def createDataset(input_file,
     writes out some statistics.
     :param input_file: the file with the annotated-demultiplexed records in BAM format
     :param qa_stats: the Stats object to add some stats (THIS IS PASSED BY REFERENCE)
+    :param gff_filename: the annotation reference file
     :param umi_cluster_algorithm: the clustering algorithm to cluster UMIs
     :param umi_allowed_mismatches: the number of miss matches allowed to remove
                                   duplicates by UMIs
@@ -79,6 +82,7 @@ def createDataset(input_file,
     :param output_template: the name of the dataset
     :param verbose: True if we can to collect the stats in the logger
     :type input_file: str
+    :type gff_filename: str
     :type umi_cluster_algorithm: str
     :type umi_allowed_mismatches: boolean
     :type umi_counting_offset: integer
@@ -118,8 +122,8 @@ def createDataset(input_file,
     elif umi_cluster_algorithm == "Affinity":
         group_umi_func = affinity_umi_removal
     else:
-        error = "Error creating dataset.\n" \
-        "Incorrect clustering algorithm {}".format(umi_cluster_algorithm)
+        error = "Error creating dataset.\n " \
+                "Incorrect clustering algorithm {}".format(umi_cluster_algorithm)
         logger.error(error)
         raise RuntimeError(error)
  
@@ -134,7 +138,7 @@ def createDataset(input_file,
         for gene, spots in unique_events:
             transcript_counts_by_spot = {}
             for spot_coordinates, reads in list(spots.items()):
-                (x,y) = spot_coordinates
+                x,y = spot_coordinates
                 # Re-compute the read count accounting for duplicates using the UMIs
                 # Transcripts is the list of transcripts (chrom, start, end, clear_name, mapping_quality, strand, UMI)
                 # First:
@@ -180,7 +184,8 @@ def createDataset(input_file,
     # Create the data frame
     counts_table = pd.DataFrame(list_row_values, index=list_indexes)
     counts_table.fillna(0, inplace=True)
-    counts_table=counts_table.T # Transpose the dictionary to still get the spots as rows and genes as columns in the final tsv
+    # Transpose the dictionary to still get the spots as rows and genes as columns in the final tsv
+    counts_table = counts_table.T
     
     # Compute some statistics
     total_barcodes = len(counts_table.index)
diff --git a/stpipeline/common/fastq_utils.py b/stpipeline/common/fastq_utils.py
index f126ebb..f7c4c17 100755
--- a/stpipeline/common/fastq_utils.py
+++ b/stpipeline/common/fastq_utils.py
@@ -1,29 +1,24 @@
 """ 
-This module contains some specific functionalities for
-ST fastq files, mainly quality filtering functions.
+This module contains some specific functions for
+to parse and trime FASTQ files
 """
-
-from stpipeline.common.utils import safeOpenFile, fileOk, is_fifo
-from stpipeline.common.adaptors import removeAdaptor
-from stpipeline.common.sam_utils import convert_to_AlignedSegment
-from stpipeline.common.stats import qa_stats
-import logging 
-from sqlitedict import SqliteDict
-import os
 import re
-import pysam
+
 
 def coroutine(func):
     """ 
     Coroutine decorator, starts coroutines upon initialization.
     """
+
     def start(*args, **kwargs):
         cr = func(*args, **kwargs)
         cr.__next__()
         return cr
+
     return start
 
-def readfq(fp): # this is a generator function
+
+def readfq(fp):
     """ 
     Heng Li's fasta/fastq reader function.
     # https://github.com/lh3/readfq/blob/master/readfq.py
@@ -32,27 +27,27 @@ def readfq(fp): # this is a generator function
     :param fp: opened file descriptor
     :returns an iterator over tuples (name,sequence,quality)
     """
-    last = None # this is a buffer keeping the last unprocessed line
-    while True: # mimic closure; is it a bad idea?
-        if not last: # the first record or a record following a fastq
-            for l in fp: # search for the start of the next record
-                if l[0] in '>@': # fasta/q header line
-                    last = l[:-1] # save this line
+    last = None  # this is a buffer keeping the last unprocessed line
+    while True:  # mimic closure; is it a bad idea?
+        if not last:  # the first record or a record following a fastq
+            for l in fp:  # search for the start of the next record
+                if l[0] in '>@':  # fasta/q header line
+                    last = l[:-1]  # save this line
                     break
         if not last: break
-        #name, seqs, last = last[1:].partition(" ")[0], [], None
+        # name, seqs, last = last[1:].partition(" ")[0], [], None
         name, seqs, last = last[1:], [], None
-        for l in fp: # read the sequence
+        for l in fp:  # read the sequence
             if l[0] in '@+>':
                 last = l[:-1]
                 break
             seqs.append(l[:-1])
-        if not last or last[0] != '+': # this is a fasta record
-            yield name, ''.join(seqs), None # yield a fasta record
+        if not last or last[0] != '+':  # this is a fasta record
+            yield name, ''.join(seqs), None  # yield a fasta record
             if not last: break
-        else: # this is a fastq record
+        else:  # this is a fastq record
             seq, leng, seqs = ''.join(seqs), 0, []
-            for l in fp: # read the quality
+            for l in fp:  # read the quality
                 seqs.append(l[:-1])
                 leng += len(l) - 1
                 if leng >= len(seq):  # have read enough quality
@@ -63,6 +58,7 @@ def readfq(fp): # this is a generator function
                 yield name, seq, None  # yield a fasta record instead
                 break
 
+
 @coroutine
 def writefq(fp):  # This is a coroutine
     """ 
@@ -78,7 +74,8 @@ def writefq(fp):  # This is a coroutine
             fp.write(read)
     except GeneratorExit:
         return
-    
+
+
 def quality_trim_index(bases, qualities, cutoff, base=33):
     """
     Function snippet and modified from CutAdapt 
@@ -136,11 +133,12 @@ def quality_trim_index(bases, qualities, cutoff, base=33):
             max_i = i
     return max_i
 
+
 def trim_quality(sequence,
                  quality,
-                 min_qual=20, 
-                 min_length=30, 
-                 phred=33):    
+                 min_qual=20,
+                 min_length=30,
+                 phred=33):
     """
     Quality trims a fastq read using a BWA approach.
     It returns the trimmed record or None if the number of bases
@@ -169,7 +167,8 @@ def trim_quality(sequence,
         return new_seq, new_qual
     else:
         return None, None
-  
+
+
 def check_umi_template(umi, template):
     """
     Checks that the UMI (molecular barcode) given as input complies
@@ -183,4 +182,4 @@ def check_umi_template(umi, template):
     :return: True if the given molecular barcode fits the pattern given
     """
     p = re.compile(template)
-    return p.match(umi) is not None
\ No newline at end of file
+    return p.match(umi) is not None
diff --git a/stpipeline/common/gff_reader.py b/stpipeline/common/gff_reader.py
index 674e3d2..411d171 100644
--- a/stpipeline/common/gff_reader.py
+++ b/stpipeline/common/gff_reader.py
@@ -1,17 +1,21 @@
-from collections import defaultdict
+"""
+A simple module to parse a GFF/GTF file and query it
+"""
 import gzip
 import re
 
 # Code snipped from:
 # https://gist.github.com/slowkow/8101481
 
-GTF_HEADER  = ['seqname', 'source', 'feature', 'start', 'end', 'score', 'strand', 'frame']
+GTF_HEADER = ['seqname', 'source', 'feature', 'start', 'end', 'score', 'strand', 'frame']
 R_SEMICOLON = re.compile(r'\s*;\s*')
-R_COMMA     = re.compile(r'\s*,\s*')
-R_KEYVALUE  = re.compile(r'(\s+|\s*=\s*)')
+R_COMMA = re.compile(r'\s*,\s*')
+R_KEYVALUE = re.compile(r'(\s+|\s*=\s*)')
+
 
 def gff_lines(filename):
-    """Open an optionally gzipped GTF file and generate a dict for each line.
+    """
+    Opens an optionally gzipped GTF/GFF file and generate a dict for each line.
     """
     fn_open = gzip.open if filename.endswith('.gz') else open
     with fn_open(filename) as fh:
@@ -21,8 +25,10 @@ def gff_lines(filename):
             else:
                 yield gff_parse(line)
 
+
 def gff_parse(line):
-    """Parse a single GTF line and return a dict.
+    """
+    Parses a single GTF/GFF line and returns a dict.
     """
     result = {}
     fields = line.rstrip().split('\t')
@@ -43,6 +49,7 @@ def gff_parse(line):
             result[key] = _get_value(value)
     return result
 
+
 def _get_value(value):
     if not value:
         return None
@@ -54,4 +61,4 @@ def _get_value(value):
     # These values are equivalent to None.
     elif value in ['', '.', 'NA']:
         return None
-    return value
\ No newline at end of file
+    return value
diff --git a/stpipeline/common/sam_utils.py b/stpipeline/common/sam_utils.py
index 278424d..965c469 100755
--- a/stpipeline/common/sam_utils.py
+++ b/stpipeline/common/sam_utils.py
@@ -1,13 +1,12 @@
 """ 
-This module contains some functions and utilities for ST SAM/BAM files
+This module contains some functions and utilities for SAM/BAM files
 """
 
 import pysam
 import os
-import logging
-from collections import defaultdict
 import math
 
+
 def split_bam(input_bamfile_name, temp_dir, threads):
     """
     Splits a BAM file in to parts with equal read counts.
@@ -19,17 +18,17 @@ def split_bam(input_bamfile_name, temp_dir, threads):
     :retuns: the list of splitted BAM files
     """
     # Index and open the input BAM
-    pysam.index(input_bamfile_name, 
-                os.path.join(temp_dir,'{0}.bai'.format(input_bamfile_name)))
+    pysam.index(input_bamfile_name,
+                os.path.join(temp_dir, '{0}.bai'.format(input_bamfile_name)))
     input_bamfile = pysam.AlignmentFile(input_bamfile_name, mode='rb')
     assert input_bamfile.check_index()
 
-    output_file_names = {part:os.path.join(temp_dir,
-                                           "{0}.part_{1}.bam".format(input_bamfile_name,part)) 
+    output_file_names = {part: os.path.join(temp_dir,
+                                            "{0}.part_{1}.bam".format(input_bamfile_name, part))
                          for part in range(threads)}
-   # Open the output bam files
+    # Open the output bam files
     output_bamfiles = {
-        part:pysam.AlignmentFile(file_name, mode="wbu", template=input_bamfile) \
+        part: pysam.AlignmentFile(file_name, mode="wbu", template=input_bamfile) \
         for part, file_name in output_file_names.iteritems()
     }
 
@@ -47,7 +46,8 @@ def split_bam(input_bamfile_name, temp_dir, threads):
     input_bamfile.close()
     return output_file_names.values()
 
-def convert_to_AlignedSegment(header, sequence, quality, 
+
+def convert_to_AlignedSegment(header, sequence, quality,
                               barcode_sequence, umi_sequence):
     """
     This function converts the input variables 
@@ -83,6 +83,7 @@ def convert_to_AlignedSegment(header, sequence, quality,
 
     return aligned_segment
 
+
 def merge_bam(merged_file_name, files_to_merge, ubam=False):
     """
     Function for merging partial BAM files into one.
@@ -93,7 +94,7 @@ def merge_bam(merged_file_name, files_to_merge, ubam=False):
     """
     assert files_to_merge is not None and len(files_to_merge) > 0
     num_ele = 0
-    with pysam.AlignmentFile(files_to_merge[0], mode='rb', 
+    with pysam.AlignmentFile(files_to_merge[0], mode='rb',
                              check_sq=(not ubam)) as input_bamfile:
         merged_file = pysam.AlignmentFile(merged_file_name,
                                           mode="wb", template=input_bamfile)
@@ -105,4 +106,4 @@ def merge_bam(merged_file_name, files_to_merge, ubam=False):
                 num_ele += 1
             input_bamfile.close()
         merged_file.close()
-    return num_ele
\ No newline at end of file
+    return num_ele
diff --git a/stpipeline/common/saturation.py b/stpipeline/common/saturation.py
index 4385818..6e8f335 100644
--- a/stpipeline/common/saturation.py
+++ b/stpipeline/common/saturation.py
@@ -13,6 +13,7 @@
 from stpipeline.common.stats import Stats
 from stpipeline.common.utils import safeRemove
 
+
 def computeSaturation(nreads, 
                       annotated_reads,
                       gff_filename,
@@ -61,14 +62,14 @@ def computeSaturation(nreads,
         saturation_points = [p for p in sorted(saturation_points) if p < int(nreads)]
 
         if len(saturation_points) == 0:
-            error = "Error, all saturation points provided are bigger than the number" \
-            " of annotated reads {}\n".format(nreads)
+            error = "Error, all saturation points provided are bigger than the number " \
+                    "of annotated reads {}\n".format(nreads)
             logger.error(error)
             raise RuntimeError(error)     
     else:
-         # Create a list of 15 saturation points (different number of reads)
+        # Create a list of 15 saturation points (different number of reads)
         saturation_points = list()
-        for x in range(0,15):
+        for x in range(0, 15):
             spoint = int(math.floor(1e3 + (math.exp(x) * 1e3)))
             if spoint >= int(nreads):
                 break
@@ -163,5 +164,4 @@ def computeSaturation(nreads,
     logger.info("Average genes/spot per saturation point")
     logger.info(', '.join(str(a) for a in saturation_points_average_genes))
     logger.info("Average reads/spot per saturation point")
-    logger.info(', '.join(str(a) for a in saturation_points_average_reads))
-        
\ No newline at end of file
+    logger.info(', '.join(str(a) for a in saturation_points_average_reads))
\ No newline at end of file
diff --git a/stpipeline/common/stats.py b/stpipeline/common/stats.py
index 8f5c510..4a91e2f 100644
--- a/stpipeline/common/stats.py
+++ b/stpipeline/common/stats.py
@@ -5,12 +5,14 @@
 """
 import json
 
