Added support for gzipped .gsnap file
:if file name ends with '.gz', it thinks the file is compressed
Added configuration for bwa index
Source clean up for rsq2expr pipeline
Source clean-up for rsq2mut pipeline
Source clean-up for pipeline xsq2mut
Source clean-up for pipeline rsq2fusion
Removed 1st (mapping) step from pipeline (rsq2mut pipeline produces both .bam & .gsnap)
Source clean-up for pipeline rsq2skip.
Accepts gzipped .gsnap file as input.
Source clean-up for pipeline rsq2eiJunc.
Accepts gzipped .gsnap as input.
cmd change for new sample.
New utility to copy pipeline output.