fixing read metric and tests
new fastq files and analyse_read_mappings
turns out you need the header on the sam file for express
line length
scan through sam header
check the end of file hasn't already been reached
default number of pairs shouldn't be hardcoded
remove debugging prints
Merge branch 'master' of github.com:cboursnell/transrate into cboursnell-master

Conflicts:
	lib/transrate/bowtie2.rb
	test/left.fastq
	test/right.fastq
	test/test_read_metrics.rb
strip spaces from wc output for cross-platform compatibility
git push origin master
Merge branch 'cboursnell-master'