Handle GATK BAM preparation with recalibration on genome regions without aligned reads
Improve documentation on difference between hybrid_regions and variant_regions
More robust naming of ID and SM read group information to avoid downstream conflicts. Add upstream checks at configuration read time to identify issues. Move naming and preparation checking to single location. Thanks to Zhengqiu Cai for problem report
Reduce default for number of split regions until IPython file handle issue is resolved
Work around VarScan issue where it failes to generate a VCF header on regions that start with zero coverage. Thanks to @brentp for problem report
Avoid installation problem with ipython and git submodules by using editable flag. Fixes #23
Explicitly clean up ZeroMQ logging handlers used in IPython tasks, avoiding leaving open TCP connections. Fixes issues with large job numbers so revert regional splitting back to previous defaults
Initial framework for creating sample configuration files from input BAM files and template files. Work towards #22
Cleanup of metrics preparation. Handle cases without merging of BAM prepped files. Do not do in-metrics de-duplication and use pysam to count duplicates. Use variant_regions for hybrid selection metrics if explicit bait/targets not specified
Finalize initial attempt at providing a template to multi-sample configuration bridge (#22). Fix GitHub retrieval, add fastq pairing, clean up input options and provide documentation.
Ensure closing of local file handles when setting up nested local loggers
Quiet variant filtration warnings on missing filter attributes since these fill up logs and make debugging difficult
Document the method for identifying Galaxy location files for finding genome indexes (#24).
allow fastq.gz and *.gz files in template creation.
adjust pairing to handle _R1, R2 file names. strip _R from description.
set aligner to false when using bams as input.
Merge pull request #25 from brentp/sample-config

WIP: allow fastq.gz and *.gz files in template creation.
Revert change to set aligner false for BAM files since BAM is commonly used to re-alignment from Illumina inputs
Provide template command to more easily prepare a local configuration template for customization. #22
Preserve YAML comments when downloading templates for local project preparation. Supplements #26