Changes

Summary

  1. Add CRAM reference argument for loading alignments and fragments. (commit: e654884) (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/Snap.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/Freebayes.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/SamtoolsMpileup.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SingleEndBowtie2.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/SampleReads.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/Star.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/BwaMem.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/MagicBlast.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/Minimap2.scala (diff)
The file was modifiedcli/src/main/scala/org/bdgenomics/cannoli/cli/Gem.scala (diff)