Merge branch 'master' into pipeline
Merge pull request #4 from daisieh/pipeline

Pipeline works!
Merge pull request #5 from daisieh/master

Added a lot more hooks to catch problematic files in the prepare_files script.
Merge pull request #6 from daisieh/master

More tests.
Merge pull request #9 from daisieh/master

Checking to see if the fastq file is malformed.
Merge pull request #10 from daisieh/master

Un-piping things to see if that relieves the tmp device
Merge pull request #11 from daisieh/master

added sort -T flag to do the sort in our working directory.
Merge pull request #12 from daisieh/master

test script is ready to roll.
Merge pull request #13 from daisieh/master

forgot this guy.
Update README.md
Merge pull request #16 from daisieh/master

Fixes #15.
Merge pull request #18 from daisieh/master

Fixes #14.
Create 0.5-splitseq.pl
Update 0.5-splitseq.pl

this will split one sequence into three sequences. One full seq one with the first 100 bp and one with the last 100 bp.
Merge branch 'pr/20'

Conflicts:
	README.md
move 0.5-splitseq.pl to old_code
Merge branch 'juliema'
Merge branch 'master' into check_for_ends