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Author SHA1 Message Date
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