Be more agressive with system memory usage: detect total system memory instead of available and calculate fraction amounts instead of rounding to integer. Goal is to maximize memory usage in complement with previous Java memory fixes
Fix FreeBayes tumor/normal calling for MNPs. Split out MNPs prior to applying vcfsamplediff evaluation and somatic calling, otherwise VT tags do not get passed to split items and all will be filtered. Improve filtering and qualities based on FreeBayes mailing list discussion
Fix for VarDict output in regions with non-N ambiguous bases. Convert them to Ns with awk so GATK is happy
Platypus variant calling fixes: Ensure we only call in regions of interest, remove non-N ambiguous bases, decompose MNPs to allelic primitives
Remove old attempts to manage memory issues by catching re-trying. It never especially helped and new fixes actually resolve the underlying issue
Platypus variant calling: fix inputs for multisample BAMs and enable local assembly
Fall back to bcftools concat instead of GATK CombineVariants if GATK CatVariants complains about input due to VCF validity. Fixes #556. Also fixes incorrect trim reads indent, thanks to @mjafin
gzip fastq files before processing.

If FASTQ files are uncompressed, zip them first. Also recognize
.txt as a fastq file, since that is a commonly used extension.
Ensure sambamba sort during STAR alignment uses correct temporary directory. Thanks to @mjafin
Additional fixes for concatenating problem VCF files: handle VCFs with overlapping variants and correctly return full file when half finished GATK CatVariants processing is created. #556
Ensure VarScan removes duplicate alternative alleles #571. Adjustments to awk ambiguous removal script to avoid substitutions in comment regions (thanks to @mjafin)
Add documentation on curses requirement for samtools. Thanks to @sveint #558
Skip matplotlibrc updates if we lack sufficient permissions. Fixes #574
Additional CNVkit integration work: generalize single sample calls and begin work on tumor/normal calling
Merge remote-tracking branch 'upstream/master' into dev
add import for codecs