FailedChanges

Summary

  1. Modifying changelog. (commit: ed82e08) (details)
  2. Bumping R version to 0.33.0. (commit: 69d3424) (details)
  3. Modifying changelog. (commit: 4de1527) (details)
  4. Modifying pom.xml files for new development after 0.33.0 release. (commit: 7464166) (details)
  5. Default build to Hadoop version 3.2.1. (commit: 36a3484) (details)
  6. Remove Spark 2.x and Scala 2.11 from build and release profiles. (commit: 16f95d6) (details)
  7. Bump Scala 2.12 dependency version to 2.12.10. (commit: bc4f4f0) (details)
  8. Remove duplicate version 0.33.0 release notes in changelog. (commit: 909c41b) (details)
  9. Add convenience method to filter to reference name. (commit: ff180a9) (details)
  10. Add CRAM reference argument to CLI for loading alignments and fragments. (commit: 9be32ad) (details)
  11. Bump adam-python version to 0.34.0a0. (commit: 1aaa5be) (details)
  12. Refactor org.bdgenomics.adam.rdd package to org.bdgenomics.adam.ds. (commit: d760dee) (details)
  13. Replace jvmRdd with jvmDataset in adam-python. (commit: 385fda3) (details)
  14. Rename sequences SequenceDictionary field to references. (commit: 8574aaf) (details)
  15. Update Spark dependency version to 3.0.2. (commit: 9ea5f6f) (details)
  16. Modifying changelog. (commit: 39aacec) (details)
  17. Bumping R version to 0.34.0. (commit: 570ce94) (details)
  18. Modifying pom.xml files for new development after 0.34.0 release. (commit: bb0705d) (details)
  19. Provide access to header to model conversions. (commit: 90e0f83) (details)
The file was modifiedCHANGES.md (diff)
Commit 69d342480737f90fa2be5100e4a38141842fbd37 by heuermh
Bumping R version to 0.33.0.
(commit: 69d3424)
The file was modifiedadam-r/bdgenomics.adam/DESCRIPTION (diff)
The file was modifiedCHANGES.md (diff)
Commit 7464166e984008b06e50e04c716633182f2638aa by heuermh
Modifying pom.xml files for new development after 0.33.0 release.
(commit: 7464166)
The file was modifiedpom.xml (diff)
The file was modifiedadam-codegen/pom.xml (diff)
The file was modifiedadam-shade/pom.xml (diff)
The file was modifiedadam-core/pom.xml (diff)
The file was modifiedadam-python/pom.xml (diff)
The file was modifiedadam-assembly/pom.xml (diff)
The file was modifiedadam-cli/pom.xml (diff)
The file was modifiedadam-r/pom.xml (diff)
The file was modifiedadam-apis/pom.xml (diff)
The file was modifiedadam-distribution/pom.xml (diff)
Commit 36a34841ee31903be0e9443011dc5a2e60a6129f by heuermh
Default build to Hadoop version 3.2.1.
(commit: 36a3484)
The file was modifiedscripts/jenkins-test (diff)
The file was modifiedREADME.md (diff)
The file was modifieddocs/installation/source.rst (diff)
The file was modifiedpom.xml (diff)
Commit 16f95d6bda1377203040fa6df1e72e09425668c8 by heuermh
Remove Spark 2.x and Scala 2.11 from build and release profiles.
(commit: 16f95d6)
The file was modifiedscripts/jenkins-test (diff)
The file was modifieddocs/installation/source.rst (diff)
The file was modifiedscripts/release/release.sh (diff)
Commit bc4f4f0bf32e8141e744f3bf624a5966b2fb1836 by heuermh
Bump Scala 2.12 dependency version to 2.12.10.
(commit: bc4f4f0)
The file was modifiedscripts/move_to_scala_2.11.sh (diff)
The file was modifiedpom.xml (diff)
The file was modifiedscripts/move_to_scala_2.12.sh (diff)
Commit 909c41bc39b3d9d25219a1ff0a6aed690207b0bd by heuermh
Remove duplicate version 0.33.0 release notes in changelog.
(commit: 909c41b)
The file was modifiedCHANGES.md (diff)
Commit ff180a96b686b992c6fddbb231af922503fbd0c4 by heuermh
Add convenience method to filter to reference name.
(commit: ff180a9)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/GenotypeDataset.scala (diff)
Commit 9be32ad9cd1d82e6b351160f049957a9ffb74d2c by heuermh
Add CRAM reference argument to CLI for loading alignments and fragments.
