make FilterSamReads work in scenarios that create empty output files. start converting some samtools calls to pysam.
separate out tool installation tests before normal tests in Travis
revert samtools Tool wrapper to subprocess.call instead of pysam until we can fix Travis+pysam+nose
bugfix prinseq and make rmdup mvicuna work on bams with empty read groups
some more trinity thoughts, commented out for now [ci skip]
set get path for prinseq
add some logging [ci skip]
tune pipeline parameters and start consolidating some of the depletion pipe
consolidate hs_deplete steps [ci skip]
update reports and stats to be per seq run [ci skip]
argparse fixes for deplete_human
fix var
Merge remote-tracking branch 'origin/master' into dp-indels
Merge pull request #55 from broadinstitute/dp-indels

updates to pipeline structure