Skip to content
This repository has been archived by the owner on Jun 20, 2024. It is now read-only.

Commit

Permalink
Support metrics argument to ClipBam.
Browse files Browse the repository at this point in the history
  • Loading branch information
nh13 committed Jan 9, 2018
1 parent 91933f5 commit c596715
Showing 1 changed file with 3 additions and 1 deletion.
4 changes: 3 additions & 1 deletion tasks/src/main/scala/dagr/tasks/fgbio/ClipBam.scala
Original file line number Diff line number Diff line change
Expand Up @@ -25,13 +25,14 @@
package dagr.tasks.fgbio

import com.fulcrumgenomics.commons.CommonsDef.PathToFasta
import dagr.tasks.DagrDef.PathToBam
import dagr.tasks.DagrDef.{FilePath, PathToBam}

import scala.collection.mutable.ListBuffer

class ClipBam(val input: PathToBam,
val output: PathToBam,
val ref: PathToFasta,
val metrics: Option[FilePath] = None,
@deprecated("Use clipping-mode instead.", since="0.2.1")
val softClip: Option[Boolean] = None,
val clippingMode: Option[String] = None,
Expand All @@ -50,6 +51,7 @@ class ClipBam(val input: PathToBam,
buffer.append("-i", input)
buffer.append("-o", output)
buffer.append("-r", ref)
metrics.foreach (m => buffer.append("-m", m))
softClip.foreach (s => buffer.append("-s", s))
clippingMode.foreach (c => buffer.append("-c", c))
autoClipAttributes.foreach(a => buffer.append("-a", a))
Expand Down

0 comments on commit c596715

Please sign in to comment.