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
Provide per-sample metadata as part of variant calling. Enables identification of specific samples within batches for cancer tumor/normal calling. #40. Fixes #43
Support for GATK 2.6: remove recalibrator plotting command which is now covered in a separate walker
Improved reworking of configuration parameters to multi-sample calling: pass in entire configuration object for each sample to allow retrieval by name or metadata. #40
Pass full data dictionaries for multiple samples to implemented variantcallers to allow for customization. #40
Re-add the muTect file (messy history)
Add support for MuTect in the BroadRunner, and change from_config to
also use the name of the program (defaults to "gatk" for backwards
compatibility)
Adapt the MuTect support to the newest changes in bcbio-nextgen
Add MutTect to the available callers