+
 class Stats():
     """
     Stats is meant to be used
     in different part of the ST pipeline
     to collect information and statistics
     """
+
     def __init__(self):
         self.input_reads_forward = 0
         self.input_reads_reverse = 0
@@ -34,57 +36,57 @@ def __init__(self):
         self.min_reads_feature = 0
         self.average_gene_feature = 0
         self.average_reads_feature = 0
-    
+
     def __str__(self):
-        return "input_reads_forward: " +  str(self.input_reads_forward) + \
-        "\ninput_reads_reverse: " + str(self.input_reads_reverse) + \
-        "\nreads_after_trimming_forward: " + str(self.reads_after_trimming_forward) + \
-        "\nreads_after_trimming_reverse: " + str(self.reads_after_trimming_reverse) + \
-        "\nreads_after_rRNA_trimming: " + str(self.reads_after_rRNA_trimming) + \
-        "\nreads_after_mapping: " + str(self.reads_after_mapping) + \
-        "\nreads_after_annotation: " + str(self.reads_after_annotation) + \
-        "\nreads_after_demultiplexing: " + str(self.reads_after_demultiplexing) + \
-        "\nreads_after_duplicates_removal: " + str(self.reads_after_duplicates_removal) + \
-        "\ngenes_found: " + str(self.genes_found) + \
-        "\nduplicates_found: " + str(self.duplicates_found) + \
-        "\npipeline_version: " + str(self.pipeline_version) + \
-        "\nmapper_tool: " + str(self.mapper_tool) + \
-        "\nannotation_tool: " + str(self.annotation_tool) + \
-        "\ndemultiplex_tool: " + str(self.demultiplex_tool) + \
-        "\ninput_parameters: " + ''.join([str(x) for x in self.input_parameters]) + \
-        "\nmax_genes_feature: " + str(self.max_genes_feature) + \
-        "\nmin_genes_feature: " + str(self.min_genes_feature) + \
-        "\nmax_reads_feature: " + str(self.max_reads_feature) + \
-        "\nmin_reads_feature: " + str(self.min_reads_feature) + \
-        "\navergage_gene_feature: " + str(self.average_gene_feature) + \
-        "\naverage_reads_feature: " + str(self.average_reads_feature)
-        
+        return "input_reads_forward: " + str(self.input_reads_forward) + \
+               "\ninput_reads_reverse: " + str(self.input_reads_reverse) + \
+               "\nreads_after_trimming_forward: " + str(self.reads_after_trimming_forward) + \
+               "\nreads_after_trimming_reverse: " + str(self.reads_after_trimming_reverse) + \
+               "\nreads_after_rRNA_trimming: " + str(self.reads_after_rRNA_trimming) + \
+               "\nreads_after_mapping: " + str(self.reads_after_mapping) + \
+               "\nreads_after_annotation: " + str(self.reads_after_annotation) + \
+               "\nreads_after_demultiplexing: " + str(self.reads_after_demultiplexing) + \
+               "\nreads_after_duplicates_removal: " + str(self.reads_after_duplicates_removal) + \
+               "\ngenes_found: " + str(self.genes_found) + \
+               "\nduplicates_found: " + str(self.duplicates_found) + \
+               "\npipeline_version: " + str(self.pipeline_version) + \
+               "\nmapper_tool: " + str(self.mapper_tool) + \
+               "\nannotation_tool: " + str(self.annotation_tool) + \
+               "\ndemultiplex_tool: " + str(self.demultiplex_tool) + \
+               "\ninput_parameters: " + ''.join([str(x) for x in self.input_parameters]) + \
+               "\nmax_genes_feature: " + str(self.max_genes_feature) + \
+               "\nmin_genes_feature: " + str(self.min_genes_feature) + \
+               "\nmax_reads_feature: " + str(self.max_reads_feature) + \
+               "\nmin_reads_feature: " + str(self.min_reads_feature) + \
+               "\navergage_gene_feature: " + str(self.average_gene_feature) + \
+               "\naverage_reads_feature: " + str(self.average_reads_feature)
+
     def writeJSON(self, filename):
-        qa_parameters = {"input_reads_forward" : self.input_reads_forward,
-                         "input_reads_reverse" : self.input_reads_reverse,
-                         "reads_after_trimming_forward" : self.reads_after_trimming_forward,
-                         "reads_after_trimming_reverse" : self.reads_after_trimming_reverse,
-                         "reads_after_rRNA_trimming" : self.reads_after_rRNA_trimming,
-                         "reads_after_mapping" : self.reads_after_mapping,
-                         "reads_after_annotation" : self.reads_after_annotation,
-                         "reads_after_demultiplexing" : self.reads_after_demultiplexing,
-                         "reads_after_duplicates_removal" : self.reads_after_duplicates_removal,
-                         "genes_found" : self.genes_found,
-                         "duplicates_found" : self.duplicates_found,
-                         "pipeline_version" : self.pipeline_version,
-                         "mapper_tool" : self.mapper_tool,
-                         "annotation_tool" : self.annotation_tool,
-                         "demultiplex_tool" : self.demultiplex_tool,
-                         "input_parameters" : ''.join([str(x) for x in self.input_parameters]),
-                         "max_genes_feature" : self.max_genes_feature,
-                         "min_genes_feature" : self.min_genes_feature,
-                         "max_reads_feature" : self.max_reads_feature,
-                         "min_reads_feature" : self.min_reads_feature,
-                         "avergage_gene_feature" : self.average_gene_feature,
-                         "average_reads_feature" : self.average_reads_feature}
-                         
-                         
+        qa_parameters = {"input_reads_forward": self.input_reads_forward,
+                         "input_reads_reverse": self.input_reads_reverse,
+                         "reads_after_trimming_forward": self.reads_after_trimming_forward,
+                         "reads_after_trimming_reverse": self.reads_after_trimming_reverse,
+                         "reads_after_rRNA_trimming": self.reads_after_rRNA_trimming,
+                         "reads_after_mapping": self.reads_after_mapping,
+                         "reads_after_annotation": self.reads_after_annotation,
+                         "reads_after_demultiplexing": self.reads_after_demultiplexing,
+                         "reads_after_duplicates_removal": self.reads_after_duplicates_removal,
+                         "genes_found": self.genes_found,
+                         "duplicates_found": self.duplicates_found,
+                         "pipeline_version": self.pipeline_version,
+                         "mapper_tool": self.mapper_tool,
+                         "annotation_tool": self.annotation_tool,
+                         "demultiplex_tool": self.demultiplex_tool,
+                         "input_parameters": ''.join([str(x) for x in self.input_parameters]),
+                         "max_genes_feature": self.max_genes_feature,
+                         "min_genes_feature": self.min_genes_feature,
+                         "max_reads_feature": self.max_reads_feature,
+                         "min_reads_feature": self.min_reads_feature,
+                         "avergage_gene_feature": self.average_gene_feature,
+                         "average_reads_feature": self.average_reads_feature}
+
         with open(filename, "w") as filehandler:
             json.dump(qa_parameters, filehandler, indent=2, separators=(',', ': '))
-   
-qa_stats = Stats()         
\ No newline at end of file
+
+# Global object
+qa_stats = Stats()
diff --git a/stpipeline/common/utils.py b/stpipeline/common/utils.py
index d911aa1..cce4063 100755
--- a/stpipeline/common/utils.py
+++ b/stpipeline/common/utils.py
@@ -7,6 +7,7 @@
 import subprocess
 import stat
 
+
 def which_program(program):
     """ 
     Checks that a program exists and is executable
@@ -14,6 +15,7 @@ def which_program(program):
     :type program: str
     :return: The program name if the program is in the system and is executable
     """
+
     def is_exe(fpath):
         return fpath is not None and os.path.exists(fpath) and os.access(fpath, os.X_OK)
 
@@ -33,11 +35,13 @@ def ext_candidates(fpath):
                 if is_exe(candidate):
                     return candidate
     return None
-             
+
+
 class TimeStamper(object):
     """
     Thread safe time stamper 
     """
+
     def __init__(self):
         self.lock = threading.Lock()
         self.prev = None
@@ -54,6 +58,7 @@ def getTimestamp(self):
                 self.count = 1
         return ts
 
+
 def safeRemove(filename):
     """
     Safely remove a file
@@ -65,7 +70,8 @@ def safeRemove(filename):
             os.remove(filename)
     except UnboundLocalError:
         pass
-        
+
+
 def safeOpenFile(filename, atrib):
     """
     Safely opens a file
@@ -90,6 +96,7 @@ def safeOpenFile(filename, atrib):
 
     return open(filename, atrib)
 
+
 def fileOk(_file):
     """
     Checks file exists and is not zero size
@@ -97,17 +104,17 @@ def fileOk(_file):
     :return: True if the file is correct
     """
     return _file is not None and os.path.isfile(_file) and not os.path.getsize(_file) == 0
-        
+
+
 def getSTARVersion():
     """
     Tries to find the STAR binary
     and makes a system call to get its
     version and return it
     """
-    version = ""
     try:
-        proc = subprocess.Popen(["STAR", "--version"], 
-                                stdout=subprocess.PIPE, 
+        proc = subprocess.Popen(["STAR", "--version"],
+                                stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE,
                                 shell=False, close_fds=True)
         (stdout, errmsg) = proc.communicate()
@@ -116,6 +123,7 @@ def getSTARVersion():
         version = "Not available"
     return version.rstrip()
 
+
 def getTaggdCountVersion():
     """
     Tries to find the Taggd binary
@@ -124,8 +132,8 @@ def getTaggdCountVersion():
     """
     version = ""
     try:
-        proc = subprocess.Popen(["pip", "show", "taggd"], 
-                                stdout=subprocess.PIPE, 
+        proc = subprocess.Popen(["pip", "show", "taggd"],
+                                stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE,
                                 shell=False, close_fds=True)
         (stdout, errmsg) = proc.communicate()
@@ -136,6 +144,7 @@ def getTaggdCountVersion():
         version = "Not available"
     return version.rstrip()
 
+
 def getHTSeqCountVersion():
     """
     Tries to find the HTSeqCount binary
@@ -144,8 +153,8 @@ def getHTSeqCountVersion():
     """
     version = ""
     try:
-        proc = subprocess.Popen(["pip", "show", "htseq"], 
-                                stdout=subprocess.PIPE, 
+        proc = subprocess.Popen(["pip", "show", "htseq"],
+                                stdout=subprocess.PIPE,
                                 stderr=subprocess.PIPE,
                                 shell=False, close_fds=True)
         (stdout, errmsg) = proc.communicate()
@@ -156,10 +165,11 @@ def getHTSeqCountVersion():
         version = "Not available"
     return version.rstrip()
 
+
 def is_fifo(file_name):
     """
     Checks if the file name is a FIFO
     :param file_name: a file name
     :return: True if the file is a FIFO
     """
-    return (os.path.exists(file_name) and stat.S_ISFIFO(os.stat(file_name).st_mode))
\ No newline at end of file
+    return os.path.exists(file_name) and stat.S_ISFIFO(os.stat(file_name).st_mode)
diff --git a/stpipeline/core/annotation.py b/stpipeline/core/annotation.py
index 15eda66..2819839 100755
--- a/stpipeline/core/annotation.py
+++ b/stpipeline/core/annotation.py
@@ -8,18 +8,14 @@
 import pysam
 from stpipeline.common.utils import fileOk
 from stpipeline.common.stats import qa_stats
-from stpipeline.common.sam_utils import merge_bam, split_bam
-import itertools
 import HTSeq
-import multiprocessing
-import operator
-import math
-import time
 
-class UnknownChrom( Exception ):
+
+class UnknownChrom(Exception):
     pass
 
-def invert_strand( iv ):
+
+def invert_strand(iv):
     iv2 = iv.copy()
     if iv2.strand == "+":
         iv2.strand = "-"
@@ -29,17 +25,17 @@ def invert_strand( iv ):
         raise ValueError("Illegal strand")
     return iv2
 
-def count_reads_in_features(sam_filename, 
-                            gff_filename, 
+
+def count_reads_in_features(sam_filename,
+                            gff_filename,
                             samtype,
                             stranded,
-                            overlap_mode, 
-                            feature_type, 
-                            id_attribute, 
-                            quiet, 
-                            minaqual, 
-                            samout, 
-                            include_non_annotated, 
+                            overlap_mode,
+                            feature_type,
+                            id_attribute,
+                            minaqual,
+                            samout,
+                            include_non_annotated,
                             htseq_no_ambiguous,
                             outputDiscarded):
     """
@@ -66,7 +62,7 @@ def count_reads_in_features(sam_filename,
     """
     # Set up the filters
     count_reads_in_features.filter_htseq = ["__too_low_aQual", "__not_aligned"]
-    if not include_non_annotated: 
+    if not include_non_annotated:
         count_reads_in_features.filter_htseq.append("__no_feature")
     count_reads_in_features.filter_htseq_no_ambiguous = htseq_no_ambiguous
 
@@ -74,18 +70,18 @@ def count_reads_in_features(sam_filename,
     flag_write = "wb" if samtype == "bam" else "wh"
     flag_read = "rb" if samtype == "bam" else "r"
     saminfile = pysam.AlignmentFile(sam_filename, flag_read)
-    count_reads_in_features.samoutfile = pysam.AlignmentFile(samout, 
-                                                             flag_write, 
+    count_reads_in_features.samoutfile = pysam.AlignmentFile(samout,
+                                                             flag_write,
                                                              template=saminfile)
     if outputDiscarded is not None:
-        count_reads_in_features.samdiscarded = pysam.AlignmentFile(outputDiscarded, 
-                                                                   flag_write, 
+        count_reads_in_features.samdiscarded = pysam.AlignmentFile(outputDiscarded,
+                                                                   flag_write,
                                                                    template=saminfile)
     saminfile.close()
-    
+
     # Counter of annotated records
     count_reads_in_features.annotated = 0
-    
+
     # Function to write to SAM output
     def write_to_samout(read, assignment):
         # Creates the PySAM record
@@ -94,16 +90,16 @@ def write_to_samout(read, assignment):
         sam_record = read.to_pysam_AlignedSegment(count_reads_in_features.samoutfile)
         sam_record.set_tag("XF", assignment, "Z")
         if read is not None and assignment not in count_reads_in_features.filter_htseq \
-        and not (count_reads_in_features.filter_htseq_no_ambiguous and assignment.find("__ambiguous") != -1):
+                and not (count_reads_in_features.filter_htseq_no_ambiguous and assignment.find("__ambiguous") != -1):
             count_reads_in_features.samoutfile.write(sam_record)
             count_reads_in_features.annotated += 1
         elif outputDiscarded is not None:
             count_reads_in_features.samdiscarded.write(sam_record)
-                
+
     # Annotation objects
     features = HTSeq.GenomicArrayOfSets("auto", stranded != "no")
     counts = {}
-    gff = HTSeq.GFF_Reader(gff_filename)   
+    gff = HTSeq.GFF_Reader(gff_filename)
 
     try:
         for f in gff:
@@ -112,19 +108,19 @@ def write_to_samout(read, assignment):
                     feature_id = f.attr[id_attribute]
                 except KeyError:
                     raise ValueError("Feature %s does not contain a '%s' attribute" \
-                                       % (f.name, id_attribute))
+                                     % (f.name, id_attribute))
                 if stranded != "no" and f.iv.strand == ".":
                     raise ValueError("Feature %s at %s does not have strand information but you are " \
-                                       "running htseq-count in stranded mode. Use '--stranded=no'." % 
-                                       (f.name, f.iv))
+                                     "running htseq-count in stranded mode. Use '--stranded=no'." %
+                                     (f.name, f.iv))
                 features[f.iv] += feature_id
                 counts[f.attr[id_attribute]] = 0
     except:
         raise
-    
+
     if len(counts) == 0:
         raise RuntimeError("No features of type '%s' found.\n" % feature_type)
-        
+
     if samtype == "sam":
         SAM_or_BAM_Reader = HTSeq.SAM_Reader
     elif samtype == "bam":
@@ -138,7 +134,7 @@ def write_to_samout(read, assignment):
         raise RuntimeError("Error occurred when reading beginning of SAM/BAM file.")
 
