Changes

Summary

  1. Refactor org.bdgenomics.adam.rdd package to org.bdgenomics.adam.ds. (commit: f008c37) (details)
  2. Replace jvmRdd with jvmDataset in adam-python. (commit: 52e008d) (details)
Commit f008c373d85d53392c7c1adcea70b78bd99d02d6 by heuermh
Refactor org.bdgenomics.adam.rdd package to org.bdgenomics.adam.ds.
(commit: f008c37)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/InFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/RealignIndelsSuite.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/UnionConsensusGenerator.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/BAMInFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/RegionJoin.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/sequence/FlankSlicesSuite.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformVariants.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ShuffleRegionJoin.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/VariantDataset.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/OuterRegionJoinSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/DinucCovariate.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/sequence/FlankSlices.scala
The file was removedadam-r/bdgenomics.adam/R/rdd.R
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/TreeRegionJoin.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/AlignmentDataset.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FlagStat.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantContextDataset.scala
The file was addedadam-python/bdgenomics/adam/ds.py
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentDataset.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/GFF3OutFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/fragment/FragmentDatasetSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/SingleReadBucket.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/SingleReadBucketSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/recalibration/CycleCovariateSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMBAMOutputFormat.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMParquetInputFormat.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SequenceDataset.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/fragment/FragmentDataset.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/SAMHeaderWriter.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformGenotypesSuite.scala (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/OuterRegionJoinSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/CovariateSpace.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GFF3InFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/FeatureDataset.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GTFInFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/Tab6InFormatter.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fastq.scala (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/GFF3HeaderWriter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/TreeRegionJoinSuite.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformAlignmentsSuite.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/RecalibrationTable.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/TreeRegionJoin.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ReferencePartitioner.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/Features.scala
The file was modifieddocs/api/genomicDataset.rst (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/LeftOuterShuffleRegionJoinAndGroupByLeftSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/LeftOuterShuffleRegionJoinSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/recalibration/DinucCovariateSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/ModPartitioner.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/Aggregate.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureDataset.scala
The file was modifieddocs/api/adamContext.rst (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/InFormatter.scala
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromReadsSuite.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/DinucCovariate.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicBroadcast.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMInFormatter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicBroadcast.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/ModPartitionerSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/RecalibrationTable.scala
The file was modifieddocs/api/pipes.rst (diff)
The file was removedadam-r/bdgenomics.adam/tests/testthat/test_alignmentRecordDataset.R
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/sequence/SliceDataset.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/GenomicPositionPartitionerSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/CovariateKey.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/CoverageSuite.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentDatasetSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/ReferencePositionPair.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/VCFHeaderUtils.scala
The file was modifiedadam-apis/src/main/scala/org/bdgenomics/adam/api/java/GenomicRDDConverters.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/Observation.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/CoverageDataset.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/CovariateKey.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/realignment/ModPartitioner.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/CountSliceKmers.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMSaveAnyArgs.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/VariantDatasetSuite.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/ViewSuite.scala (diff)
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMCoverageConduit.java (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibrationSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/GenotypeDataset.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/Covariate.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/ReadDataset.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/GenotypeDataset.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/BEDInFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/MarkDuplicates.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMOutFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/ADAMVCFOutputFormat.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/ReadDatasetSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/RecalibratorSuite.scala
The file was modifiedadam-python/bdgenomics/adam/test/alignmentDataset_test.py (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/BinQualitiesSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/ShuffleRegionJoin.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/BinQualitiesSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/sequence/FlankSlicesSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/SAMInFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/ObservationTable.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VCFOutFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/BEDOutFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FASTQInFormatter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/RightOuterTreeRegionJoinSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/FlagStatSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMSAMOutputFormat.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/SortedGenomicDatasetSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/ReadDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/Recalibrator.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomeBins.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMGenotypeConduit.java (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/LeftOuterShuffleRegionJoinAndGroupByLeftSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicPositionPartitionerSuite.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMSequenceConduit.java (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/FragmentDataset.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTarget.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MarkDuplicates.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/CountReadKmers.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/FlagStat.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMSaveAnyArgs.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/ADAMVCFOutputFormat.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/AlignmentDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/OutFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/ADAMSAMOutputFormat.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/ReferencePartitioner.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMReadConduit.java (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/FlankSlices.scala
The file was addedadam-r/bdgenomics.adam/R/ds.R
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/ADAMCRAMOutputFormat.scala
The file was modifiedadam-r/bdgenomics.adam/R/generics.R (diff)
The file was modifiedadam-r/bdgenomics.adam/R/adam-context.R (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/NarrowPeakInFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GFF3OutFormatter.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMSliceConduit.java (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/FlagStat.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/FeatureParser.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/GFF3HeaderWriterSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/fragment/Tab5InFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/TreeRegionJoinSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/GFF3InFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/RepairPartitions.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/RepairPartitionsSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/sequence/SequenceDatasetSuite.scala
