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Add two new GroupReadsByUmi task options #388

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Mar 1, 2021
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Add two new GroupReadsByUmi task options #388

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4 changes: 4 additions & 0 deletions tasks/src/main/scala/dagr/tasks/fgbio/GroupReadsByUmi.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,8 @@ class GroupReadsByUmi(val in: PathToBam,
val minMapQ: Option[Int] = None,
val strategy: AssignmentStrategy = AssignmentStrategy.Adjacency,
val edits: Option[Int] = None,
val minUmiLength: Option[Int] = None,
val allowInterContig: Boolean = false,
tmpDir: Option[DirPath] = None) extends FgBioTask(tmpDir=tmpDir) with Pipe[SamOrBam, SamOrBam] {

/** Implement this to add the tool-specific arguments */
Expand All @@ -58,6 +60,8 @@ class GroupReadsByUmi(val in: PathToBam,
minMapQ.foreach(m => buffer.append("-m", m))
buffer.append("-s", strategy.toString.toLowerCase)
edits.foreach(e => buffer.append("-e", e))
minUmiLength.foreach(m => buffer.append("-l", m))
if (allowInterContig) buffer.append("-x")
tmpDir.foreach(d => buffer.append(s"--tmp-dir=${d}"))
}
}