     try:
-        
+
         for r in read_seq:
             if not r.aligned:
                 write_to_samout(r, "__not_aligned")
@@ -149,9 +145,9 @@ def write_to_samout(read, assignment):
             if stranded != "reverse":
                 iv_seq = (co.ref_iv for co in r.cigar if co.type == "M" and co.size > 0)
             else:
-                iv_seq = (invert_strand(co.ref_iv) 
-                          for co in r.cigar 
-                          if co.type in ["M","=","X"] and co.size > 0)
+                iv_seq = (invert_strand(co.ref_iv)
+                          for co in r.cigar
+                          if co.type in ["M", "=", "X"] and co.size > 0)
             try:
                 if overlap_mode == "union":
                     fs = set()
@@ -173,14 +169,14 @@ def write_to_samout(read, assignment):
                                     fs = fs.intersection(fs2)
                 else:
                     raise RuntimeError("Illegal overlap mode.")
-                
+
                 if fs is None or len(fs) == 0:
                     write_to_samout(r, "__no_feature")
                 elif len(fs) > 1:
                     write_to_samout(r, "__ambiguous[" + '+'.join(fs) + "]")
                 else:
                     write_to_samout(r, list(fs)[0])
-                    
+
             except UnknownChrom:
                 write_to_samout(r, "__no_feature")
                 pass
@@ -191,19 +187,18 @@ def write_to_samout(read, assignment):
         count_reads_in_features.samoutfile.close()
         if outputDiscarded is not None:
             count_reads_in_features.samdiscarded.close()
-            
+
     return count_reads_in_features.annotated
 
-def annotateReads(mappedReads, 
+
+def annotateReads(mappedReads,
                   gtfFile,
                   outputFile,
                   outputDiscarded,
                   mode,
                   strandness,
-                  htseq_no_ambiguous, 
-                  include_non_annotated,
-                  temp_dir,
-                  threads):
+                  htseq_no_ambiguous,
+                  include_non_annotated):
     """
     Annotates a file with mapped reads (BAM) using a modified 
     version of the htseq-count tool. It writes the annotated records to a file.
@@ -219,8 +214,6 @@ def annotateReads(mappedReads,
     :param include_non_annotated: true if we want to include 
     non annotated reads as __no_feature in the output
     :param outputFile: the name/path to the output file
-    :param temp_dir: path to the folder where to put the created files
-    :param threads: the number of CPU cores to use
     :type mappedReads: str
     :type gtfFile: str
     :type outputFile: str
@@ -230,28 +223,25 @@ def annotateReads(mappedReads,
     :type htseq_no_ambiguos: boolean
     :type include_non_annotated: str
     :type outputFile: str
-    :type temp_dir: str
-    :type threads: int
     :raises: RuntimeError, ValueError
     """
-    
+
     logger = logging.getLogger("STPipeline")
-    
+
     if not os.path.isfile(mappedReads):
         error = "Error during annotation, input file not present {}\n".format(mappedReads)
         logger.error(error)
         raise RuntimeError(error)
-    
+
     try:
         annotated = count_reads_in_features(mappedReads,
                                             gtfFile,
-                                            "bam", # Type BAM for filesz
-                                            strandness, # Strand yes/no/reverse
-                                            mode, # intersection_nonempty, union, intersection_strict
-                                            "exon", # feature type in GFF
-                                            "gene_id", # gene_id or gene_name
-                                            True, # Quiet mode
-                                            0, # Min quality score
+                                            "bam",  # Type BAM for filesz
+                                            strandness,  # Strand yes/no/reverse
+                                            mode,  # intersection_nonempty, union, intersection_strict
+                                            "exon",  # feature type in GFF
+                                            "gene_id",  # gene_id or gene_name
+                                            0,  # Min quality score
                                             outputFile,
                                             include_non_annotated,
                                             htseq_no_ambiguous,
@@ -260,11 +250,11 @@ def annotateReads(mappedReads,
         error = "Error during annotation. HTSEQ execution failed\n"
         logger.error(error)
         raise e
-    
+
     if not fileOk(outputFile) or annotated == 0:
         error = "Error during annotation. Output file not present {}\n".format(outputFile)
         logger.error(error)
         raise RuntimeError(error)
-    
+
     logger.info("Annotated reads: {}".format(annotated))
-    qa_stats.reads_after_annotation = annotated
\ No newline at end of file
+    qa_stats.reads_after_annotation = annotated
diff --git a/stpipeline/core/mapping.py b/stpipeline/core/mapping.py
index 717d384..7154db2 100755
--- a/stpipeline/core/mapping.py
+++ b/stpipeline/core/mapping.py
@@ -2,7 +2,7 @@
 This module contains functions related to sequence alignment and barcode
 demultiplexing in the ST pipeline
 """
-import logging 
+import logging
 import subprocess
 from subprocess import CalledProcessError
 from stpipeline.common.utils import fileOk
@@ -10,7 +10,8 @@
 import os
 import shutil
 
-def alignReads(reverse_reads, 
+
+def alignReads(reverse_reads,
                ref_map,
                outputFile,
                annotation,
@@ -70,12 +71,12 @@ def alignReads(reverse_reads,
     :raises: RuntimeError,ValueError,OSError,CalledProcessError
     """
     logger = logging.getLogger("STPipeline")
-    
+
     if not os.path.isfile(reverse_reads):
         error = "Error mapping with STAR, input file not present {}\n".format(reverse_reads)
         logger.error(error)
         raise RuntimeError(error)
-    
+
     # STAR has predefined output names for the files
     tmpOutputFile = "Aligned.sortedByCoord.out.bam"
     tmpOutputFileDiscarded = "Unmapped.out.mate1"
@@ -84,27 +85,26 @@ def alignReads(reverse_reads,
     log_sj = "SJ.out.tab"
     log_final = "Log.final.out"
     log_progress = "Log.progress.out"
-    
+
     if outputFolder is not None and os.path.isdir(outputFolder):
         tmpOutputFile = os.path.join(outputFolder, tmpOutputFile)
-        tmpOutputFileDiscarded = os.path.join(outputFolder, tmpOutputFileDiscarded)
         log_std = os.path.join(outputFolder, log_std)
         log = os.path.join(outputFolder, log)
         log_sj = os.path.join(outputFolder, log_sj)
         log_final = os.path.join(outputFolder, log_final)
         log_progress = os.path.join(outputFolder, log_progress)
-    
-    multi_map_number = 1 if disable_multimap else 20 # 10 is the STAR default
+
+    multi_map_number = 1 if disable_multimap else 20  # 10 is the STAR default
     alignment_mode = "EndToEnd" if diable_softclipping else "Local"
-    
+
     flags = ["--clip3pNbases", invTrimReverse,
              "--clip5pNbases", trimReverse,
              "--runThreadN", str(max(cores, 1)),
-             "--outFilterType", "Normal", 
+             "--outFilterType", "Normal",
              "--outSAMtype", "BAM", "SortedByCoordinate",
              "--alignEndsType", alignment_mode,
-             "--outSAMorder", "Paired",    
-             "--outSAMprimaryFlag", "OneBestScore", 
+             "--outSAMorder", "Paired",
+             "--outSAMprimaryFlag", "OneBestScore",
              "--outFilterMultimapNmax", multi_map_number,
              "--alignIntronMin", min_intron_size,
              "--alignIntronMax", max_intron_size,
@@ -112,29 +112,29 @@ def alignReads(reverse_reads,
              "--outSAMmultNmax", 1,
              "--outMultimapperOrder", "Random",
              "--readMatesLengthsIn", "NotEqual",
-             "--outFilterMismatchNoverLmax", 0.1, ## (0.3 default)
+             "--outFilterMismatchNoverLmax", 0.1,  # (0.3 default)
              "--genomeLoad", star_genome_loading,
              "--limitBAMsortRAM", star_sort_mem_limit,
-             "--readFilesType", "SAM","SE", # Input in BAM format
-             "--readFilesCommand", "samtools", "view", "-h"] 
-    
+             "--readFilesType", "SAM", "SE",  # Input in BAM format
+             "--readFilesCommand", "samtools", "view", "-h"]
+
     if twopassMode:
         flags += ["--twopassMode", "Basic"]
 
     if annotation is not None:
         flags += ["--sjdbGTFfile", annotation]
-       
+
     if include_non_mapped:
         flags += ["--outSAMunmapped", "Within"]
     else:
         flags += ["--outSAMunmapped", "None"]
-        
+
     args = ["STAR",
             "--genomeDir", ref_map,
             "--readFilesIn", reverse_reads,
-            "--outFileNamePrefix", outputFolder + os.sep]  
+            "--outFileNamePrefix", outputFolder + os.sep]
     args += flags
-    
+
     try:
         proc = subprocess.Popen([str(i) for i in args],
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE,
@@ -149,25 +149,29 @@ def alignReads(reverse_reads,
     except CalledProcessError as e:
         logger.error("Error mapping with STAR\n Program returned error.")
         raise e
-        
+
     if not fileOk(tmpOutputFile):
         error = "Error mapping with STAR.\n" \
-        "Output file not present {}\n{}\n".format(tmpOutputFile, errmsg)
+                "Output file not present {}\n{}\n".format(tmpOutputFile, errmsg)
         logger.error(error)
         raise RuntimeError(error)
 
     if len(errmsg) > 0:
         logger.warning("STAR has generated error messages during mapping.\n{}\n".format(errmsg))
-        
+
     # Rename output files.
     shutil.move(tmpOutputFile, outputFile)
-        
+
     # Remove temp files from STAR
-    if os.path.isfile(log_std): os.remove(log_std)
-    if os.path.isfile(log): os.remove(log)
-    if os.path.isfile(log_progress): os.remove(log_progress)
-    if os.path.isfile(log_sj): os.remove(log_sj)
-    
+    if os.path.isfile(log_std):
+        os.remove(log_std)
+    if os.path.isfile(log):
+        os.remove(log)
+    if os.path.isfile(log_progress):
+        os.remove(log_progress)
+    if os.path.isfile(log_sj):
+        os.remove(log_sj)
+
     if not os.path.isfile(log_final):
         logger.warning("Log output file from STAR is not present")
     else:
@@ -180,22 +184,24 @@ def alignReads(reverse_reads,
         with open(log_final, "r") as star_log:
             for line in star_log.readlines():
                 if line.find("Uniquely mapped reads %") != -1 \
-                or line.find("Uniquely mapped reads number") != -1 \
-                or line.find("Number of reads mapped to multiple loci") != -1 \
-                or line.find("% of reads mapped to multiple loci") != -1 \
-                or line.find("% of reads unmapped: too short") != -1:
+                        or line.find("Uniquely mapped reads number") != -1 \
+                        or line.find("Number of reads mapped to multiple loci") != -1 \
+                        or line.find("% of reads mapped to multiple loci") != -1 \
+                        or line.find("% of reads unmapped: too short") != -1:
                     logger.info(str(line).rstrip())
                 # Some duplicated code here; TODO refactor
                 if line.find("Uniquely mapped reads number") != -1:
                     uniquely_mapped = int(str(line).rstrip().split()[-1])
                 if line.find("Number of reads mapped to multiple loci") != -1:
                     multiple_mapped = int(str(line).rstrip().split()[-1])
-            logger.info("Total mapped reads: {}".format(uniquely_mapped + multiple_mapped))   
-             
-    # Remove log file       
-    if os.path.isfile(log_final): os.remove(log_final)
+            logger.info("Total mapped reads: {}".format(uniquely_mapped + multiple_mapped))
+
+    # Remove log file
+    if os.path.isfile(log_final):
+        os.remove(log_final)
 
