Commit d28ac4f0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix insertsize metrics

parent 5e001a6e
......@@ -57,6 +57,13 @@ trait SummaryQScript extends BiopetQScript {
//TODO: add more checksums types
}
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList) {
summarizable match {
case f: BiopetCommandLineFunctionTrait => f.beforeGraph
case _ =>
}
}
//Automatic checksums
for ((_, summarizableList) <- summarizables; summarizable <- summarizableList; (_, file) <- summarizable.summaryFiles)
addChecksum(file)
......
......@@ -26,13 +26,13 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
javaMainClass = "picard.analysis.CollectInsertSizeMetrics"
@Input(doc = "The input SAM or BAM files to analyze. Must be coordinate sorted.", required = true)
var input: File = _
var input: File = null
@Output(doc = "The output file to write statistics to", required = true)
var output: File = _
var output: File = null
@Output(doc = "Output histogram", required = true)
def outputHistogram: File = new File(output + ".pdf")
protected var outputHistogram: File = null
@Argument(doc = "Reference file", required = false)
var reference: File = config("reference")
......@@ -56,6 +56,7 @@ class CollectInsertSizeMetrics(val root: Configurable) extends Picard with Summa
var histogramWidth: Option[Int] = config("histogramWidth")
override def beforeGraph {
outputHistogram = new File(output + ".pdf")
//if (outputHistogram == null) outputHistogram = new File(output + ".pdf")
//require(reference.exists)
}
......
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