(commit: 9be32ad)
The file was addedadam-cli/src/main/scala/org/bdgenomics/adam/cli/CramArgs.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/CountReadKmers.scala (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/FlagStat.scala (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFragments.scala (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fastq.scala (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/View.scala (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/Coverage.scala (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala (diff)
Commit 1aaa5bea0de03dcc3d09b4f59c030144ba064a69 by heuermh
Bump adam-python version to 0.34.0a0.
(commit: 1aaa5be)
The file was modifiedadam-python/version.py (diff)
Commit d760dee99b8829486c40c2cadff0925aae2d3316 by heuermh
Refactor org.bdgenomics.adam.rdd package to org.bdgenomics.adam.ds.
(commit: d760dee)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AnySAMInFormatter.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/variant/GenotypeDataset.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/ADAMContextSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/RightOuterTreeRegionJoinSuite.scala
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/util/ParallelFileMergerSuite.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTargetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/Covariate.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/sequence/SequenceDatasetSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/GenotypeDatasetSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/CycleCovariate.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/InnerShuffleRegionJoinSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/RightOuterTreeRegionJoinSuite.scala
The file was modifiedadam-r/bdgenomics.adam/R/generics.R (diff)
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/feature/GFF3HeaderWriter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/SortedGenomicDatasetSuite.scala
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnownsSuite.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/FlagStatSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/MarkDuplicates.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/MarkDuplicatesSuite.scala
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/BAMInFormatter.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/fragment/FragmentDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/BaseQualityRecalibration.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GTFOutFormatter.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/UnionConsensusGenerator.scala (diff)
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/read/recalibration/Recalibrator.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/GenotypeDatasetSuite.scala
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/read/ReferencePositionPair.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/CovariateKey.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantContextDataset.scala
The file was modifiedadam-python/bdgenomics/adam/__init__.py (diff)
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/feature/NarrowPeakInFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Covariate.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/BinQualities.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMInFormatter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/CoverageDatasetSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/recalibration/CycleCovariateSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/sequence/SliceDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/ADAMBAMOutputFormat.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/sequence/FlankSlicesSuite.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/ADAMParquetInputFormat.scala
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/feature/CoverageDataset.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/sequence/SliceDatasetSuite.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromReads.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/BEDInFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Aggregate.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/ADAMCRAMOutputFormat.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/RealignIndelsSuite.scala
The file was modifieddocs/api/pipes.rst (diff)
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/variant/VariantDataset.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/ReferencePositionPair.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMVariantConduit.java (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/View.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/CycleCovariateSuite.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/FlagStat.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/Tab5InFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/LeftOuterShuffleRegionJoinSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/BEDOutFormatter.scala
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromReadsSuite.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/RegionJoin.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/ObservationTable.scala
The file was addedadam-python/bdgenomics/adam/ds.py
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/SingleReadBucket.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/sequence/SequenceDatasetSuite.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/ReadDataset.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/FlagStat.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/Tab6InFormatter.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/feature/Features.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/FeatureParser.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.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/SortedGenomicDatasetSuite.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMFeatureConduit.java (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/realignment/RealignmentTargetFinder.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/ObservationTable.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/RepairPartitions.scala
The file was modifiedadam-apis/src/main/scala/org/bdgenomics/adam/api/java/GenomicDatasetConverters.scala (diff)
The file was modifiedadam-apis/src/main/scala/org/bdgenomics/adam/api/java/JavaADAMContext.scala (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAM2Fastq.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDataset.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/SAMInFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SliceDataset.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/NarrowPeakOutFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/LeftOuterShuffleRegionJoinAndGroupByLeftSuite.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFragments.scala (diff)
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/realignment/ModPartitionerSuite.scala
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 modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMCoverageConduit.java (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/BinQualities.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/FlagStatSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/recalibration/RecalibratorSuite.scala
The file was modifiedadam-python/setup.py (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/ADAMVCFOutputFormat.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/OutFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/VCFHeaderUtils.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/GTFOutFormatter.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/ADAMSAMOutputFormat.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/FlankSlices.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/ADAMSAMOutputFormat.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/FASTAInFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/Aggregate.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/CoverageSuite.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantDataset.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/ADAM2FastqSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnowns.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GFF3InFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/DinucCovariate.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/ViewSuite.scala (diff)
The file was modifiedadam-r/bdgenomics.adam/NAMESPACE (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/ReferencePartitioner.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/RepairPartitionsSuite.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/feature/FeatureDataset.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMGenotypeConduit.java (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/RegionJoin.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MarkDuplicates.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ReferencePartitioner.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/ADAMShell.scala (diff)
The file was removedadam-r/bdgenomics.adam/R/rdd.R
