Changes

Summary

  1. Add CRAM reference argument for loading alignments and fragments. (commit: e654884) (details)
  2. Update ADAM dependency version to 0.34.0. (commit: ce83e0c) (details)
  3. Modifying changelog. (commit: 14e118e) (details)
  4. Modifying pom.xml files for new development after 0.12.0 release. (commit: c6d0d09) (details)
  5. Update cannoli-shell example per ADAM 0.34.0 release. (commit: 6fe3a6b) (details)
Commit e654884af62ce114fa725bd6d5342cafe6a474a1 by heuermh
Add CRAM reference argument for loading alignments and fragments.
(commit: e654884)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/BwaMem.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SingleEndBowtie2.scala (diff)
The file was addedcli/src/main/scala/org/bdgenomics/cannoli/cli/CramArgs.scala
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SingleEndStar.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Snap.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Minimap2.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Star.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Gem.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SamtoolsMpileup.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/BwaMem2.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/MagicBlast.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SampleReads.scala (diff)
Commit ce83e0c5171bd5d213e982ab36eba2be64b36ac4 by heuermh
Update ADAM dependency version to 0.34.0.
(commit: ce83e0c)
The file was modifiedcli/src/test/scala/org/bdgenomics/cannoli/cli/InterleaveFastqSuite.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Blastn.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SingleEndStar.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/BcftoolsNorm.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/Bowtie2.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/Bowtie.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/SingleEndBowtie2.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Vep.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/SamtoolsMpileup.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/Snap.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Snap.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Star.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/Gem.scala (diff)
The file was modifiedpom.xml (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/VtNormalize.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/Blastn.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/BwaMem2.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/BedtoolsIntersect.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/SingleEndStar.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/VtNormalize.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/MagicBlast.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/BcftoolsCall.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/BwaMem.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Minimap2.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/Minimap2.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Bowtie2.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/BcftoolsMpileup.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/BcftoolsMpileup.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/Freebayes.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/MagicBlast.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/SnpEff.scala (diff)
The file was modifiedscripts/move_to_spark_2.sh (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/Cannoli.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SingleEndBowtie2.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/Vep.scala (diff)
The file was modifiedscripts/move_to_spark_3.sh (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SampleReads.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/BwaMem.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/BcftoolsNorm.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Freebayes.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SamtoolsMpileup.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/util/QuerynameGrouper.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Gem.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/BwaMem2.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/BedtoolsIntersect.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/BcftoolsCall.scala (diff)
The file was modifiedcore/src/main/scala/org/bdgenomics/cannoli/Star.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SnpEff.scala (diff)
The file was modifiedCHANGES.md (diff)
Commit c6d0d09f11210b40f5a8177b341d349362f99ccd by heuermh
Modifying pom.xml files for new development after 0.12.0 release.
(commit: c6d0d09)
The file was modifiedcli/pom.xml (diff)
The file was modifiedassembly/pom.xml (diff)
The file was modifieddistribution/pom.xml (diff)
The file was modifiedcore/pom.xml (diff)
The file was modifiedbuilder/pom.xml (diff)
The file was modifiedpom.xml (diff)
Commit 6fe3a6b50f29b68ded7528a52b2478a6fa42136b by heuermh
Update cannoli-shell example per ADAM 0.34.0 release.
(commit: 6fe3a6b)
The file was modifiedREADME.md (diff)