Document supported inputs (single BAM and single or paired fastq). Raise useful error messages for input configurations with other file specifications. #209
Update contributors to add Miika, Jakub and Paul. Thank you
Update get_paired_bams to return a namedtuple if the analysis is paired, and None if there is missing metadata
Rename is_sample_pair to is_sample_analysis
Added strand-specific RNA sequencing support.
Added strandedness documentation.
Skip reconstituting the index file if it already exists.
Added Cufflinks support.
Updated with note about Cufflinks.
Swapped htseq-count flag to match the Tophat strandedness flag.
Use sambamba for downsampling instead of GATK. Avoids memory ussage problems and issues with RNA-seq reads, plus mulithreaded
Added example settings of the strandedness flag.
Switch to simple sed approach for illumina to sanger quality conversion for fastq. fastx_toolkit approach does not appear to work. (again) fixes #190
Documentation clarifications on depth, reference genomes and no alignment templates. Thanks to Severine Catreux
Added minimal requirements checking.

Extra metadata on the multicore/ipythontask functions
under {"resources": {"ensure": "prog": fn}} can specify
a function which takes cores_per_job and memory_per_core
as arguments and sets them to the minimal requirements
for that tool if they do not meet them.

Fixes a bug with not allocating enough memory to
Tophat.
Removed deprecated total_memory block.
Update with Tophat memory fix.
Link to Mt Sinai scaling slides
Update to human dbSNP 138 available in latest Broad GATK bundle
Add support for Freebayes paired tumor/normal variant calling

Currently untested and not plugged into the main pipeline yet