Changes

Summary

  1. Added an optimisation to not spare not required shuffle of the reads (commit: cc4a711) (details)
  2. added mergePairedReads as a parameter to Python API (commit: d6a6678) (details)
  3. code format fix (commit: e6332ef) (details)
Commit cc4a7110282bb2cf1ff14925f7ceda1cea5e15c5 by brahamim
Added an optimisation to not spare not required shuffle of the reads when they are unpaired
(commit: cc4a711)
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.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/SingleReadBucket.scala (diff)
The file was modifiedadam-core/src/test/scala/org/bdgenomics/adam/rdd/fragment/FragmentDatasetSuite.scala (diff)
The file was addedadam-core/src/test/resources/unpaired.sam
The file was modifiedadam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentDataset.scala (diff)
Commit d6a66783de76e23a184fbb2760a3d7d5ea79a7fb by brahamim
added mergePairedReads as a parameter to Python API
(commit: d6a6678)
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)