Ensure merging of overlapping intervals from variant_regions input for cn.mops. Thanks to @mjafin
use the name in the yaml file in the final files
remove space
Merge pull request #589 from lpantano/upstream

use the name than in the yaml file for the final files of qsignature
Platypus variant calling: more lenient filters to improve sensitivity relative to GATK/FreeBayes/samtools. Do streaming post-processing of output
Support samtools-driven joint calling. Fix checks for using bcbio-variation-recall to ensure resources used in calculating requirements
Avoid race conditions when preparing tabix indexed files during initial BED prep steps. Thanks to @mjafin
Bring unit tests up to date with latest changes to trimming and transactions. Fixes #590. Fixes #591
v0.8.2 release
Provide improved sensitivity for Platypus calling by removing allele bias, qual by depth and mapping quality filters. These remove a number of true positives in NA12878 evaluations
Avoid race conditions during bedprep work on samples with shared input BED files. Fixes #595
Update testing.rst

Updated the RNASeq example for a typo
Merge pull request #599 from pfaucon/patch-1

Update testing.rst