Improvements to java memory usage for VarScan and MuTect to help scale tumor/normal variant calling
Added proper readgroup information in bowtie2 alignment.
Closes #552.
Added @matted to the contributor list.
Actually add Matt to the contributor list.
Edge case fixes for somatic variant calling: FreeBayes somatic correction restarts when partially finished and scalpel region preparation from tuples
Add dependencies for cnvkit installation and provide target to only update conda deps
Initial work on CNVkit integration -- support for testing single sample calls (cc @etal)
Update speedseq lumpy calling to match command line arguments in latest version
Do not require cutadapt on PATH and use the command relative to Python installation. Fixes #561