fixed typo
Removed BadCigar filter from mutect as it's no longer present in the latest revision from Appistry
Added oncofuse update to changelog.
Discard reads trimmed with AlienTrimmer that are < 20 bases.
Give AlienTrimmer full length adapters to trim.

AlienTrimmer uses a kmer matching algorithm so it needs the full
length adapters to match the entire sequence and not just get the
ends. This should resolve some incomplete adapter removal issues.
Fix for missing oncofuse file.
Ensure discordant and split read BAMs are passed through pipeline for output and storage to enable later structural variation calling
Updates to support bcbio-nextgen in Docker: ensure nested regions are turned into tuples and bump conda package
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