Halfway through refactoring to jip pipeline
Pipeline refactorings
Updated the pipeline to support cleanup
jip refactorings
Pipeline cleanup
New Jip job names
Fixed minor things on the pipeline
More cleanup and refactored teh execution
All the pipeline stuff
Fixed log file issue
Pipeline update
Fixed exon overlap option type
fixed annotation filtering
Removed some unused paramters from the split mapper
Parameterized the rna seq pipeline
VS pipeline
Added API for TAG annotation with SAM flags
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into develop
Bug fix in stats_merge + initial bisulfite code
Ensure map/alignment attributes are initialized and tag strings are not
static