Merge pull request #586 from kern3020/master

doc change wrt rna-seq.
Support Psuedomonas genome build
Decoupled scalpel from mutect and enabled pairing via indelcaller argument
Merge branch 'master' into decouple_mutect
Merge pull request #587 from mjafin/decouple_mutect

Decouple mutect
Generalize indelcaller addition to enable usage from other callers. #587
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
remove chanjo from list