Split all imports of tools|engine from utils, and all tools from engine.

Browse Source

First of two commits, renaming files only.

...

This commit is contained in:

Khalid Shakir 2014-10-22 00:40:42 +08:00

parent b69b256003

commit bb7151192a

818 changed files with 0 additions and 0 deletions

Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL

Show Stats Download Patch File Download Diff File Expand all files Collapse all files

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRGatherer.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRGatherer.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BQSRReadTransformer.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BQSRReadTransformer.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/BaseRecalibration.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/BaseRecalibration.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizer.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizer.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/QuantizationInfo.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/QuantizationInfo.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariates.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariates.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatum.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatum.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumNode.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumNode.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalUtils.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalUtils.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/bqsr/RecalibrationArgumentCollection.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationArgumentCollection.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReport.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReport.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTables.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTables.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ContextCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ContextCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/Covariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/Covariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/CycleCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/CycleCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ExperimentalCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ExperimentalCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/QualityScoreCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/QualityScoreCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/ReadGroupCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/ReadGroupCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatLengthCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatLengthCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitAndLengthCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitAndLengthCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RepeatUnitCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RepeatUnitCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/RequiredCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/RequiredCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/recalibration/covariates/StandardCovariate.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/recalibration/covariates/StandardCovariate.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/StandardCallerArgumentCollection.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/StandardCallerArgumentCollection.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculator.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculator.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/LDMerger.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMerger.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/haplotype/MergeVariantsAcrossHaplotypes.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/MergeVariantsAcrossHaplotypes.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinder.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/graphs/EmptyPathHaplotypeFinderNode.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/variant/ReferenceConfidenceVariantContextMerger.java → protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ReferenceConfidenceVariantContextMerger.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ContextCovariateUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ContextCovariateUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/CycleCovariateUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/CycleCovariateUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/QualQuantizerUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/QualQuantizerUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadCovariatesUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadCovariatesUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/ReadGroupCovariateUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/ReadGroupCovariateUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalDatumUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalDatumUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalUtilsUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalUtilsUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationReportUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationReportUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTablesUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTablesUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RecalibrationTestUtils.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RecalibrationTestUtils.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/recalibration/RepeatCovariatesUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/recalibration/RepeatCovariatesUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/nanoScheduler/NanoSchedulerIntegrationTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/NanoSchedulerIntegrationTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/genotyper/ReadLikelihoodsUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/genotyper/ReadLikelihoodsUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/ActiveRegionTestDataSet.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/ActiveRegionTestDataSet.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/FastLoglessPairHMMUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/FastLoglessPairHMMUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeBaseComparatorUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeBaseComparatorUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeLDCalculatorUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeLDCalculatorUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeScoreComparatorUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeScoreComparatorUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/HaplotypeSizeAndBaseComparatorUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeSizeAndBaseComparatorUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/haplotype/LDMergerUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/LDMergerUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/pairhmm/PairHMMProbabilityBugIntegrationTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/PairHMMProbabilityBugIntegrationTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/variant/VariantContextMergerUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantContextMergerUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffEngineUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffEngineUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffNodeUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffNodeUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DiffableReaderUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DiffableReaderUnitTest.java

Unescape Escape View File

0

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/engine/walkers/diffengine/DifferenceUnitTest.java → protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/utils/diffengine/DifferenceUnitTest.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java → public/gatk-engine/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKBin.java → public/gatk-engine/src/main/java/htsjdk/samtools/GATKBin.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/htsjdk/samtools/GATKChunk.java → public/gatk-engine/src/main/java/htsjdk/samtools/GATKChunk.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java → public/gatk-engine/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineExecutable.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFUtils.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GATKVCFUtils.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/SampleUtils.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/SampleUtils.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/WalkerManager.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Aligner.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/Alignment.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAAligner.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWAConfiguration.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/BWTFiles.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentMatchSequence.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignmentState.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAAlignment.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/BWAJavaAligner.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/LowerBound.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/package-info.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/AMBWriter.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/ANNWriter.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWT.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTReader.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTSupplementaryFileGenerator.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/BWTWriter.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Bases.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/Counts.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/CreateBWTFromReference.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SequenceBlock.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArray.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayReader.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/bwt/SuffixArrayWriter.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedInputStream.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/BasePackedOutputStream.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/CreatePACFromReference.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/PackUtils.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedInputStream.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/alignment/reference/packing/UnsignedIntPackedOutputStream.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/DbsnpArgumentCollection.java

Unescape Escape View File

0

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java → public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java

Unescape Escape View File

Some files were not shown because too many files have changed in this diff Show More