Commit 8b40a367 authored by Wai Yi Leung's avatar Wai Yi Leung

Style fix

parent dd458aef
...@@ -42,10 +42,10 @@ class WipeReads(val root: Configurable) extends ToolCommandFunction { ...@@ -42,10 +42,10 @@ class WipeReads(val root: Configurable) extends ToolCommandFunction {
var readgroup: Set[String] = config("read_group", default = Nil) var readgroup: Set[String] = config("read_group", default = Nil)
@Argument(doc = "Whether to remove multiple-mapped reads outside the target regions (default: yes)") @Argument(doc = "Whether to remove multiple-mapped reads outside the target regions (default: yes)")
var limitRemoval: Boolean = config("limit_removal", default=false) var limitRemoval: Boolean = config("limit_removal", default = false)
@Argument(doc = "Whether to index output BAM file or not") @Argument(doc = "Whether to index output BAM file or not")
var noMakeIndex: Boolean = config("no_make_index", default=false) var noMakeIndex: Boolean = config("no_make_index", default = false)
@Argument(doc = "GTF feature containing intervals (default: exon)") @Argument(doc = "GTF feature containing intervals (default: exon)")
var featureType: Option[String] = config("feature_type") var featureType: Option[String] = config("feature_type")
...@@ -67,7 +67,7 @@ class WipeReads(val root: Configurable) extends ToolCommandFunction { ...@@ -67,7 +67,7 @@ class WipeReads(val root: Configurable) extends ToolCommandFunction {
override def beforeGraph() { override def beforeGraph() {
super.beforeGraph() super.beforeGraph()
if (! noMakeIndex) outputIndex = Some(new File(outputBam.getPath.stripSuffix(".bam") + ".bai")) if (!noMakeIndex) outputIndex = Some(new File(outputBam.getPath.stripSuffix(".bam") + ".bai"))
} }
override def cmdLine = super.cmdLine + override def cmdLine = super.cmdLine +
......
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