Changes

Summary

  1. Provide access to header to model conversions. (commit: e9dada4) (details)
  2. Bump commons-io from 2.6 to 2.7 (commit: c121515) (details)
  3. Bump guava from 27.0-jre to 29.0-jre (commit: d89a1a7) (details)
  4. Update guava to 30.1.1-jre, commons-io to 2.8.0, commons-codec to 1.15 (commit: fbe647a) (details)
  5. Update maven plugin dependency versions, remove coverage profiles (commit: 47494a6) (details)
  6. Add paired fastq argument to transformFragments. (commit: 0d53586) (details)
Commit e9dada41f481dd29b0e063b2c7d926917a3cc4e6 by heuermh
Provide access to header to model conversions.
(commit: e9dada4)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/models/ReadGroupDictionary.scala (diff)
The file was removedadam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMOutFormatter.scala (diff)
The file was removedadam-core/src/test/scala/org/bdgenomics/adam/converters/SAMRecordConverterSuite.scala
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/converters/AlignmentConverter.scala (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/converters/AlignmentConverterSuite.scala (diff)
Commit c121515a71629db3a9703c75fd1a1539376cae50 by heuermh
Bump commons-io from 2.6 to 2.7

Bumps commons-io from 2.6 to 2.7.

Signed-off-by: dependabot[bot] <support@github.com>
(commit: c121515)
The file was modifiedpom.xml (diff)
Commit d89a1a706c6bc2de6b52a462dfeff5c7c34c9640 by heuermh
Bump guava from 27.0-jre to 29.0-jre

Bumps [guava](https://github.com/google/guava) from 27.0-jre to 29.0-jre.
- [Release notes](https://github.com/google/guava/releases)
- [Commits](https://github.com/google/guava/commits)

Signed-off-by: dependabot[bot] <support@github.com>
(commit: d89a1a7)
The file was modifiedpom.xml (diff)
Commit fbe647a6134187cdd3a5b339af50137943291596 by heuermh
Update guava to 30.1.1-jre, commons-io to 2.8.0, commons-codec to 1.15
(commit: fbe647a)
The file was modifiedpom.xml (diff)
Commit 47494a6b3c95feb43248c30de65118c5e946b267 by heuermh
Update maven plugin dependency versions, remove coverage profiles
(commit: 47494a6)
The file was modifiedpom.xml (diff)
Commit 0d53586426bfce1a9062d8e0664d4a6358db985c by heuermh
Add paired fastq argument to transformFragments.
(commit: 0d53586)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFragments.scala (diff)