-def barcodeDemultiplexing(reads, 
+
+def barcodeDemultiplexing(reads,
                           idFile,
                           mismatches,
                           kmer,
@@ -235,53 +241,53 @@ def barcodeDemultiplexing(reads,
     :raises: RuntimeError,ValueError,OSError,CalledProcessError
     """
     logger = logging.getLogger("STPipeline")
-    
+
     if not os.path.isfile(reads):
         error = "Error, input file not present {}\n".format(reads)
         logger.error(error)
         raise RuntimeError(error)
-    
+
     # Taggd options
-    #--metric (subglobal (default) , Levenshtein or Hamming)
-    #--slider-increment (space between kmer searches, 0 is default = kmer length)
-    #--seed
-    #--overhang additional flanking bases around read barcode to allow
-    #--estimate-min-edit-distance is set estimate the min edit distance among true barcodes
-    #--no-offset-speedup turns off speed up, 
+    # --metric (subglobal (default) , Levenshtein or Hamming)
+    # --slider-increment (space between kmer searches, 0 is default = kmer length)
+    # --seed
+    # --overhang additional flanking bases around read barcode to allow
+    # --estimate-min-edit-distance is set estimate the min edit distance among true barcodes
+    # --no-offset-speedup turns off speed up,
     #  it might yield more hits (exactly as findIndexes)
-    #--homopolymer-filter if set excludes reads where barcode 
+    # --homopolymer-filter if set excludes reads where barcode
     #  contains a homolopymer of the given length (0 no filter), default 8
-    
-    if taggd_metric == "Hamming": over_hang = 0 
+
+    if taggd_metric == "Hamming": over_hang = 0
     args = ['taggd_demultiplex.py']
-    
+
     if taggd_trim_sequences is not None:
-        args.append("--trim-sequences") 
+        args.append("--trim-sequences")
         for pos in taggd_trim_sequences:
-            args.append(pos) 
-            
+            args.append(pos)
+
     args += ["--max-edit-distance", mismatches,
-            "--k", kmer,
-            "--barcode-tag", "B0", # if input is BAM we tell taggd what tag contains the barcode
-            "--homopolymer-filter", 0,
-            "--subprocesses", cores,
-            "--metric", taggd_metric,
-            "--overhang", over_hang] #,
-            #'--use-samtools-merge'] # Could be added to merge using samtools instead of pysam WIP on taggd
-            
+             "--k", kmer,
+             "--barcode-tag", "B0",  # if input is BAM we tell taggd which tag contains the barcode
+             "--homopolymer-filter", 0,
+             "--subprocesses", cores,
+             "--metric", taggd_metric,
+             "--overhang", over_hang]
+    # --use-samtools-merge Could be added to merge using samtools instead of pysam WIP on taggd
+
     if taggd_multiple_hits_keep_one:
-        args.append("--multiple-hits-keep-one")  
-            
+        args.append("--multiple-hits-keep-one")
+
     if not keep_discarded_files:
         args.append("--no-unmatched-output")
         args.append("--no-ambiguous-output")
         args.append("--no-results-output")
-        
+
     args += [idFile, reads, outputFilePrefix]
 
     try:
-        proc = subprocess.Popen([str(i) for i in args], 
-                                stdout=subprocess.PIPE, stderr=subprocess.PIPE, 
+        proc = subprocess.Popen([str(i) for i in args],
+                                stdout=subprocess.PIPE, stderr=subprocess.PIPE,
                                 close_fds=True, shell=False)
         (stdout, errmsg) = proc.communicate()
     except ValueError as e:
@@ -293,23 +299,23 @@ def barcodeDemultiplexing(reads,
     except CalledProcessError as e:
         logger.error("Error demultiplexing with TAGGD\n Program returned error.")
         raise e
-    
+
     # We know the output file from the prefix and suffix
     outputFile = "{}_matched{}".format(outputFilePrefix, os.path.splitext(reads)[1].lower())
     if not fileOk(outputFile):
         error = "Error demultiplexing with TAGGD.\n" \
-        "Output file is not present {}\n{}\n".format(outputFile, errmsg)
+                "Output file is not present {}\n{}\n".format(outputFile, errmsg)
         logger.error(error)
         raise RuntimeError(error)
- 
+
     if len(errmsg) > 0:
         logger.warning("Taggd has generated error messages during " \
                        "demultiplexing.\n{}\n".format(errmsg))
-           
+
     # TODO must be a cleaner way to get the stats from the output file
     procOut = stdout.decode().split("\n")
     logger.info("Demultiplexing Mapping stats:")
-    for line in procOut: 
+    for line in procOut:
         if line.find("Total reads:") != -1:
             logger.info(str(line))
         if line.find("Total reads written:") != -1:
diff --git a/stpipeline/core/pipeline.py b/stpipeline/core/pipeline.py
index b01f42d..7cf2c6d 100755
--- a/stpipeline/core/pipeline.py
+++ b/stpipeline/core/pipeline.py
@@ -24,36 +24,38 @@
 import pysam
 import inspect
 
-FILENAMES = {"mapped" : "mapped.bam",
-             "annotated" : "annotated.bam",
-             "contaminated_clean" : "contaminated_clean.bam",
-             "demultiplexed_prefix" : "demultiplexed",
-             "demultiplexed_matched" : "demultiplexed_matched.bam",
-             "quality_trimmed_R2" : "R2_quality_trimmed.bam"}
-
-FILENAMES_DISCARDED = {"mapped_discarded" : "mapping_discarded.bam",
-                       "contaminated_discarded" : "contaminated.bam",
-                       "demultiplexed_ambiguos" : "demultiplexed_ambiguos.bam",
-                       "demultiplexed_unmatched" : "demultiplexed_unmatched.bam",
-                       "demultiplexed_results" : "demultiplexed_results.tsv",
-                       "quality_trimmed_discarded" : "R2_quality_trimmed_discarded.fastq",
+FILENAMES = {"mapped": "mapped.bam",
+             "annotated": "annotated.bam",
+             "contaminated_clean": "contaminated_clean.bam",
+             "demultiplexed_prefix": "demultiplexed",
+             "demultiplexed_matched": "demultiplexed_matched.bam",
+             "quality_trimmed_R2": "R2_quality_trimmed.bam"}
+
+FILENAMES_DISCARDED = {"mapped_discarded": "mapping_discarded.bam",
+                       "contaminated_discarded": "contaminated.bam",
+                       "demultiplexed_ambiguos": "demultiplexed_ambiguos.bam",
+                       "demultiplexed_unmatched": "demultiplexed_unmatched.bam",
+                       "demultiplexed_results": "demultiplexed_results.tsv",
+                       "quality_trimmed_discarded": "R2_quality_trimmed_discarded.fastq",
                        "annotated_discarded": "annotated_discarded.bam"}
 
+
 class Pipeline():
-    """ This class contains all the ST pipeline
+    """
+    This class contains all the ST pipeline
     attributes and a bunch of methods to parse
     the input parameters, do sanity check and
     run the pipeline steps.
     """
     LogName = "STPipeline"
-    
+
     def __init__(self):
         self.allowed_missed = 2
         self.allowed_kmer = 6
         self.overhang = 0
         self.min_length_trimming = 20
         self.trimming_rv = 0
-        self.min_quality_trimming = 20 
+        self.min_quality_trimming = 20
         self.clean = True
         self.barcode_start = 0
         self.threads = 8
@@ -110,7 +112,7 @@ def __init__(self):
         self.disable_barcode = False
         self.transcriptome = False
         self.saturation_points = None
-        
+
     def clean_filenames(self):
         """ Just makes sure to remove
         all temp files
@@ -122,8 +124,8 @@ def clean_filenames(self):
             for file_name in list(FILENAMES_DISCARDED.values()):
                 safeRemove(file_name)
         if self.temp_folder is not None and os.path.isdir(self.temp_folder):
-            safeRemove(os.path.join(self.temp_folder,"unzipped_fastq_fw.fastq"))
-            safeRemove(os.path.join(self.temp_folder,"unzipped_fastq_rv.fastq"))
+            safeRemove(os.path.join(self.temp_folder, "unzipped_fastq_fw.fastq"))
+            safeRemove(os.path.join(self.temp_folder, "unzipped_fastq_rv.fastq"))
             star_temp1 = os.path.join(self.temp_folder, "_STARgenome")
             star_temp2 = os.path.join(self.temp_folder, "_STARpass1")
             if os.path.isdir(star_temp1):
@@ -131,68 +133,68 @@ def clean_filenames(self):
             if os.path.isdir(star_temp2):
                 shutil.rmtree(star_temp2)
             if self.clean and not self.keep_discarded_files \
-            and self.temp_folder != self.output_folder:
+                    and self.temp_folder != self.output_folder:
                 shutil.rmtree(self.temp_folder)
-          
+
     def sanityCheck(self):
         """ 
         Performs some basic sanity checks on the input parameters
         """
 
         if self.ref_annotation is not None and (not os.path.isfile(self.ref_annotation) or \
-        (not self.ref_annotation.endswith(".gtf") \
-        and not self.ref_annotation.endswith(".gff3") \
-        and not self.ref_annotation.endswith(".gff"))):
+                                                (not self.ref_annotation.endswith(".gtf") \
+                                                 and not self.ref_annotation.endswith(".gff3") \
+                                                 and not self.ref_annotation.endswith(".gff"))):
             error = "Error parsing parameters.\n" \
-            "Invalid annotation file {}".format(self.ref_annotation)
+                    "Invalid annotation file {}".format(self.ref_annotation)
             self.logger.error(error)
             raise RuntimeError(error)
-        
+
         if self.ref_annotation is None and not self.transcriptome:
             error = "Error, annotation file is missing but the transcriptome option is disabled\n"
             self.logger.error(error)
             raise RuntimeError(error)
-            
+
         if self.ref_map is None and not self.disable_mapping:
             error = "Error, genome reference is missing but the disable_mapping option is disabled\n"
             self.logger.error(error)
             raise RuntimeError(error)
-          
+
         if not os.path.isfile(self.fastq_fw) or not os.path.isfile(self.fastq_rv):
             error = "Error parsing parameters.\n" \
-            "Invalid input files {} {}".format(self.fastq_fw, self.fastq_rv)
+                    "Invalid input files {} {}".format(self.fastq_fw, self.fastq_rv)
             self.logger.error(error)
             raise RuntimeError(error)
-                     
-        if (not self.fastq_fw.endswith(".fastq") \
-        and not self.fastq_fw.endswith(".fq") \
-        and not self.fastq_fw.endswith(".gz") \
-        and not self.fastq_rv.endswith(".bz2")) \
-        or (not self.fastq_rv.endswith(".fastq") \
-        and not self.fastq_rv.endswith(".fq") \
-        and not self.fastq_rv.endswith(".gz") \
-        and not self.fastq_rv.endswith(".bz2")):
+
+        if (not self.fastq_fw.endswith(".fastq")
+            and not self.fastq_fw.endswith(".fq")
+            and not self.fastq_fw.endswith(".gz")
+            and not self.fastq_rv.endswith(".bz2")) \
+                or (not self.fastq_rv.endswith(".fastq")
+                    and not self.fastq_rv.endswith(".fq")
+                    and not self.fastq_rv.endswith(".gz")
+                    and not self.fastq_rv.endswith(".bz2")):
             error = "Error parsing parameters.\n" \
-            "Incorrect format for input files {} {}".format(self.fastq_fw, self.fastq_rv)
+                    "Incorrect format for input files {} {}".format(self.fastq_fw, self.fastq_rv)
             self.logger.error(error)
             raise RuntimeError(error)
-             
+
         if not self.disable_barcode and not os.path.isfile(self.ids):
             error = "Error parsing parameters.\n" \
-            "Invalid IDs file {}".format(self.ids)
+                    "Invalid IDs file {}".format(self.ids)
             self.logger.error(error)
-            raise RuntimeError(error)      
-        
+            raise RuntimeError(error)
+
         if not self.disable_barcode and self.ids is None:
             error = "Error IDs file is missing but the option to disable the " \
-            "demultiplexing step is not activated\n"
+                    "demultiplexing step is not activated\n"
             self.logger.error(error)
-            raise RuntimeError(error)   
-           
+            raise RuntimeError(error)
+
         if self.saturation_points is not None and not self.compute_saturation:
-            self.logger.warning("Saturation points are provided but the option" \
+            self.logger.warning("Saturation points are provided but the option"
                                 "to compute saturation is disabled.")
-            
+
         if not self.disable_umi and self.umi_filter:
             # Check template validity
             import re
@@ -200,14 +202,14 @@ def sanityCheck(self):
             if re.search(regex, self.umi_filter_template) is not None:
                 error = "Error invalid UMI template given {}.\n".format(self.umi_filter_template)
                 self.logger.error(error)
-                raise RuntimeError(error)                
-            # Check template length
+                raise RuntimeError(error)
+                # Check template length
             if len(self.umi_filter_template) != (self.umi_end_position - self.umi_start_position):
                 error = "Error the UMI template given does not have the same " \
-                "length as the UMIs {}.\n".format(self.umi_filter_template)
+                        "length as the UMIs {}.\n".format(self.umi_filter_template)
                 self.logger.error(error)
-                raise RuntimeError(error) 
-            # Convert the template into a reg-exp
+                raise RuntimeError(error)
+                # Convert the template into a reg-exp
             temp_reg_exp = ""
             for ele in self.umi_filter_template:
                 if ele == "W":
@@ -243,41 +245,40 @@ def sanityCheck(self):
                 elif ele == "H":
                     temp_reg_exp += "[ACT]"
             self.umi_filter_template = temp_reg_exp
-                         
+
         # Add checks for trimming parameters, demultiplex parameters and UMI parameters
         if self.allowed_missed > self.allowed_kmer and not self.disable_barcode:
             error = "Error starting the pipeline.\n" \
-            "Taggd allowed mismatches is bigger or equal than the Taggd k-mer size"
+                    "Taggd allowed mismatches is bigger or equal than the Taggd k-mer size"
             self.logger.error(error)
             raise RuntimeError(error)
-        
-        if self.barcode_start > self.umi_start_position \
-        and self.barcode_start < self.umi_end_position \
-        and not self.disable_barcode and not self.disable_umi:
+
+        if self.umi_start_position < self.barcode_start < self.umi_end_position \
+                and not self.disable_barcode and not self.disable_umi:
             error = "Error starting the pipeline.\n" \
-            "The start position of the barcodes is between the UMIs start-end position"
+                    "The start position of the barcodes is between the UMIs start-end position"
             self.logger.error(error)
             raise RuntimeError(error) 
-        
+
         if self.umi_allowed_mismatches > (self.umi_end_position - self.umi_start_position) \
-        and not self.disable_umi:
+                and not self.disable_umi:
             error = "Error starting the pipeline.\n" \
-            "The allowed UMI mismatches is bigger than the UMI size"
+                    "The allowed UMI mismatches is bigger than the UMI size"
             self.logger.error(error)
-            raise RuntimeError(error)              
-                     
-        # Test the presence of the scripts 
+            raise RuntimeError(error)
+
+            # Test the presence of the scripts
         required_scripts = set(['STAR'])
         unavailable_scripts = set()
         for script in required_scripts:
-            if which_program(script) is None: 
+            if which_program(script) is None:
                 unavailable_scripts.add(script)
         if len(unavailable_scripts) != 0:
             error = "Error starting the pipeline.\n" \
-            "Required software not found:\t".join(unavailable_scripts)
+                    "Required software not found:\t".join(unavailable_scripts)
             self.logger.error(error)
             raise RuntimeError(error)
-            
+
     def createParameters(self, parser):
         """
         Adds the pipeline's parameters to a given
@@ -285,6 +286,7 @@ def createParameters(self, parser):
         :param parser: the Argparse object
         :return: a new Argparse object with the parameters
         """
+
         class readable_dir(argparse.Action):
             def __call__(self, parser, namespace, values, option_string=None):
                 prospective_dir = values
@@ -296,178 +298,380 @@ def __call__(self, parser, namespace, values, option_string=None):
                     raise argparse.ArgumentTypeError("{0} is not a readable dir".format(prospective_dir))
 