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/GenomicDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/OutFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FASTQInFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMSaveAnyArgs.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/sequence/SequenceDataset.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/BinQualitiesSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDatasetConversion.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformGenotypesSuite.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/DinucCovariate.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/InnerShuffleRegionJoinSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/BAMInFormatter.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/fragment/Tab5InFormatter.scala
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/models/SnpTableSuite.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/BEDInFormatter.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMReadConduit.java (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/GFF3HeaderWriterSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/SAMHeaderWriter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/LeftOuterShuffleRegionJoinAndGroupByLeftSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/sequence/SliceDataset.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/VCFInFormatter.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/models/SAMFileHeaderWritable.scala (diff)
The file was modifieddocs/api/genomicDataset.rst (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MarkDuplicatesSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/ReadDatasetSuite.scala
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/MergeShardsSuite.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/NarrowPeakOutFormatter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/ADAMContextSuite.scala
The file was removedadam-r/bdgenomics.adam/tests/testthat/test_alignmentRecordDataset.R
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VCFInFormatter.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/fragment/FragmentDataset.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/AlignmentDataset.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/feature/CoverageDatasetSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/feature/FeatureDatasetSuite.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFeatures.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/GTFInFormatter.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/TransformGenotypes.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTarget.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/test/scala/org/bdgenomics/adam/rdd/read/realignment/ModPartitionerSuite.scala
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMSliceConduit.java (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/fragment/Tab6InFormatter.scala
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/read/recalibration/CovariateSpace.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureParser.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/AlignmentDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/InFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomeBins.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentDataset.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/feature/GFF3OutFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/ADAMCRAMOutputFormat.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/FASTQInFormatter.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicPartitioners.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/read/SingleReadBucket.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/SingleReadBucketSuite.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/variant/VCFOutFormatter.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/read/AnySAMOutFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/MDTaggingSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/GTFInFormatter.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/CountReadKmers.scala (diff)
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformFeaturesSuite.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantContextDatasetSuite.scala
The file was modifiedadam-python/bdgenomics/adam/test/coverageDataset_test.py (diff)
The file was modifiedadam-apis/src/test/java/org/bdgenomics/adam/api/java/JavaADAMSequenceConduit.java (diff)
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/MDTagging.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/models/IndelTable.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/FeatureDataset.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/IndelRealignmentTargetSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/ADAMVCFOutputFormat.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/CountSliceKmers.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/GenomicPositionPartitionerSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/VariantDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/Observation.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicDatasetConversion.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/GenomicBroadcast.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/TreeRegionJoin.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/recalibration/DinucCovariateSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/SAMHeaderWriter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/LeftOuterShuffleRegionJoinSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/feature/Features.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/sequence/SequenceDataset.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/feature/NarrowPeakInFormatter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndelsSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/ReadDatasetSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/RecalibratorSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/Observation.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/feature/GFF3HeaderWriterSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/BinQualitiesSuite.scala
The file was modifiedadam-python/bdgenomics/adam/test/alignmentDataset_test.py (diff)
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/sequence/FlankSlicesSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/VariantContextDatasetSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/TreeRegionJoin.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignmentTargetFinder.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/AnySAMOutFormatter.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/InFormatter.scala
The file was modifiedadam-r/bdgenomics.adam/R/adam-context.R (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/DinucCovariateSuite.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/read/SAMInFormatter.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/OuterRegionJoinSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/variant/VariantDatasetSuite.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/InterleavedFASTQInFormatter.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/recalibration/BaseQualityRecalibrationSuite.scala
The file was modifiedadam-python/bdgenomics/adam/adamContext.py (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/recalibration/CovariateKey.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/sequence/FlankSlices.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/GenomicPositionPartitionerSuite.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/recalibration/BaseQualityRecalibrationSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/RepairPartitions.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/ShuffleRegionJoin.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/VCFHeaderUtils.scala
The file was addedadam-r/bdgenomics.adam/R/ds.R
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/ModPartitioner.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/RecalibrationTable.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/read/recalibration/RecalibrationTable.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/RepairPartitionsSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMSaveAnyArgs.scala
The file was modifieddocs/api/adamContext.rst (diff)
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/sequence/FASTAInFormatter.scala
The file was removedadam-python/bdgenomics/adam/rdd.py
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/FlagStat.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/GFF3OutFormatter.scala
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/recalibration/CovariateSpace.scala
The file was addedadam-core/src/test/scala/org/bdgenomics/adam/ds/InnerTreeRegionJoinSuite.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/MDTagging.scala
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/realignment/RealignIndels.scala
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala (diff)
The file was modifiedadam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformFragmentsSuite.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/TreeRegionJoinSuite.scala
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/SingleReadBucketSuite.scala
Commit 385fda35224f956ee974818550dc3de58ad9c64c by heuermh
Replace jvmRdd with jvmDataset in adam-python.
