Changes

Summary

  1. Rename sequences SequenceDictionary field to references. (commit: 8574aaf) (details)
  2. Update Spark dependency version to 3.0.2. (commit: fc9b1cf) (details)
Commit 8574aaf88157dc1bf5e1a1410c4638e888cd4004 by heuermh
Rename sequences SequenceDictionary field to references.
(commit: 8574aaf)
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/variant/VariantContextDatasetSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/ADAMShell.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/ds/variant/GenotypeDataset.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/VCFInFormatter.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMInFormatter.scala (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/TwoBitFileSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/TwoBitFile.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/util/ReferenceContigMap.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/SequenceDictionaryReader.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/util/ReferenceFile.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/sequence/SequenceDataset.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/util/IndexedFastaFileSuite.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/models/ReferenceRegion.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/GenomicDataset.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/variant/VariantContextDataset.scala (diff)
The file was modifiedadam-r/bdgenomics.adam/R/ds.R (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/GenomicPositionPartitionerSuite.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/GenotypeDatasetSuite.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/AlignmentDatasetSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/AlignmentDataset.scala (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/serialization/ADAMKryoRegistrator.scala (diff)
The file was modifieddocs/cli/actions.rst (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformAlignments.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/util/IndexedFastaFile.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/models/SequenceDictionary.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/sequence/SliceDataset.scala (diff)
The file was modifieddocs/api/adamContext.rst (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/realignment/RealignIndelsSuite.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/fragment/FragmentDataset.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/feature/FeatureDatasetSuite.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/read/MDTaggingSuite.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/ds/variant/VariantDatasetSuite.scala (diff)
Commit fc9b1cfe074c22ee1930de17001f02d287b5728c by heuermh
Update Spark dependency version to 3.0.2.
(commit: fc9b1cf)
The file was modifiedpom.xml (diff)
The file was modifiedscripts/move_to_spark_3.sh (diff)
The file was modifiedscripts/jenkins-test (diff)