Handle calculation of excessive coverage regions when none found in input. Provide ploidy estimates when no metadata present in configuration
Initial framework to support cn.mops CNV calling
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Subset analysis regions by chromosomal section, ensuring that internal regions truncate at the end of the overall chrom/start/end section. Replaces custom code with pybedtools for intersections
Initial support for CNV calling with cn.mops. Needs additional testing since requires datasets with multiple samples