The file was modifiedadam-python/bdgenomics/adam/test/coverageDataset_test.py (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMParquetInputFormat.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/OutFormatter.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMFragmentConduit.java (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/NarrowPeakOutFormatter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala
The file was modifiedadam-r/bdgenomics.adam/NAMESPACE (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/RegionJoin.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/DinucCovariateSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/LeftOuterShuffleRegionJoinSuite.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GTFOutFormatter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/sequence/SliceDatasetSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/GenotypeDatasetSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/FASTAInFormatter.scala
The file was modifiedadam-python/bdgenomics/adam/adamContext.py (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/recalibration/RecalibratorSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/ModPartitionerSuite.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnowns.scala (diff)
The file was modifiedadam-python/bdgenomics/adam/__init__.py (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/CycleCovariate.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MDTaggingSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMInFormatter.scala
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/models/SnpTableSuite.scala (diff)
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/MergeShardsSuite.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/feature/FeatureDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDatasetConversion.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/BinQualities.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureParser.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/FASTQInFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/BEDOutFormatter.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformFeaturesSuite.scala (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/GenomicDatasetSuite.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/models/IndelTable.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/NarrowPeakOutFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/CovariateSpace.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/realignment/RealignmentTargetFinder.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/View.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/util/ParallelFileMergerSuite.scala (diff)
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/ADAM2FastqSuite.scala (diff)
The file was modifiedadam-apis/src/main/scala/org/bdgenomics/adam/api/java/GenomicDatasetConverters.scala (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/SortedGenomicDatasetSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SliceDataset.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/models/SnpTable.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicPartitioners.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/NarrowPeakInFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/GTFInFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Recalibrator.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDatasetConversion.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicPartitioners.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/VCFOutFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/recalibration/BaseQualityRecalibrationSuite.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala (diff)
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMVariantConduit.java (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/MarkDuplicatesSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/CycleCovariateSuite.scala
The file was modifiedadam-r/bdgenomics.adam/DESCRIPTION (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGenerator.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/BEDInFormatter.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFragments.scala (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/feature/CoverageDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/MDTagging.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/FlagStatSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/VCFHeaderUtils.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformSequences.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/SingleReadBucket.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Observation.scala
The file was modifiedadam-apis/src/main/scala/org/bdgenomics/adam/api/java/JavaADAMContext.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/GenomeBins.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ReadDataset.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibration.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/BaseQualityRecalibration.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/recalibration/RecalibrationTableSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformFragmentsSuite.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/fragment/Tab6InFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/ADAMBAMOutputFormat.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VCFInFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignmentTargetFinder.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformGenotypes.scala (diff)
The file was removedadam-python/bdgenomics/adam/rdd.py
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantContextDatasetSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Covariate.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/ObservationTable.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/MDTaggingSuite.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromReads.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/SAMHeaderWriter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/GTFOutFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/InnerTreeRegionJoinSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/feature/GFF3HeaderWriterSuite.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMFeatureConduit.java (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ReferencePositionPair.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/realignment/RealignIndels.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMCRAMOutputFormat.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/ADAMContextSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/sequence/SequenceDataset.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFeatures.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/VariantContextDataset.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantDataset.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/InnerTreeRegionJoinSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Aggregate.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GFF3HeaderWriter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDataset.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/InnerShuffleRegionJoinSuite.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/ADAMShell.scala (diff)
The file was modifiedadam-python/setup.py (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformSlices.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/SAMInFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/sequence/SequenceDatasetSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/RepairPartitionsSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/BAMInFormatter.scala
The file was modifiedadam-apis/src/test/scala/org/bdgenomics/adam/api/java/JavaADAMContextSuite.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/CycleCovariate.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/BinQualities.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/VariantContextDatasetSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MarkDuplicatesSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/CoverageDataset.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/SingleReadBucketSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/fragment/InterleavedFASTQInFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/RightOuterTreeRegionJoinSuite.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/Coverage.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicDatasetSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/sequence/SliceDatasetSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/RecalibrationTableSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/RepairPartitions.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMOutFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/VCFInFormatter.scala
The file was addedadam-r/bdgenomics.adam/tests/testthat/test_alignmentDataset.R
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/sequence/FASTAInFormatter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/InnerShuffleRegionJoinSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/Tab5InFormatter.scala
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnownsSuite.scala (diff)
Commit 52e008d129b980bcecafbc28688d8fb93e2a6bd9 by heuermh
Replace jvmRdd with jvmDataset in adam-python.
(commit: 52e008d)
The file was modifiedadam-python/bdgenomics/adam/test/featureDataset_test.py (diff)
The file was modifiedadam-python/bdgenomics/adam/test/genotypeDataset_test.py (diff)
The file was modifiedadam-python/bdgenomics/adam/test/alignmentDataset_test.py (diff)
The file was modifiedadam-python/bdgenomics/adam/test/adamContext_test.py (diff)
The file was modifiedadam-python/bdgenomics/adam/ds.py (diff)
The file was modifiedadam-python/bdgenomics/adam/test/variantDataset_test.py (diff)