Changes

Summary

  1. Added an optimisation to not spare not required shuffle of the reads (details)
  2. added mergePairedReads as a parameter to Python API (details)
  3. code format fix (details)
Commit cc4a7110282bb2cf1ff14925f7ceda1cea5e15c5 by brahamim
Added an optimisation to not spare not required shuffle of the reads when they are unpaired
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala (diff)
The file was modifiedadam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFragments.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/read/MarkDuplicatesSuite.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/read/SingleReadBucket.scala (diff)
The file was addedadam-core/src/test/resources/unpaired.sam
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala (diff)
Commit d6a66783de76e23a184fbb2760a3d7d5ea79a7fb by brahamim
added mergePairedReads as a parameter to Python API
The file was modifiedadam-python/bdgenomics/adam/rdd.py (diff)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/SingleReadBucket.scala (diff)