These are commits before pull from github.
Merge branch 'osu' of github.com:sgivan/RNA-Seq-Toolkit into osu

Conflicts:
	bin/RNAseq_process_data.sh
Commented --segment-mismatches lines.
Added error and output files in bsub invocation
Modified adapter_trim.pl to trim lowercase nucleotides.
Added option to leave temporary files in place.
When using --printall, sequences must be greater than a user-specified minimum length.
Add line to use gnu parallel sort and /scratch as a temporary directory on IRCF BioCluster.
Added -tempdir and -sort options.
Refactored to faciliate receiving input as a piped stream.
Added -q option to no generate as much output on STDOUT.
Added --nofilter option.
Added --quiet option to not generate output to STDOUT.
Added shell script to count mapped reads in a SAM file.
Added -J | --ignore_single_exons to RNAseq_process_data.sh.
Use -J option in test scripts.
There was a call to cufflinks that wasn't outputting STDOUT to a log file.
Add -J option to cmd script in remaining test directories.
Updated test_result scripts to reflect recent changes.