vagrant test machines
updated to latest version of snap; removed p_unique
clean up pipeline of bam file creation
Added Gitter badge
Merge pull request #105 from gitter-badger/gitter-badge

Add a Gitter chat badge to README.md
Update README.md
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
test express data loading
Merge branch 'master' of github.com:cboursnell/transrate into cboursnell-master

Conflicts:
	deps/deps.yaml
Merge branch 'cboursnell-master'
fixed possible bug in fasta defline parsing
contigs require more than 1 fragment mapped to get a p_good > 0
express results now parsed when transrate rerun
latest version of snap (dev61) and bumped alpha to 10
variable name typo
fixed deps for change in bam-read repo name