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
Use zip_safe=False to keep the installation unzipped for easier
debugging. Fixes issue #41.
Some PEP8 fixes
Merge pull request #42 from cswegger/setup_no_zip

Set installation as zip_safe=False
Document code internals with tips for plugging in new aligners and variant callers. #43
Do not remove duplicates as part of duplication marking during variant pipeline. Fixes #35
Avoid automatic sleep when setting up logging, only needed when creating directory. Attempt to work on causes for #37
Additional IPython logging, including moving IPython logs inside standard project directory for easier diagnosis of cluster related errors
Generalize passing associated files to specific variant callers. Allows usage of configured files beyond only DbSNP
Correctly catch CmdNotFound errors when retrieving gemini information from configuration. Thanks to @tanglingfung. Fixes #45