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Khalid Shakir 1e25a758f5 Moved files to maven directories. 
Here are the git moved directories in case other files need to be moved during a merge:
  git-mv private/java/src/        private/gatk-private/src/main/java/
  git-mv private/R/scripts/       private/gatk-private/src/main/resources/
  git-mv private/java/test/       private/gatk-private/src/test/java/
  git-mv private/testdata/        private/gatk-private/src/test/resources/
  git-mv private/scala/qscript/   private/queue-private/src/main/qscripts/
  git-mv private/scala/src/       private/queue-private/src/main/scala/
  git-mv protected/java/src/      protected/gatk-protected/src/main/java/
  git-mv protected/java/test/     protected/gatk-protected/src/test/java/
  git-mv public/java/src/         public/gatk-framework/src/main/java/
  git-mv public/java/test/        public/gatk-framework/src/test/java/
  git-mv public/testdata/         public/gatk-framework/src/test/resources/
  git-mv public/scala/qscript/    public/queue-framework/src/main/qscripts/
  git-mv public/scala/src/        public/queue-framework/src/main/scala/
  git-mv public/scala/test/       public/queue-framework/src/test/scala/
 		2014-02-03 13:50:44 -05:00
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c 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
chainFiles
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doc Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
gatk-framework/src Moved files to maven directories. 2014-02-03 13:50:44 -05:00
gatk-queue-extgen/src/main/java/org/broadinstitute/sting/queue/extensions/gatk Moved gsalib, R and other resources, Queue GATK extensions generator, Queue version java files. 2014-02-03 13:49:21 -05:00
gsalib/src/R Moved gsalib, R and other resources, Queue GATK extensions generator, Queue version java files. 2014-02-03 13:49:21 -05:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework/src Moved files to maven directories. 2014-02-03 13:50:44 -05:00