updated to latest version of snap; removed p_unique
clean up pipeline of bam file creation
fix bam file names
fix parsing of contig name from bam-read output
fix parsing of contig name from express output
fix read count parsing for new version of snap
set nullprior to 0.7 for bam-read
Merge branch 'master' of github.com:cboursnell/transrate into cboursnell-master

Conflicts:
	deps/deps.yaml
Merge branch 'cboursnell-master'