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
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bwa	Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-07-19 20:25:33 -04:00
reference	Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-07-19 20:25:33 -04:00
Aligner.java	Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-07-19 20:25:33 -04:00
Alignment.java	Merge branch 'master' of ssh://chartl@tin.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2011-07-19 20:25:33 -04:00
AlignmentValidationWalker.java	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
AlignmentWalker.java	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
CountBestAlignmentsWalker.java	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
package-info.java	BWA bindings and tests moved to public (was required for ValidationAmplicons)	2011-07-19 20:11:31 -04:00