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Commit 9c2720bf authored by Peter van 't Hof's avatar Peter van 't Hof
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Fix RGPI config var

parent 8b4d55c2
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public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+ 2
− 2
View file @ 9c2720bf
...@@ -89,7 +89,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript { ...@@ -89,7 +89,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
var RGDT: Date = _ var RGDT: Date = _
@Argument(doc = "Readgroup predicted insert size", shortName = "RGPI", required = false) @Argument(doc = "Readgroup predicted insert size", shortName = "RGPI", required = false)
var RGPI: Int = config("RGPI") var RGPI: Option[Int] = config("RGPI")
var paired: Boolean = false var paired: Boolean = false
val flexiprep = new Flexiprep(this) val flexiprep = new Flexiprep(this)
...@@ -300,7 +300,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript { ...@@ -300,7 +300,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
if (RGCN != null) RG += "CN:" + RGCN + "\\t" if (RGCN != null) RG += "CN:" + RGCN + "\\t"
if (RGDS != null) RG += "DS" + RGDS + "\\t" if (RGDS != null) RG += "DS" + RGDS + "\\t"
if (RGDT != null) RG += "DT" + RGDT + "\\t" if (RGDT != null) RG += "DT" + RGDT + "\\t"
if (RGPI > 0) RG += "PI" + RGPI + "\\t" if (RGPI.isDefined) RG += "PI" + RGPI.get + "\\t"
return RG.substring(0, RG.lastIndexOf("\\t")) return RG.substring(0, RG.lastIndexOf("\\t"))
} }
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