Avoid calculating hybrid metrics unless project specifically identified as exome. Avoids out of memory errors on CalculateHsMetrics when used with large intervals
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Only calculate hybrid metrics on exome samples, since regional can also refer to large problematic blocks for CalculateHsMetrics
Added do.run logging instead of bare subprocess/sh calls.
Handle ipython installation outside of standard requirements.txt to avoid issues with current ipython build process
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Allow processing of inputs without preparation or variantcalling. More cleanly regular errors we're seeing from HsMetrics calculation
Pass all of names to aligners, not just the rg.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Added RNA-SeQC to the final output metrics for RNA-seq.
Allow samples crossing multiple lanes in RNA-seq pipeline.
Handle custom JVM options properly for RNA-SeQC.
Provide explicit skipping of regional bam preparation for inputs that do not need variant calling or preparation
Add snpeff reference genome for mm10
Provide flexible memory adjustment for GATK runs during initial alignment post-processing steps: maximize memory usage for multicore processes and avoid memory issues for highly parallel work
Enable logging for multiprocessing/future processing running within ipython environments: create process local references to ZeroMQ logger. Move to concurrent.future for multiprocessing to improve error messages for debugging.
Avoid picking up tarballs located in snpeff data directory. Fixes #38. Clean up logging test code for multiprocessing inside ipython
Document workaround for Git when git protocol is blocked or behind proxy. Thanks to James Cuff
Small plink to VCF cleanups: handle file inputs with alternative characters and more intuitive output files
Use joblib for multicore parallelization instead of custom multiprocessing/concurrent.futures implementation. Work on #37