         parser.add_argument('fastq_files', nargs=2)
-        parser.add_argument('--ids', metavar="[FILE]", required=False,
+        parser.add_argument('--ids',
+                            metavar="[FILE]",
+                            required=False,
                             help='Path to the file containing the map of barcodes to the array coordinates')
-        parser.add_argument('--ref-map', metavar="[FOLDER]", action=readable_dir, required=False,
-                            help="Path to the folder with the STAR index " \
-                            "for the genome that you want to use to align the reads")
-        parser.add_argument('--ref-annotation', metavar="[FILE]", required=False,
-                            help="Path to the reference annotation file " \
-                            "(GTF or GFF format is required) to be used to annotated the reads")
-        parser.add_argument('--expName', type=str, metavar="[STRING]", required=True,
-                            help="Name of the experiment/dataset (The output files will prepend this name)")
-        parser.add_argument('--allowed-missed', default=2, metavar="[INT]", type=int, choices=range(0, 31),
-                            help="Number of allowed mismatches when demultiplexing " \
-                            "against the barcodes with TaggD (default: %(default)s)")
-        parser.add_argument('--allowed-kmer', default=6, metavar="[INT]", type=int, choices=range(1, 51),
-                            help="KMer length when demultiplexing against the barcodes with TaggD (default: %(default)s)")
-        parser.add_argument('--overhang', default=0, metavar="[INT]", type=int, choices=range(0, 11),
-                            help="Extra flanking bases added when demultiplexing against the barcodes with TaggD (default: %(default)s)")
-        parser.add_argument('--min-length-qual-trimming', default=20, metavar="[INT]", type=int, choices=range(10, 101),
-                            help="Minimum length of the reads after trimming, " \
-                            "shorter reads will be discarded (default: %(default)s)")
-        parser.add_argument('--mapping-rv-trimming', default=0, metavar="[INT]", type=int, choices=range(0, 51),
-                            help="Number of bases to trim in the reverse reads for the mapping step (5' end) (default: %(default)s)")
-        parser.add_argument('--contaminant-index', metavar="[FOLDER]", action=readable_dir, default=None,
-                            help="Path to the folder with a STAR index with a contaminant genome. Reads will be filtered "
-                            "against the specified genome and mapping reads will be descarded")
-        parser.add_argument('--qual-64', action="store_true", default=False,
-                            help="Use phred-64 quality instead of phred-33(default)")
-        parser.add_argument('--htseq-mode', default="intersection-nonempty", type=str, metavar="[STRING]",
-                            choices=["union", "intersection-nonempty", "intersection-strict"],
-                            help="Mode of Annotation when using HTSeq. "
-                            "Modes = {union,intersection-nonempty(default),intersection-strict}")
-        parser.add_argument('--htseq-no-ambiguous', action="store_true", default=False,
-                            help="When using htseq discard reads annotating ambiguous genes (default False)")
-        parser.add_argument('--start-id', default=0, metavar="[INT]", type=int,
-                            help="Start position of the IDs (Barcodes) in the R1 (counting from 0) (default: %(default)s)")
-        parser.add_argument('--no-clean-up', action="store_false", default=True,
+        parser.add_argument('--ref-map',
+                            metavar="[FOLDER]",
+                            action=readable_dir,
+                            required=False,
+                            help="Path to the folder with the STAR index "
+                                 "for the genome that you want to use as reference")
+        parser.add_argument('--ref-annotation',
+                            metavar="[FILE]",
+                            required=False,
+                            help="Path to the reference annotation file "
+                                 "(GTF or GFF format is required) to be used to annotated the mapped reads")
+        parser.add_argument('--expName',
+                            type=str,
+                            metavar="[STRING]",
+                            required=True,
+                            help="Name of the dataset (The output files will prepend this name)")
+        parser.add_argument('--contaminant-index',
+                            metavar="[FOLDER]",
+                            action=readable_dir,
+                            default=None,
+                            help="Path to the folder with a STAR index with a contaminant genome reference.\n"
+                                 "Reads will be filtered using the specified genome and mapping reads will be discarded")
+        parser.add_argument('--no-clean-up',
+                            action="store_false",
+                            default=True,
                             help="Do not remove temporary/intermediary files (useful for debugging)")
-        parser.add_argument('--verbose', action="store_true", default=False,
+        parser.add_argument('--verbose',
+                            action="store_true",
+                            default=False,
                             help="Show extra information on the log file")
-        parser.add_argument('--mapping-threads', default=4, metavar="[INT]", type=int, choices=range(1, 33),
-                            help="Number of threads to use in the mapping step (default: %(default)s)")
-        parser.add_argument('--min-quality-trimming', default=20, metavar="[INT]", type=int, choices=range(1, 61),
-                            help="Minimum phred quality a base must have in the trimming step (default: %(default)s)")
-        parser.add_argument('--bin-path', metavar="[FOLDER]", action=readable_dir, default=None,
+        parser.add_argument('--threads',
+                            default=4,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(1, 81),
+                            help="Number of threads to use (default: %(default)s)")
+        parser.add_argument('--bin-path',
+                            metavar="[FOLDER]",
+                            action=readable_dir,
+                            default=None,
                             help="Path to folder where binary executables are present (system path by default)")
-        parser.add_argument('--log-file', metavar="[STR]", default=None,
+        parser.add_argument('--log-file',
+                            metavar="[STR]",
+                            default=None,
                             help="Name of the file that we want to use to store the logs (default output to screen)")
-        parser.add_argument('--output-folder', metavar="[FOLDER]", action=readable_dir, default=None,
+        parser.add_argument('--output-folder',
+                            metavar="[FOLDER]",
+                            action=readable_dir,
+                            default=None,
                             help='Path of the output folder')
-        parser.add_argument('--temp-folder', metavar="[FOLDER]", action=readable_dir, default=None,
+        parser.add_argument('--temp-folder',
+                            metavar="[FOLDER]",
+                            action=readable_dir,
+                            default=None,
                             help='Path of the location for temporary files')
-        parser.add_argument('--umi-allowed-mismatches', default=1, metavar="[INT]", type=int, choices=range(0, 9),
-                            help="Number of allowed mismatches (hamming distance) " \
-                            "that UMIs of the same gene-spot must have in order to cluster together (default: %(default)s)")
-        parser.add_argument('--umi-start-position', default=18, metavar="[INT]", type=int,
-                            help="Position in R1 (base wise) of the first base of the " \
-                            "UMI (starting by 0) (default: %(default)s)")
-        parser.add_argument('--umi-end-position', default=27, metavar="[INT]", type=int,
-                            help="Position in R1 (base wise) of the last base of the "\
-                            "UMI (starting by 1) (default: %(default)s)")
-        parser.add_argument('--keep-discarded-files', action="store_true", default=False,
-                            help='Writes down unaligned, un-annotated and un-demultiplexed reads to files')
-        parser.add_argument('--remove-polyA', default=10, metavar="[INT]", type=int, choices=range(0, 35),
-                            help="Remove PolyA stretches of the given length from R2 (Use 0 to disable it) (default: %(default)s)")
-        parser.add_argument('--remove-polyT', default=10, metavar="[INT]", type=int, choices=range(0, 35),
-                            help="Remove PolyT stretches of the given length from R2 (Use 0 to disable it) (default: %(default)s)")
-        parser.add_argument('--remove-polyG', default=10, metavar="[INT]", type=int, choices=range(0, 35),
-                            help="Remove PolyG stretches of the given length from R2 (Use 0 to disable it) (default: %(default)s)")
-        parser.add_argument('--remove-polyC', default=10, metavar="[INT]", type=int, choices=range(0, 35),
-                            help="Remove PolyC stretches of the given length from R2 (Use 0 to disable it) (default: %(default)s)")
-        parser.add_argument('--remove-polyN', default=10, metavar="[INT]", type=int, choices=range(0, 35),
-                            help="Remove PolyN stretches of the given length from R2 (Use 0 to disable it) (default: %(default)s)")
-        parser.add_argument('--filter-AT-content', default=90, metavar="[INT%]", type=int, choices=range(0, 100),
-                            help="Discards reads whose number of A and T bases in total are more " \
-                            "or equal than the number given in percentage (default: %(default)s)")
-        parser.add_argument('--filter-GC-content', default=90, metavar="[INT%]", type=int, choices=range(0, 100),
-                            help="Discards reads whose number of G and C bases in total are more " \
-                            "or equal than the number given in percentage (default: %(default)s)")
-        parser.add_argument('--disable-multimap', action="store_true", default=False,
-                            help="If activated, multiple aligned reads obtained during mapping will be all discarded. " \
-                            "Otherwise the highest scored one will be kept")
-        parser.add_argument('--disable-clipping', action="store_true", default=False,
+        parser.add_argument('--keep-discarded-files',
+                            action="store_true",
+                            default=False,
+                            help='Keep files with discarded reads in every step')
+        parser.add_argument('--qual-64',
+                            action="store_true",
+                            default=False,
+                            help="Use phred-64 quality instead of phred-33(default) in the quality trimming step")
+        parser.add_argument('--min-length-qual-trimming',
+                            default=20,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(5, 151),
+                            help="Minimum length of the reads after trimming, "
+                                 "shorter reads will be discarded (default: %(default)s)")
+        parser.add_argument('--min-quality-trimming',
+                            default=20,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(1, 61),
+                            help="Minimum phred quality a base must have in order to be kept "
+                                 "in the quality trimming step (default: %(default)s)")
+        parser.add_argument('--remove-polyA',
+                            default=10,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 35),
+                            help="Remove PolyA stretches of the given length from R2 "
+                                 "(Use 0 to disable it) (default: %(default)s)")
+        parser.add_argument('--remove-polyT',
+                            default=10,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 35),
+                            help="Remove PolyT stretches of the given length from R2 "
+                                 "(Use 0 to disable it) (default: %(default)s)")
+        parser.add_argument('--remove-polyG',
+                            default=10,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 35),
+                            help="Remove PolyG stretches of the given length from R2 "
+                                 "(Use 0 to disable it) (default: %(default)s)")
+        parser.add_argument('--remove-polyC',
+                            default=10,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 35),
+                            help="Remove PolyC stretches of the given length from R2 "
+                                 "(Use 0 to disable it) (default: %(default)s)")
+        parser.add_argument('--remove-polyN',
+                            default=10,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 35),
+                            help="Remove PolyN stretches of the given length from R2 "
+                                 "(Use 0 to disable it) (default: %(default)s)")
+        parser.add_argument('--homopolymer-mismatches',
+                            default=0,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 9),
+                            help="Number of mismatches allowed when removing "
+                                 "homopolymers (A, T, G, C or N) (default: %(default)s)")
+        parser.add_argument('--filter-AT-content',
+                            default=90,
+                            metavar="[INT%]",
+                            type=int,
+                            choices=range(0, 101),
+                            help="Discards reads whose number of A and T bases in total are more "
+                                 "or equal than the percentage given as input (0-100) (default: %(default)s)")
+        parser.add_argument('--filter-GC-content',
+                            default=90,
+                            metavar="[INT%]",
+                            type=int,
+                            choices=range(0, 100),
+                            help="Discards reads whose number of G and C bases in total are more "
+                                 "or equal the percentage given as input (0-100) (default: %(default)s)")
+        parser.add_argument('--mapping-rv-trimming',
+                            default=0,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 51),
+                            help="Number of bases to trim in the reverse reads (R2) for "
+                                 "the mapping step (5' end) (default: %(default)s)")
+        parser.add_argument('--inverse-mapping-rv-trimming',
+                            default=0,
+                            type=int,
+                            metavar="[INT]",
+                            choices=range(0, 51),
+                            help="Number of bases to trim in the reverse reads (R2) for "
+                                 "the mapping step (3' end) (default: %(default)s)")
+        parser.add_argument('--disable-multimap',
+                            action="store_true",
+                            default=False,
+                            help="If activated, multiple aligned reads obtained during mapping will be all discarded. "
+                                 "Otherwise the highest scored one will be kept")
+        parser.add_argument('--disable-clipping',
+                            action="store_true",
+                            default=False,
                             help="If activated, disable soft-clipping (local alignment) in the mapping step")
-        parser.add_argument('--umi-cluster-algorithm', default="AdjacentBi", metavar="[STRING]", 
-                            type=str, choices=["naive", "hierarchical", "Adjacent", "AdjacentBi", "Affinity"],
-                            help="Type of clustering algorithm to use when performing UMIs duplicates removal.\n" \
-                            "Options = {naive, hierarchical(default), Affinity, Adjacent and AdjacentBi}\n"
-                            "Note that for the affinity method the umi allowed mismatches parameter will be ignored.")
-        parser.add_argument('--min-intron-size', default=1, metavar="[INT]", type=int, choices=range(1, 1000),
-                            help="Minimum allowed intron size when searching for splice variants with STAR\n" \
-                            "Splices alignments are disabled by default (=1) but to turn it on set this parameter\n" \
-                            "to a bigger number, for example 10 or 20. (default: %(default)s)")
-        parser.add_argument('--max-intron-size', default=1, metavar="[INT]", type=int, choices=range(1, 1000000),
-                            help="Maximum allowed intron size when searching for splice variants with STAR\n" \
-                            "Splices alignments are disabled by default (=1) but to turn it on set this parameter\n" \
-                            "to a big number, for example 10000 or 100000. (default: %(default)s)")
-        parser.add_argument('--umi-filter', action="store_true", default=False,
+        parser.add_argument('--min-intron-size',
+                            default=1,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(1, 1000),
+                            help="Minimum allowed intron size when searching for splice variants with STAR\n"
+                                 "Splices alignments are disabled by default (=1) but to turn it on set this parameter\n"
+                                 "to a bigger number, for example 10 or 20. (default: %(default)s)")
+        parser.add_argument('--max-intron-size',
+                            default=1,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(1, 1000000),
+                            help="Maximum allowed intron size when searching for splice variants with STAR\n"
+                                 "Splices alignments are disabled by default (=1) but to turn it on set this parameter\n"
+                                 "to a big number, for example 10000 or 100000. (default: %(default)s)")
+        parser.add_argument('--star-two-pass-mode',
+                            default=False,
+                            action="store_true",
+                            help="Activates the 2-pass mode in STAR to improve mapping accuracy")
+        parser.add_argument('--star-genome-loading',
+                            default="NoSharedMemory",
+                            metavar="[STRING]",
+                            type=str,
+                            choices=["NoSharedMemory", "LoadAndKeep", "LoadAndRemove", "LoadAndExit"],
+                            help="Similar to the STAR option --genomeLoad. It allows to load the genome index\n"
+                                 "into memory so it can easily be shared by other jobs to save loading time.\n"
+                                 "Read the STAR manual for more info on this. (default: %(default)s)")
+        parser.add_argument('--star-sort-mem-limit',
+                            default=0,
+                            type=int,
+                            help="The maximum available RAM for sorting BAM during mapping with STAR."
+                                 "\nDefault is 0 which means that it will be set to the genome index size")
+        parser.add_argument('--demultiplexing-mismatches',
+                            default=2,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 31),
+                            help="Number of allowed mismatches when demultiplexing the reads "
+                                 "against the barcodes with TaggD (default: %(default)s)")
+        parser.add_argument('--demultiplexing-kmer',
+                            default=6,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(1, 51),
+                            help="KMer size to use when demultiplexing against the "
+                                 "barcodes with TaggD (default: %(default)s)")
+        parser.add_argument('--demultiplexing-overhang',
+                            default=0,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 11),
+                            help="Extra flanking bases added on each side of the barcode when demultiplexing against "
+                                 "the barcodes with TaggD (default: %(default)s)")
+        parser.add_argument('--demultiplexing-start',
+                            default=0,
+                            metavar="[INT]",
+                            type=int,
+                            help="Start position of the IDs (Barcodes) in R1 (counting from 0) (default: %(default)s)")
+        parser.add_argument('--demultiplexing-metric',
+                            default="Subglobal",
+                            metavar="[STRING]",
+                            type=str,
+                            choices=["Subglobal", "Levenshtein", "Hamming"],
+                            help="Distance metric to use for TaggD demultiplexing:\n"
+                                 "Options:\n" \
+                                 "  Subglobal, Levenshtein or Hamming (default: Subglobal)")
+        parser.add_argument("--demultiplexing-multiple-hits-keep-one",
+                            default=False,
+                            action="store_true",
+                            help="When multiple ambiguous hits with same score are "
+                                 "found in the demultiplexing step, keep only one (random).")
+        parser.add_argument('--demultiplexing-trim-sequences',
+                            nargs='+',
+                            type=int,
+                            default=None,
+                            help="Trim the barcodes in the input file when doing demultiplexing.\n"
+                                 "The input given is a list of tuples: START END START END .. where\n"
+                                 "START is the integer position of the first base (0 based) and END is the integer\n"
+                                 "position of the last base (1 based).\n"
+                                 "The final barcode will be obtained by combining all the sequences given in the input.\n"
+                                 "This is useful when having a barcode composed of multiple sequences in the read"
+                                 "or when the barcode needs to be trimmed out.\n"
+                                 "Trimmng sequences can be given several times.")
+        parser.add_argument('--htseq-mode',
+                            default="intersection-nonempty",
+                            type=str,
+                            metavar="[STRING]",
