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7 Commits (20601f034e97456ba5f2c5d30b4ca0eca1348d76)

Author SHA1 Message Date
Eric Banks ded0e11b45 Killing off some FindBugs 'Realiability' issues 2012-08-16 14:00:48 -04:00
Eric Banks 79195b97a3 Adding categories for the remaining uncategorized walkers 2012-07-30 11:35:08 -04:00
Mauricio Carneiro 116885a450 Removed the "Walker" suffix from all walkers that had it. 
* Did not touch archived walkers... those can be named whatever.
   * Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...)
   * Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
 2012-07-20 17:27:11 -04:00
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