fixed typo
Removed BadCigar filter from mutect as it's no longer present in the latest revision from Appistry
Enable export of results in binned CRAM format for space storage on large projects. Provide generalized approach for setting default argument parameters in pipeline.run_info
Merge pull request #418 from mjafin/master

Removed BadCigar filter from mutect as it's no longer present in the lat...
Provide 'tools_off' algorithm parameter to turn off processing components. Add support for avoiding gemini database creation. Fixes #401
fixed typo
picard metric definitions moved
one sentence
Merge branch 'master' of https://github.com/kern3020/bcbio-nextgen
Add the commands run to the upload directory.
Lumpy post filtering: split into sample and filter by evidence and read counts. Enable removal of low complexity regions from analysis. Add toolz dependency for better functional programming. Clean up upload of log files
Provide full set of samples as background for cn.mops calculation. Improves estimation and avoids missing copy number changes specific to a family
Merge pull request #419 from kern3020/master

small fixes for docs
Parallelize delly and cn.mops by chromosome over multiple cores. Use variant regions to provide exclude regions for delly and lumpy calling. Integrates low complexity regions if configured
Provide resiliency to Galaxy API errors when uploading bcbio-nextgen results
Avoid adding *-orig files when merging from subparts instead of incorporating new file name
Fix split/recombine variant calling with BAM post-alignment preparation steps. Correctly pass multiple regional BAMs. Generally clean up process to use align BAMs and multiple keys instead of re-using work_bam. Thanks to Severine Catreux
Initial work to support CRAM input to pipelines. Not yet finished
Futher fixes for parallelizing by regions with post-alignment BAM preparation: handle single samples correctly and correctly handle special cases in structural variant calling and upload. Thanks to Severine Catreux
Return proper name of rRNA interval list file.