index_ref function needed bwa_path argument as well
sai_to_bam now with ability to specify samtools path as well as better error handling and output
Forgot to remove debug statement and added completed message at end
Check to see if samtools path is set and if samtools is available
Whatever
Merge remote branch 'temp/dev'
ignore env directory if iexists
This is why you should write tests for everything. Instead manual checking it is
Starting tests for install module. Only tests which function at this time
Trying to track down a bug with bwa index not actually running
Hopefully fixing a nasty bug with is_indexed where it would say a reference was indexed when it actually was not
hack for missing .git directory and version stuff
changing to setuptools
Merge branch 'dev'
Readme