+                            choices=["union", "intersection-nonempty", "intersection-strict"],
+                            help="Mode of annotation when using htseq-count. "
+                                 "Modes = {union, intersection-nonempty(default), intersection-strict}")
+        parser.add_argument('--htseq-no-ambiguous',
+                            action="store_true",
+                            default=False,
+                            help="When using htseq-count discard reads annotating ambiguous genes (default False)")
+        parser.add_argument('--strandness',
+                            default="yes",
+                            type=str,
+                            metavar="[STRING]",
+                            choices=["no", "yes", "reverse"],
+                            help="What strandness mode to use when annotating "
+                                 "with htseq-count [no, yes(default), reverse]")
+        parser.add_argument('--include-non-annotated',
+                            action="store_true",
+                            default=False,
+                            help="Do not discard un-annotated reads (they will be labeled __no_feature)")
+        parser.add_argument('--umi-cluster-algorithm',
+                            default="AdjacentBi",
+                            metavar="[STRING]",
+                            type=str,
+                            choices=["naive", "hierarchical", "Adjacent", "AdjacentBi", "Affinity"],
+                            help="Type of clustering algorithm to use when performing UMIs duplicates removal.\n"
+                                 "Options = {naive, hierarchical, Affinity, Adjacent and AdjacentBi(default)}\n"
+                                 "Note that for the affinity method the umi allowed mismatches parameter will be ignored.")
+        parser.add_argument('--umi-allowed-mismatches',
+                            default=1,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 9),
+                            help="Number of allowed mismatches (hamming distance) "
+                                 "that UMIs of the same gene-spot must have in order to "
+                                 "cluster together (default: %(default)s)")
+        parser.add_argument('--umi-start-position',
+                            default=18,
+                            metavar="[INT]",
+                            type=int,
+                            help="Position in R1 (base wise) of the first base of the "
+                                 "UMI (starting by 0) (default: %(default)s)")
+        parser.add_argument('--umi-end-position',
+                            default=27,
+                            metavar="[INT]",
+                            type=int,
+                            help="Position in R1 (base wise) of the last base of the "
+                                 "UMI (starting by 1) (default: %(default)s)")
+        parser.add_argument('--umi-filter',
+                            action="store_true",
+                            default=False,
                             help="Enables the UMI quality filter based on the template given in --umi-filter-template")
-        parser.add_argument('--umi-filter-template', default="WSNNWSNNV", type=str, metavar="[STRING]",
+        parser.add_argument('--umi-filter-template',
+                            default="WSNNWSNNV",
+                            type=str,
+                            metavar="[STRING]",
                             help="UMI template (IUPAC nucleotide code) for the UMI filter, default = WSNNWSNNV")
-        parser.add_argument('--compute-saturation', action="store_true", default=False,
-                            help="Performs a saturation curve computation by sub-sampling the annotated reads, computing " \
-                            "unique molecules and then a saturation curve (included in the log file)")
-        parser.add_argument("--saturation-points", default=None, nargs='+', type=int,
-                            help="Saturation points can be provided instead of using default values.\n" \
-                            "Provide separate values like this for example: 10000 20000 50000 100000")
-        parser.add_argument('--include-non-annotated', action="store_true", default=False,
-                            help="Do not discard un-annotated reads (they will be labeled __no_feature)")
-        parser.add_argument('--inverse-mapping-rv-trimming', default=0, type=int, metavar="[INT]", choices=range(0, 50),
-                            help="Number of bases to trim in the reverse reads for the mapping step on the 3' end")
-        parser.add_argument('--two-pass-mode', default=False, action="store_true",
-                            help="Activates the 2-pass mode in STAR to improve mapping accuracy")
-        parser.add_argument('--strandness', default="yes", type=str, metavar="[STRING]", choices=["no", "yes", "reverse"],
-                            help="What strandness mode to use when annotating with htseq-count [no, yes(default), reverse]")
-        parser.add_argument('--umi-quality-bases', default=6, metavar="[INT]", type=int, choices=range(0, 10),
+        parser.add_argument('--umi-quality-bases',
+                            default=6,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 13),
                             help="Maximum number of low quality bases allowed in an UMI (default: %(default)s)")
-        parser.add_argument('--umi-counting-offset', default=250, metavar="[INT]", type=int, choices=range(0, 1000),
-                            help="Expression count for each gene-spot combination is expressed " \
-                            "as the number of unique UMIs in each strand/start position. However " \
-                            "some reads might have slightly different start positions due to " \
-                            "amplification artifacts. This parameters allows to define an " \
-                            "offset window from where to count unique UMIs. You can set it to a very" \
-                            "high value +9999 to count unique UMIs for the whole gene (default: %(default)s)")
-        parser.add_argument('--demultiplexing-metric', default="Subglobal", metavar="[STRING]", type=str,
-                            help="Distance metric for TaggD demultiplexing: Subglobal, Levenshtein or Hamming (default: Subglobal)",
-                            choices=["Subglobal","Levenshtein","Hamming"])
-        parser.add_argument("--demultiplexing-multiple-hits-keep-one", default=False, action="store_true",
-                            help="When multiple ambiguous hits with same score are found in the demultiplexing, keep one (random)." )
-        parser.add_argument('--demultiplexing-trim-sequences', nargs='+', type=int, default=None, 
-                            help="Trims from the barcodes in the input file when doing demultiplexing.\n" \
-                            "The bases given in the list of tuples as START END START END .. where\n" \
-                            "START is the integer position of the first base (0 based) and END is the integer\n" \
-                            "position of the last base (1 based).\nTrimmng sequences can be given several times.")
-        parser.add_argument('--homopolymer-mismatches', default=0, metavar="[INT]", type=int, choices=range(0, 9),
-                            help="Number of mismatches allowed when removing homopolymers (default: %(default)s)")
-        parser.add_argument('--star-genome-loading', default="NoSharedMemory", metavar="[STRING]", type=str,
-                            help="Similar to the STAR option --genomeLoad. It allows to load the genome index\n"
-                            " into memory so it can easily be shared by other jobs so to save loading time.\n"
-                            " Read the STAR manual for more info on this. (default: NoSharedMemory)",
-                            choices=["NoSharedMemory","LoadAndKeep","LoadAndRemove", "LoadAndExit"])
-        parser.add_argument('--star-sort-mem-limit', default=0, type=int,
-                            help="The maximum available RAM for sorting BAM during mapping. Default is 0\n" \
-                            "which means that it will be set to the genome index size")
-        parser.add_argument("--disable-trimming", default=False, action="store_true",
-                            help="Use this flag if you want to skip the trimming step" )
-        parser.add_argument("--disable-mapping", default=False, action="store_true",
-                            help="Use this flag if you want to skip the mapping step" )
-        parser.add_argument("--disable-annotation", default=False, action="store_true",
-                            help="Use this flag if you want to skip the annotation" )
-        parser.add_argument("--disable-barcode", default=False, action="store_true",
-                            help="Use this flag if you want to skip the barcode demultiplexing step" )
-        parser.add_argument("--disable-umi", default=False, action="store_true",
-                            help="Use this flag if you want to skip the UMI filtering step" )
-        parser.add_argument("--transcriptome", default=False, action="store_true",
-                            help="Use a transcriptome instead of a genome, the gene tag will be obtained from the transcriptome file" )
+        parser.add_argument('--umi-counting-offset',
+                            default=250,
+                            metavar="[INT]",
+                            type=int,
+                            choices=range(0, 1001),
+                            help="UMI count for each gene-spot combination is computed "
+                                 "as the number of unique UMIs in each strand/start position. However "
+                                 "some reads might have slightly different start positions due to "
+                                 "amplification artifacts. This parameters allows to define an "
+                                 "offset window from where to count unique UMIs. You can set it to a very "
+                                 "high value +9999 to count unique UMIs for the whole gene (default: %(default)s)")
+        parser.add_argument('--compute-saturation',
+                            action="store_true",
+                            default=False,
+                            help="Performs a saturation curve computation by sub-sampling the annotated reads, computing "
+                                 "unique UMIs and adding the stats to the log file (this can be used to plot saturation curves)")
+        parser.add_argument("--saturation-points",
+                            default=None,
+                            nargs='+',
+                            type=int,
+                            help="Saturation points for the saturation curve computation can be "
+                                 "provided instead of using default values.\n"
+                                 "Provide a list of values like this for example: 10000 20000 50000 100000")
+        parser.add_argument("--disable-trimming",
+                            default=False,
+                            action="store_true",
+                            help="Use this flag if you want to skip the trimming step")
+        parser.add_argument("--disable-mapping",
+                            default=False,
+                            action="store_true",
+                            help="Use this flag if you want to skip the mapping step")
+        parser.add_argument("--disable-annotation",
+                            default=False,
+                            action="store_true",
+                            help="Use this flag if you want to skip the annotation")
+        parser.add_argument("--disable-barcode",
+                            default=False,
+                            action="store_true",
+                            help="Use this flag if you want to skip the barcode demultiplexing step")
+        parser.add_argument("--disable-umi",
+                            default=False,
+                            action="store_true",
+                            help="Use this flag if you want to skip the UMI filtering step")
+        parser.add_argument("--transcriptome",
+                            default=False,
+                            action="store_true",
+                            help="Use this flag if you want to use transcriptome instead of a genome, the gene tag will be "
+                                 "obtained from the transcriptome file")
         parser.add_argument('--version', action='version', version='%(prog)s ' + str(version_number))
         return parser
-         
+
     def load_parameters(self, options):
         """
         Load the input parameters from the argparse object given as parameter
         :param options: a Argparse object
         """
-        self.allowed_missed = options.allowed_missed
-        self.allowed_kmer = options.allowed_kmer
-        self.overhang = options.overhang
+        self.allowed_missed = options.demultiplexing_mismatches
+        self.allowed_kmer = options.demultiplexing_kmer
+        self.overhang = options.demultiplexing_overhang
         self.min_length_trimming = options.min_length_qual_trimming
         self.trimming_rv = options.mapping_rv_trimming
         self.min_quality_trimming = options.min_quality_trimming
         self.clean = options.no_clean_up
-        self.barcode_start = options.start_id
-        self.threads = options.mapping_threads
+        self.barcode_start = options.demultiplexing_start
+        self.threads = options.threads
         self.verbose = options.verbose
         self.ids = os.path.abspath(options.ids)
         if options.ref_map is not None:
@@ -481,17 +685,17 @@ def load_parameters(self, options):
         if options.contaminant_index is not None:
             self.contaminant_index = os.path.abspath(options.contaminant_index)
         # Load the given path into the system PATH
-        if options.bin_path is not None and os.path.isdir(options.bin_path): 
+        if options.bin_path is not None and os.path.isdir(options.bin_path):
             os.environ["PATH"] += os.pathsep + options.bin_path
         if options.log_file is not None:
-            self.logfile = os.path.abspath(options.log_file)  
+            self.logfile = os.path.abspath(options.log_file)
         self.fastq_fw = os.path.abspath(options.fastq_files[0])
         self.fastq_rv = os.path.abspath(options.fastq_files[1])
         if options.output_folder is not None and os.path.isdir(options.output_folder):
             self.output_folder = os.path.abspath(options.output_folder)
         else:
-            self.output_folder = os.path.abspath(os.getcwd())      
-        if options.temp_folder is not None and os.path.isdir(options.temp_folder): 
+            self.output_folder = os.path.abspath(os.getcwd())
+        if options.temp_folder is not None and os.path.isdir(options.temp_folder):
             self.temp_folder = os.path.abspath(options.temp_folder)
         else:
             self.temp_folder = tempfile.mkdtemp(prefix="st_pipeline_temp")
@@ -516,7 +720,7 @@ def load_parameters(self, options):
         self.compute_saturation = options.compute_saturation
         self.include_non_annotated = options.include_non_annotated
         self.inverse_trimming_rv = options.inverse_mapping_rv_trimming
-        self.two_pass_mode = options.two_pass_mode
+        self.two_pass_mode = options.star_two_pass_mode
         self.strandness = options.strandness
         self.umi_quality_bases = options.umi_quality_bases
         self.umi_counting_offset = options.umi_counting_offset
@@ -536,28 +740,28 @@ def load_parameters(self, options):
         if options.saturation_points is not None:
             self.saturation_points = [int(p) for p in options.saturation_points]
         # Assign class parameters to the QA stats object
-        attributes = inspect.getmembers(self, lambda a:not(inspect.isroutine(a)))
-        attributes_filtered = [a for a in attributes if not(a[0].startswith('__') and a[0].endswith('__'))]
+        attributes = inspect.getmembers(self, lambda a: not (inspect.isroutine(a)))
+        attributes_filtered = [a for a in attributes if not (a[0].startswith('__') and a[0].endswith('__'))]
         # Assign general parameters to the qa_stats object
         qa_stats.input_parameters = attributes_filtered
         qa_stats.annotation_tool = "htseq-count {}".format(getHTSeqCountVersion())
         qa_stats.demultiplex_tool = "Taggd {}".format(getTaggdCountVersion())
         qa_stats.pipeline_version = version_number
-        qa_stats.mapper_tool = getSTARVersion()    
-        
+        qa_stats.mapper_tool = getSTARVersion()
+
     def createLogger(self):
         """
         Creates a logging object and logs some information from the input parameters
-        """    
+        """
         # Create a logger
         if self.logfile is not None:
             logging.basicConfig(filename=self.logfile, level=logging.DEBUG)
         else:
             logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
-            
+
         self.logger = logging.getLogger(self.__class__.LogName)
         self.logger.info("ST Pipeline {}".format(version_number))
-        
+
         # Some info
         self.logger.info("Output directory: {}".format(self.output_folder))
         self.logger.info("Temporary directory: {}".format(self.temp_folder))
@@ -579,19 +783,22 @@ def createLogger(self):
             if self.taggd_multiple_hits_keep_one:
                 self.logger.info("TaggD multiple hits keep one (random) is enabled")
             if self.taggd_trim_sequences is not None:
-                self.logger.info("TaggD trimming from the barcodes " + '-'.join(str(x) for x in self.taggd_trim_sequences))
+                self.logger.info(
+                    "TaggD trimming from the barcodes " + '-'.join(str(x) for x in self.taggd_trim_sequences))
         if not self.disable_mapping:
             self.logger.info("Mapping reverse trimming: {}".format(self.trimming_rv))
             self.logger.info("Mapping inverse reverse trimming: {}".format(self.inverse_trimming_rv))
             self.logger.info("Mapping tool: STAR")
-            self.logger.info("Mapping minimum intron size allowed (splice alignments) with STAR: {}".format(self.min_intron_size))
-            self.logger.info("Mapping maximum intron size allowed (splice alignments) with STAR: {}".format(self.max_intron_size))
+            self.logger.info(
+                "Mapping minimum intron size allowed (splice alignments) with STAR: {}".format(self.min_intron_size))
+            self.logger.info(
+                "Mapping maximum intron size allowed (splice alignments) with STAR: {}".format(self.max_intron_size))
             self.logger.info("STAR genome loading strategy {}".format(self.star_genome_loading))
             if self.disable_clipping:
                 self.logger.info("Not allowing soft clipping when mapping with STAR")
             if self.disable_multimap:
                 self.logger.info("Not allowing multiple alignments when mapping with STAR")
-            if self.two_pass_mode :
+            if self.two_pass_mode:
                 self.logger.info("Using the STAR 2-pass mode for the mapping step")
         if not self.disable_annotation:
             self.logger.info("Annotation tool: HTSeq")
@@ -602,7 +809,8 @@ def createLogger(self):
         if self.compute_saturation:
             self.logger.info("Computing saturation curve with several sub-samples...")
             if self.saturation_points is not None:
-                self.logger.info("Using the following points {}".format(' '.join(str(p) for p in self.saturation_points)))
+                self.logger.info(
+                    "Using the following points {}".format(' '.join(str(p) for p in self.saturation_points)))
         if not self.disable_umi:
             self.logger.info("UMIs start position: {}".format(self.umi_start_position))
             self.logger.info("UMIs end position: {}".format(self.umi_end_position))
@@ -611,20 +819,26 @@ def createLogger(self):
             self.logger.info("Allowing an offset of {} when clustering UMIs " \
                              "by strand-start in a gene-spot".format(self.umi_counting_offset))
             self.logger.info("Allowing {} low quality bases in an UMI".format(self.umi_quality_bases))
-            self.logger.info("Discarding reads that after trimming are shorter than {}".format(self.min_length_trimming))
+            self.logger.info(
+                "Discarding reads that after trimming are shorter than {}".format(self.min_length_trimming))
             if self.umi_filter:
                 self.logger.info("UMIs using filter: {}".format(self.umi_filter_template))
         if not self.disable_trimming:
             if self.remove_polyA_distance > 0:
-                self.logger.info("Removing polyA sequences of a length of at least: {}".format(self.remove_polyA_distance))                        
+                self.logger.info(
+                    "Removing polyA sequences of a length of at least: {}".format(self.remove_polyA_distance))
             if self.remove_polyT_distance > 0:
-                self.logger.info("Removing polyT sequences of a length of at least: {}".format(self.remove_polyT_distance))
+                self.logger.info(
+                    "Removing polyT sequences of a length of at least: {}".format(self.remove_polyT_distance))
             if self.remove_polyG_distance > 0:
-                self.logger.info("Removing polyG sequences of a length of at least: {}".format(self.remove_polyG_distance))
+                self.logger.info(
+                    "Removing polyG sequences of a length of at least: {}".format(self.remove_polyG_distance))
             if self.remove_polyC_distance > 0:
-                self.logger.info("Removing polyC sequences of a length of at least: {}".format(self.remove_polyC_distance))
+                self.logger.info(
+                    "Removing polyC sequences of a length of at least: {}".format(self.remove_polyC_distance))
             if self.remove_polyN_distance > 0:
-                self.logger.info("Removing polyN sequences of a length of at least: {}".format(self.remove_polyN_distance))
+                self.logger.info(
+                    "Removing polyN sequences of a length of at least: {}".format(self.remove_polyN_distance))
             self.logger.info("Allowing {} mismatches when removing homopolymers".format(self.adaptor_missmatches))
             self.logger.info("Remove reads whose AT content is {}%".format(self.filter_AT_content))
             self.logger.info("Remove reads whose GC content is {}%".format(self.filter_GC_content))
@@ -642,13 +856,13 @@ def run(self):
                 FILENAMES[key] = os.path.join(self.temp_folder, value)
             for key, value in list(FILENAMES_DISCARDED.items()):
                 FILENAMES_DISCARDED[key] = os.path.join(self.temp_folder, value)
-                      
+
         # Get the starting time to compute total execution time
         globaltime = TimeStamper()
 
