gatk-3.8

Author	SHA1	Message	Date
Matt Hanna	41d70abe4e	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
Mauricio Carneiro	e89ff063fc	GATKSAMRecord refactor The GATK engine will now provide a GATKSAMRecord to all tools which incorporates the functionality used by the GATK to the bam file (ReadGroups, Reduced Reads, ...). * No tools should create SAMRecord anymore, use GATKSAMRecord instead *	2011-11-03 15:43:26 -04:00
Christopher Hartl	5d706c9e92	Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable Removing PSP and CSM Conflicts: public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java public/java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java	2011-07-19 20:25:33 -04:00
Christopher Hartl	92c7cfa1c8	BWA bindings and tests moved to public (was required for ValidationAmplicons) Integration tests for ValidationAmplicons. New argument to disable BWA, lowercase letters only for repetitiveness instead.	2011-07-19 20:11:31 -04:00