Update platypus and lock on stable version. Update samblaster
Update Platypus to patched 0.7.9.2 release
Merge pull request #12 from lpantano/master

add recipe for pindel
Update pindel build to use lightweight tag from @liangkaiye (fixes genome/pindel#4) and explicitly use samtools 0.1.19 for build. #12
Update gatk-framework to 3.2-4 with support for SomaticPindelFilter
Clean up pindel recipe to avoid using local LDFLAGS and included samtools 1.0 libraries in build. Avoid delay in build by creating Makefile.local
Build target for bcbio.variation.recall v0.0.1
Update STAR to 2.4.0.c.
Pull latest VarDict...

with bug fixes to amplicon calling
Update bcbio.variation.recall to v0.0.2
Update vardict.rb
Update vcflib and vt to latest development versions from GitHub
Swap vt to use tarball download instead of git clone to avoid build error on recent update. Thanks to Moshe Einhorn
Update vt to include htslib with fixes for large numbers of contigs. chapmanb/bcbio-nextgen#639
Update cramtools SHA1 hash.
Update to 2.4.0d.

This addresses chapmanb/bcbio-nextgen#625.
The issue seemed to be spaces in the read names:

https://groups.google.com/forum/#!topic/rna-star/mlcu7j4bocI
Update SNAP aligner to latest beta release to avoid compile errors with newest development version. Thanks to Severine Catreux
Build target for WHAM 1.0 release
THetA2: initial install recipe. Estimates tumor heterogeneity
WHAM 1.1.0: ensure bamtools properly linked when not found in library path. Fixes #13