-        #=================================================================
+        # =================================================================
         # START PIPELINE
-        #=================================================================
+        # =================================================================
         start_exe_time = globaltime.getTimestamp()
         self.logger.info("Starting the pipeline: {}".format(start_exe_time))
 
@@ -657,26 +871,26 @@ def run(self):
         try:
             temp_r1_fifo_name = os.path.join(self.temp_folder, "R1_TMP_FIFO.fq")
             temp_r2_fifo_name = os.path.join(self.temp_folder, "R2_TMP_FIFO.fq")
-            
+
             if self.fastq_fw.endswith(".gz"):
                 r1_decompression_command = "gzip --decompress --stdout {} > {}".format(
-                                                                                       self.fastq_fw.replace(' ','\ '),
-                                                                                       temp_r1_fifo_name)
+                    self.fastq_fw.replace(' ', '\ '),
+                    temp_r1_fifo_name)
             elif self.fastq_fw.endswith(".bz2"):
                 r1_decompression_command = "bzip2 --decompress --stdout {} > {}".format(
-                                                                                        self.fastq_fw.replace(' ','\ '),
-                                                                                        temp_r1_fifo_name)
+                    self.fastq_fw.replace(' ', '\ '),
+                    temp_r1_fifo_name)
             else:
                 r1_decompression_command = None
-                
+
             if self.fastq_rv.endswith(".gz"):
                 r2_decompression_command = "gzip --decompress --stdout {} > {}".format(
-                                                                                       self.fastq_rv.replace(' ','\ '),
-                                                                                       temp_r2_fifo_name)
+                    self.fastq_rv.replace(' ', '\ '),
+                    temp_r2_fifo_name)
             elif self.fastq_rv.endswith(".bz2"):
                 r2_decompression_command = "bzip2 --decompress --stdout {} > {}".format(
-                                                                                        self.fastq_rv.replace(' ','\ '),
-                                                                                        temp_r2_fifo_name)
+                    self.fastq_rv.replace(' ', '\ '),
+                    temp_r2_fifo_name)
             else:
                 r2_decompression_command = None
 
@@ -684,7 +898,7 @@ def run(self):
                 os.mkfifo(temp_r1_fifo_name)
                 subprocess.Popen(r1_decompression_command, shell=True, preexec_fn=os.setsid)
                 self.fastq_fw = temp_r1_fifo_name
-            
+
             if r2_decompression_command:
                 os.mkfifo(temp_r2_fifo_name)
                 subprocess.Popen(r2_decompression_command, shell=True, preexec_fn=os.setsid)
@@ -692,13 +906,13 @@ def run(self):
 
         except Exception as e:
             self.logger.error("Error while starting the decompression of "
-            "GZIP/BZIP2 input files {0} {1}".format(self.fastq_fw, self.fastq_rv))
+                              "GZIP/BZIP2 input files {0} {1}".format(self.fastq_fw, self.fastq_rv))
             raise e
 
-        #=================================================================
+        # =================================================================
         # STEP: FILTERING 
         # Applies different filters : sanity, quality, short, adaptors, UMI...
-        #=================================================================
+        # =================================================================
         # Get the barcode length
         barcode_length = len(list(read_barcode_file(self.ids).values())[0].sequence)
         if not self.disable_trimming:
@@ -707,7 +921,8 @@ def run(self):
                 InputReadsFilter(self.fastq_fw,
                                  self.fastq_rv,
                                  FILENAMES["quality_trimmed_R2"],
-                                 FILENAMES_DISCARDED["quality_trimmed_discarded"] if self.keep_discarded_files else None,
+                                 FILENAMES_DISCARDED[
+                                     "quality_trimmed_discarded"] if self.keep_discarded_files else None,
                                  barcode_length,
                                  self.barcode_start,
                                  self.filter_AT_content,
@@ -731,16 +946,16 @@ def run(self):
                                  self.disable_barcode)
             except Exception:
                 raise
-        
+
             # After filtering is completed remove the temporary FIFOs
-            if is_fifo(temp_r1_fifo_name): 
+            if is_fifo(temp_r1_fifo_name):
                 os.remove(temp_r1_fifo_name)
-            if is_fifo(temp_r2_fifo_name): 
+            if is_fifo(temp_r2_fifo_name):
                 os.remove(temp_r2_fifo_name)
-        
-        #=================================================================
+
+        # =================================================================
         # CONDITIONAL STEP: Filter out contaminated reads, e.g. typically bacterial rRNA
-        #=================================================================
+        # =================================================================
         if self.contaminant_index:
             # To remove contaminants sequence we align the reads to the contaminant genome
             # and keep the un-mapped reads
@@ -750,20 +965,20 @@ def run(self):
                 alignReads(FILENAMES["quality_trimmed_R2"],
                            self.contaminant_index,
                            FILENAMES_DISCARDED["contaminated_discarded"],
-                           None, # Do not pass the annotation file in contaminant filter
+                           None,  # Do not pass the annotation file in contaminant filter
                            self.temp_folder,
                            self.trimming_rv,
                            self.inverse_trimming_rv,
                            self.threads,
-                           1, # Disable splice alignments in contaminant filter
-                           1, # Disable splice alignments in contaminant filter
-                           False, # Disable multimap in contaminant filter
-                           False, # Disable softclipping in contaminant filter
-                           False, # Disable 2-pass mode in contaminant filter
+                           1,  # Disable splice alignments in contaminant filter
+                           1,  # Disable splice alignments in contaminant filter
+                           False,  # Disable multimap in contaminant filter
+                           False,  # Disable softclipping in contaminant filter
+                           False,  # Disable 2-pass mode in contaminant filter
                            self.min_length_trimming,
-                           True, # Include un-aligned reads in the output     
+                           True,  # Include un-aligned reads in the output
                            self.star_genome_loading,
-                           self.star_sort_mem_limit) 
+                           self.star_sort_mem_limit)
                 # Extract the contaminant free reads (not aligned) from the output of STAR
                 # NOTE: this will not be needed when STAR allows to chose the discarded
                 # reads format (BAM)
@@ -793,10 +1008,10 @@ def run(self):
                 shutil.move(temp_name, FILENAMES_DISCARDED["contaminated_discarded"])
             except Exception:
                 raise
-             
-        #=================================================================
+
+        # =================================================================
         # STEP: Maps against the genome using STAR
-        #=================================================================
+        # =================================================================
         if not self.disable_mapping:
             self.logger.info("Starting genome alignment {}".format(globaltime.getTimestamp()))
             input_reads = FILENAMES["contaminated_clean"] if self.contaminant_index else FILENAMES["quality_trimmed_R2"]
@@ -818,7 +1033,7 @@ def run(self):
                            self.min_length_trimming,
                            self.keep_discarded_files,
                            self.star_genome_loading,
-                           self.star_sort_mem_limit)        
+                           self.star_sort_mem_limit)
                 # Remove secondary alignments and un-mapped
                 # NOTE: this will not be needed when STAR allows to chose the discarded
                 # reads format (BAM)
@@ -827,16 +1042,17 @@ def run(self):
                     # Note use 260 to also discard multiple-alignments
                     command = "samtools view -b -h -F 4 -@ {} -o {} -U {} {}".format(self.threads,
                                                                                      temp_name,
-                                                                                     FILENAMES_DISCARDED["mapped_discarded"],
+                                                                                     FILENAMES_DISCARDED[
+                                                                                         "mapped_discarded"],
                                                                                      FILENAMES["mapped"])
                     subprocess.check_call(command, shell=True)
-                    os.rename(temp_name, FILENAMES["mapped"])                
+                    os.rename(temp_name, FILENAMES["mapped"])
             except Exception:
                 raise
-                      
-        #=================================================================
+
+        # =================================================================
         # STEP: DEMULTIPLEX READS Map against the barcodes
-        #=================================================================
+        # =================================================================
         if not self.disable_barcode:
             self.logger.info("Starting barcode demultiplexing {}".format(globaltime.getTimestamp()))
             try:
@@ -849,22 +1065,23 @@ def run(self):
                                       self.taggd_multiple_hits_keep_one,
                                       self.taggd_trim_sequences,
                                       self.threads,
-                                      FILENAMES["demultiplexed_prefix"], # Prefix for output files
+                                      FILENAMES["demultiplexed_prefix"],  # Prefix for output files
                                       self.keep_discarded_files)
                 # TaggD does not output the BAM file sorted
                 command = "samtools sort -T {}/sort_bam -@ {} -o {} {}".format(self.temp_folder,
-                                                                            self.threads,
-                                                                            FILENAMES["demultiplexed_matched"],
-                                                                            FILENAMES["demultiplexed_matched"])
+                                                                               self.threads,
+                                                                               FILENAMES["demultiplexed_matched"],
+                                                                               FILENAMES["demultiplexed_matched"])
                 subprocess.check_call(command, shell=True)
             except Exception:
-                raise 
-        
-        #=================================================================
+                raise
+
+                # =================================================================
         # STEP: annotate using htseq-count or the transcriptome
-        #=================================================================
+        # =================================================================
         if not self.disable_annotation:
-            input_file = FILENAMES["demultiplexed_matched"] if FILENAMES["demultiplexed_matched"] else FILENAMES["mapped"]
+            input_file = FILENAMES["demultiplexed_matched"] if FILENAMES["demultiplexed_matched"] else FILENAMES[
+                "mapped"]
             if self.transcriptome:
                 self.logger.info("Assigning gene names from transcriptome {}".format(globaltime.getTimestamp()))
                 # Iterate the BAM file to set the gene name as the transcriptome's entry
@@ -873,7 +1090,7 @@ def run(self):
                 infile = pysam.AlignmentFile(input_file, flag_read)
                 outfile = pysam.AlignmentFile(FILENAMES["annotated"], flag_write, template=infile)
                 for rec in infile.fetch(until_eof=True):
-                    #NOTE chrom may have to be trimmed to 250 characters max
+                    # NOTE chrom may have to be trimmed to 250 characters max
                     chrom = infile.getrname(rec.reference_id).split()[0]
                     rec.set_tag("XF", chrom, "Z")
                     outfile.write(rec)
@@ -883,20 +1100,18 @@ def run(self):
                 self.logger.info("Starting annotation {}".format(globaltime.getTimestamp()))
                 try:
                     annotateReads(input_file,
-                                  self.ref_annotation, 
-                                  FILENAMES["annotated"], 
+                                  self.ref_annotation,
+                                  FILENAMES["annotated"],
                                   FILENAMES_DISCARDED["annotated_discarded"] if self.keep_discarded_files else None,
-                                  self.htseq_mode, self.strandness, 
-                                  self.htseq_no_ambiguous, 
-                                  self.include_non_annotated, 
-                                  self.temp_folder, 
-                                  self.threads)
+                                  self.htseq_mode, self.strandness,
+                                  self.htseq_no_ambiguous,
+                                  self.include_non_annotated)
                 except Exception:
                     raise
 
