attempted faster coverage calculation
Merge branch 'master' of github.com:Blahah/transrate
smaller test dataset with uncovered bases
Merge branch 'master' of github.com:cboursnell/transrate into cboursnell-master

Conflicts:
	test/test_read_metrics.rb
Merge branch 'cboursnell-master'
remove old classes no longer used
don't require removed classes
allow 100 byte delta in bowtie test sam filesize
remove accidentally added file
new chimera detection algorithm