Add paired fastq argument to transformFragments.

bigdatagenomics · Apr 28, 2021 · 0d53586 · 0d53586
1 parent 47494a6
commit 0d53586
Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFragments.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/TransformFragments.scala
@@ -47,6 +47,9 @@ class TransformFragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with Parque
  @Args4jOption(required = false, name = "-load_as_alignments", usage = "Treats the input data as alignments")
  var loadAsAlignments: Boolean = false
 
+ @Args4jOption(required = false, name = "-paired_fastq", usage = "When converting two (paired) FASTQ files, pass the path to the second file here.")
+ var pairedFastqFile: String = null
+
  @Args4jOption(required = false, name = "-save_as_alignments", usage = "Saves the output data as alignments")
  var saveAsAlignments: Boolean = false
 
@@ -130,8 +133,9 @@ class TransformFragments(protected val args: TransformFragmentsArgs) extends BDG
 
  args.configureCramFormat(sc)
 
- val rdd = if (args.loadAsAlignments) {
- sc.loadAlignments(args.inputPath)
+ val optPairedFastqFile = Option(args.pairedFastqFile)
+ val rdd = if (args.loadAsAlignments || optPairedFastqFile.isDefined) {
+ sc.loadAlignments(args.inputPath, optPathName2 = optPairedFastqFile)
  .toFragments
  } else {
  sc.loadFragments(args.inputPath)