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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/

...

This commit is contained in:

Khalid Shakir 2014-01-29 13:36:16 -05:00 committed by David Roazen

parent faaef236ea

commit 1e25a758f5

1437 changed files with 0 additions and 0 deletions

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcFactory.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACcounts.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactACset.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java

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protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java → protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java

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