documentation for bam_vs_bed.py
Documentation for bam2bed
added test_commandline.py
pep8 changes
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10
Documentation for bam_vs_bed and bam_vs_gtf
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10
bam2fastq documentation
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10
added cgat_get_options.py and changed some scripts to permit parsing
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10
Documentation fixed for bed2bed
improve documentation for fastq2fastq #issue35
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-20140-10
style guide update for script options;
improve docs for fastq2fastq.py
Update documentation for bam2bam and bam_vs_gtf
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10
Documentation for diff_gtf
Merge branch 'Scrum-2014-10' of ssh://github.com/CGATOxford/cgat into Scrum-2014-10