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.
Look up rRNA in GTF file instead of using BWA and mapping

This was not functional, it always returned NA. This method
should work for the genome files we support so there is no need
to do anything more complicated.
Bump canFam3 resource to use new dbSNP
Documentation: update todo list with latest work. Add suggestion for recent gcc to intall docs (chapmanb/homebrew-cbl#9). Improve VM instructions for MacOSX, thanks to Glen Otero
Support CRAM files as input to pipeline, including retrieval of sub-regions based on variant_region input. Uses new CRAM region support in biobambam (gt1/biobambam#36)
Baseline support for SNAP aligner for testing purposes. Does not yet include automatic index creation as part of integration.
Ensure memory specification modifier is uppercase to be compatible with sambamba. Tries to introduce forward compatibility for any swaps from samtools to sambamba. Fixes #425
Ensure input CRAM files have indexes, splitting indexing from compression and using scramble C indexing implementation
Fixes for FreeBayes filtering AF extraction and sample selection test to support latest bcftools release candidate