Initial commit
Now paralellizes individual steps of the pipeline.
Fixed NAs on gene list
Fixed chromosome numbering
Fixed indel calling bug
Added pipeline_multisample.py implementing GATK multisample variant calling pipeline
Bugfixing
Fixed not reporting zero coverage exons
Fixed bug when there is only one gene in the region
Report coverage when given a list of genes
Fixes and fixes
bugfixes
post-pipeline cleanup task
missing one file to cleanup
Cleanups
Fixed help text
Fixed docs
Changed error throwing slightly
Various fixes
Merge branch 'master' of github.com:fsroque/NGS-pipeline