basic tests for fastqs2fast[a|qs].py
added recipe for stripping bam files
added notebook recipes
pep8 refactoring
bam2bam tests
Merge branch 'Scrum-apr-14' of ssh://github.com/CGATOxford/cgat into Scrum-apr-14
fixed path in CGATRecipes.rst
added Mikes changes to styleguide
Merge branch 'Scrum-apr-14' of ssh://github.com/CGATOxford/cgat into Scrum-apr-14
Added tests for gtf2gff.py. Altered cgat_script_template.py to reflect new documentation format
Merge branch 'Scrum-apr-14' of ssh://github.com/CGATOxford/cgat into Scrum-apr-14
Kath changes to fastq2fastq.py unit tests and changes to bam2fastq.py documentation
Merge branch 'Scrum-apr-14' of ssh://github.com/CGATOxford/cgat into Scrum-apr-14
bam2bed.py original test files
Merge branch 'Scrum-apr-14' of ssh://github.com/CGATOxford/cgat into Scrum-apr-14
Added new tests for index_fasta.py. Translators still untested
Various minor fixes to index_fasta, mostly pointing the main script to IndexFasta rather than internal functions
Merge branch 'index_fasta_fixes' into ian_tests
Removed extranous file
Merge branch 'index_fasta_fixes' into Scrum-apr-14