-        #=================================================================
+        # =================================================================
         # STEP: compute saturation (Optional)
-        #=================================================================
+        # =================================================================
         # To compute saturation points we need the number of annotated reads
         # the fastest way is to get that information from the stats object
         if self.compute_saturation and os.path.isfile(FILENAMES["annotated"]):
@@ -915,15 +1130,15 @@ def run(self):
                                   self.saturation_points)
             except Exception:
                 raise
-                
-        #=================================================================
+
+        # =================================================================
         # STEP: Create dataset and remove duplicates
-        #=================================================================
+        # =================================================================
         if os.path.isfile(FILENAMES["annotated"]):
             self.logger.info("Starting creating dataset {}".format(globaltime.getTimestamp()))
             try:
                 createDataset(FILENAMES["annotated"],
-                              qa_stats, # Passed as reference
+                              qa_stats,  # Passed as reference
                               self.ref_annotation,
                               self.umi_cluster_algorithm,
                               self.umi_allowed_mismatches,
@@ -931,18 +1146,18 @@ def run(self):
                               self.disable_umi,
                               self.output_folder,
                               self.expName,
-                              True) # Verbose
+                              True)  # Verbose
             except Exception:
                 raise
 
-        #=================================================================
+        # =================================================================
         # END PIPELINE
-        #=================================================================
+        # =================================================================
         # Write stats to JSON
         print(qa_stats)
         # TODO this is giving problems in Python3
-        #qa_stats.writeJSON(os.path.join(self.output_folder, self.expName + "_qa_stats.json"))
-        
+        # qa_stats.writeJSON(os.path.join(self.output_folder, self.expName + "_qa_stats.json"))
+
         finish_exe_time = globaltime.getTimestamp()
         total_exe_time = finish_exe_time - start_exe_time
         self.logger.info("Total Execution Time: {}".format(total_exe_time))
diff --git a/stpipeline/version.py b/stpipeline/version.py
index d663bac..59ec158 100644
--- a/stpipeline/version.py
+++ b/stpipeline/version.py
@@ -1,1 +1,1 @@
-version_number = "1.8.0"
+version_number = "1.8.1"


Test patch:
diff --git a/testrun.py b/testrun.py
index e1a68ce..88f48ae 100755
--- a/testrun.py
+++ b/testrun.py
@@ -2,7 +2,7 @@
 """ 
 Unit-test for run-tests, it just tests that the pipeline runs and produces correct results
 """
- 
+
 import unittest
 import urllib
 import tempfile
@@ -14,8 +14,9 @@
 import os
 from shutil import copyfile
 
+
 class TestPipeline(unittest.TestCase):
- 
+
     @classmethod
     def setUpClass(self):
         # Obtain paths and files.
@@ -25,7 +26,7 @@ def setUpClass(self):
         self.annotfile = os.path.join(testdir, 'config/annotations/Homo_sapiens.GRCh38.79_chr19.gtf')
         self.chipfile = os.path.join(testdir, 'config/idfiles/150204_arrayjet_1000L2_probes.txt')
         self.expname = "test"
-        
+
         # Obtain temp dir
         self.tmpdir = tempfile.mkdtemp(prefix="st_pipeline_test_temp")
         print("ST Pipeline Test Temporary directory {}".format(self.tmpdir))
@@ -34,61 +35,62 @@ def setUpClass(self):
         self.error_file = os.path.join(self.tmpdir, 'error.log')
         self.logFile = tempfile.mktemp(prefix="st_pipeline_test_log")
         print("ST Pipeline Test Log file {}".format(self.logFile))
-   
+
         # Create genome index dirs.
         self.genomedir = os.path.join(self.tmpdir, 'config/genomes/mouse_grcm38')
         os.makedirs(self.genomedir)
-   
+
         # STAR contaminant dir
         self.contamdir = os.path.join(self.tmpdir, 'config/contaminant_genomes/R45S5_R5S1')
         os.makedirs(self.contamdir)
-   
+
         genomefasta = os.path.join(self.genomedir, "human_grcm38_chromosome19.fasta")
         genomefastagz = os.path.join(self.genomedir, "human_grcm38_chromosome19.fasta.gz")
-          
+
         # Change dir to the temp folder
         os.chdir(self.tmpdir)
-          
+
         # Download and unpack fasta files
         try:
             print("ST Pipeline Test Downloading genome files...")
-            copyfile(os.path.join(testdir, "config/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz"), 
+            copyfile(os.path.join(testdir, "config/Homo_sapiens.GRCh38.dna.chromosome.19.fa.gz"),
                      genomefastagz)
             check_call(['gunzip', genomefastagz])
         except Exception as e:
             print(str(e))
             self.assertTrue(0, "Downloading genome files failed \n")
-   
+
         # Make genome indexes
         try:
             print("ST Pipeline Test Creating genome index...")
-            check_call(["STAR", 
+            check_call(["STAR",
                         "--runMode", "genomeGenerate",
                         "--genomeSAindexNbases", "11",
                         "--runThreadN", "4",
                         "--genomeDir", self.genomedir,
                         "--genomeFastaFiles", genomefasta])
-   
+
             print("ST Pipeline Test Creating contaminant genome index...")
             contamfasta = os.path.join(testdir, "config/contaminant_genomes/R45S5_R5S1/Rn45s_Rn5s.fasta")
-            check_call(["STAR", "--runMode", "genomeGenerate",
-                    "--genomeSAindexNbases", "8",
-                    "--runThreadN", "4",
-                    "--genomeDir", self.contamdir,
-                    "--genomeFastaFiles", contamfasta])
+            check_call(["STAR",
+                        "--runMode", "genomeGenerate",
+                        "--genomeSAindexNbases", "8",
+                        "--runThreadN", "4",
+                        "--genomeDir", self.contamdir,
+                        "--genomeFastaFiles", contamfasta])
         except Exception as e:
             print(str(e))
             self.assertTrue(0, "Creating genome index failed \n")
-                  
+
         # Verify existence of input files
-        assert(os.path.exists(self.infile_fw))
-        assert(os.path.exists(self.infile_rv))
-        assert(os.path.isdir(self.genomedir))
-        assert(os.path.isdir(self.contamdir))
-        assert(os.path.exists(self.annotfile))
-        assert(os.path.exists(self.chipfile))
-        assert(os.path.isdir(self.outdir))
-        assert(os.path.isdir(self.tmpdir))
+        assert (os.path.exists(self.infile_fw))
+        assert (os.path.exists(self.infile_rv))
+        assert (os.path.isdir(self.genomedir))
+        assert (os.path.isdir(self.contamdir))
+        assert (os.path.exists(self.annotfile))
+        assert (os.path.exists(self.chipfile))
+        assert (os.path.isdir(self.outdir))
+        assert (os.path.isdir(self.tmpdir))
 
     @classmethod
     def tearDownClass(self):
@@ -99,8 +101,8 @@ def tearDownClass(self):
             for name in dirs:
                 os.rmdir(os.path.join(root, name))
         if os.path.exists(self.outdir):
-            os.rmdir(self.outdir)  
-            
+            os.rmdir(self.outdir)
+
         print("ST Pipeline Test Remove temporary directory {}".format(self.tmpdir))
         for root, dirs, files in os.walk(self.tmpdir, topdown=False):
             for name in files:
@@ -108,9 +110,9 @@ def tearDownClass(self):
             for name in dirs:
                 os.rmdir(os.path.join(root, name))
         if os.path.exists(self.tmpdir):
-            os.rmdir(self.tmpdir) 
-            
-        # Remove STAR log files 
+            os.rmdir(self.tmpdir)
+
+            # Remove STAR log files
         log_std = "Log.std.out"
         log = "Log.out"
         log_sj = "SJ.out.tab"
@@ -125,8 +127,8 @@ def tearDownClass(self):
         if os.path.isfile(log_progress):
             os.remove(log_progress)
         if os.path.isfile(log_final):
-            os.remove(log_final)   
-      
+            os.remove(log_final)
+
     def test_run(self):
         # Run st_pipeline_run.py
         try:
@@ -134,10 +136,10 @@ def test_run(self):
             check_call(["st_pipeline_run.py",
                         "--verbose",
                         "--no-clean-up",
-                        "--two-pass-mode",
+                        "--star-two-pass-mode",
                         "--htseq-no-ambiguous",
                         "--keep-discarded-files",
-                        "--mapping-threads", "4",
+                        "--threads", "4",
                         "--log-file", self.logFile,
                         "--expName", self.expname,
                         "--ids", self.chipfile,
@@ -150,19 +152,19 @@ def test_run(self):
         except Exception as e:
             print(str(e))
             self.assertTrue(0, "Running st_pipeline_run.py failed \n")
-        
+
         # Verify existence of output files and temp files
         self.assertNotEqual(os.listdir(self.outdir), [], "Output folder is not empty")
         self.assertNotEqual(os.listdir(self.tmpdir), [], "Tmp folder is not empty")
         datafile = os.path.join(self.outdir, self.expname + "_stdata.tsv")
         readsfile = os.path.join(self.outdir, self.expname + "_reads.bed")
-        statsfile = os.path.join(self.outdir, self.expname + "_qa_stats.json")
+        # statsfile = os.path.join(self.outdir, self.expname + "_qa_stats.json")
         self.assertTrue(os.path.exists(datafile), "ST Data file exists")
         self.assertTrue(os.path.getsize(datafile) > 1024, "ST Data file is not empty")
         self.assertTrue(os.path.exists(readsfile), "ST Data BED file exists")
         self.assertTrue(os.path.getsize(readsfile) > 1024, "ST Data BED file is not empty")
-        #self.assertTrue(os.path.exists(statsfile), "Stats JSON file exists")
-            
+        # self.assertTrue(os.path.exists(statsfile), "Stats JSON file exists")
+
         # Run st_qa.py
         try:
             print("Running st_qa.py")
@@ -172,22 +174,21 @@ def test_run(self):
             self.assertTrue(0, "Running st_qa.py failed \n")
         # TODO verify all output files are present
         self.assertTrue(os.path.exists("{}_qa_stats.txt".format(
-            os.path.basename(datafile).split(".")[0])), 
-                        "Output of st_qa.py file exists")
-        
+            os.path.basename(datafile).split(".")[0])),
+            "Output of st_qa.py file exists")
+
         # Run convertEnsemblToNames.py
         try:
             print("Running convertEnsemblToNames.py")
             check_call(["convertEnsemblToNames.py",
-                        "--annotation", self.annotfile, 
+                        "--annotation", self.annotfile,
                         datafile])
         except Exception as e:
             print(str(e))
             self.assertTrue(0, "Running convertEnsemblToNames.py failed \n")
-        self.assertTrue(os.path.exists("output.tsv"), 
+        self.assertTrue(os.path.exists("output.tsv"),
                         "Output of convertEnsemblToNames.py file exists")
-        
-        
+
         # Run filter_gene_type_matrix.py
         try:
             print("Running filter_gene_type_matrix.py")
@@ -199,10 +200,9 @@ def test_run(self):
         except Exception as e:
             print(str(e))
             self.assertTrue(0, "Running filter_gene_type_matrix.py failed \n")
-        self.assertTrue(os.path.exists("output2.tsv"), 
+        self.assertTrue(os.path.exists("output2.tsv"),
                         "Output of filter_gene_type_matrix.py file exists")
 
-        
         # TODO complete run tests for adjust_matrix_coordinates.py, merge_fastq.py and multi_qa.py
         try:
             print("Running adjust_matrix_coordinates.py")
@@ -210,20 +210,21 @@ def test_run(self):
         except Exception as e:
             print(str(e))
             self.assertTrue(0, "Running adjust_matrix_coordinates.py failed \n")
-            
+
         try:
             print("Running merge_fastq.py")
             check_call(["merge_fastq.py", "--help"])
         except Exception as e:
             print(str(e))
             self.assertTrue(0, "Running merge_fastq.py failed \n")
-            
+
         try:
             print("Running multi_qa.py")
             check_call(["multi_qa.py", "--help"])
         except Exception as e:
             print(str(e))
             self.assertTrue(0, "Running multi_qa.py failed \n")
-        
+
+
 if __name__ == '__main__':
     unittest.main()