(commit: 385fda3)
The file was modifiedadam-python/bdgenomics/adam/test/alignmentDataset_test.py (diff)
The file was modifiedadam-python/bdgenomics/adam/test/genotypeDataset_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)
The file was modifiedadam-python/bdgenomics/adam/test/adamContext_test.py (diff)
The file was modifiedadam-python/bdgenomics/adam/test/featureDataset_test.py (diff)
Commit 8574aaf88157dc1bf5e1a1410c4638e888cd4004 by heuermh
Rename sequences SequenceDictionary field to references.
(commit: 8574aaf)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/VariantContextDatasetSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/VariantDataset.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/feature/FeatureDatasetSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/FeatureDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/AlignmentDataset.scala (diff)
The file was modifieddocs/api/adamContext.rst (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/ADAMContextSuite.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/util/IndexedFastaFileSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMInFormatter.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/IndexedFastaFile.scala (diff)
The file was addedadam-core/src/main/scala/org/bdgenomics/adam/util/ReferenceMap.scala
The file was modifieddocs/cli/conversions.rst (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/GenotypeDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/fragment/FragmentDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/feature/CoverageDatasetSuite.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/AlignmentDatasetSuite.scala (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/ADAMShell.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/RealignIndelsSuite.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/fragment/FragmentDatasetSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/sequence/SequenceDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/feature/CoverageDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDataset.scala (diff)
The file was modifiedadam-r/bdgenomics.adam/R/ds.R (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/sequence/SliceDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/util/ReferenceContigMap.scala
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/MDTaggingSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/ADAMContext.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/TwoBitFile.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/VCFInFormatter.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/ReferenceFile.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/GenotypeDatasetSuite.scala (diff)
The file was modifieddocs/cli/actions.rst (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/ReadDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/VariantContextDataset.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/VariantDatasetSuite.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/util/TwoBitFileSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/SequenceDictionaryReader.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/GenomicPositionPartitionerSuite.scala (diff)
Commit 9ea5f6f3f09702d8f037b1b7c46842e259b82b0e by heuermh
Update Spark dependency version to 3.0.2.
(commit: 9ea5f6f)
The file was modifiedpom.xml (diff)
The file was modifiedscripts/jenkins-test (diff)
The file was modifiedscripts/move_to_spark_3.sh (diff)
The file was modifiedCHANGES.md (diff)
Commit 570ce941483bed616b5c2204c894333882e230ee by heuermh
Bumping R version to 0.34.0.
(commit: 570ce94)
The file was modifiedadam-r/bdgenomics.adam/DESCRIPTION (diff)
Commit bb0705d5ec9e27943ce0a12151febc771d76952e by heuermh
Modifying pom.xml files for new development after 0.34.0 release.
(commit: bb0705d)
The file was modifiedadam-python/pom.xml (diff)
The file was modifiedadam-core/pom.xml (diff)
The file was modifiedadam-r/pom.xml (diff)
The file was modifiedadam-shade/pom.xml (diff)
The file was modifiedadam-apis/pom.xml (diff)
The file was modifiedadam-codegen/pom.xml (diff)
The file was modifiedpom.xml (diff)
The file was modifiedadam-assembly/pom.xml (diff)
The file was modifiedadam-distribution/pom.xml (diff)
The file was modifiedadam-cli/pom.xml (diff)
Commit 90e0f83806afa2be04801c548258fdbd80ca6fdf by heuermh
Provide access to header to model conversions.
(commit: 90e0f83)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala (diff)