Commit 819bada6 authored by Peter van 't Hof's avatar Peter van 't Hof

Added output files to bamstats

parent 8654affb
......@@ -3,10 +3,10 @@ package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
import nl.lumc.sasc.biopet.core.summary.Summarizable
import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.Input
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
/**
* Created by pjvanthof on 18/11/2016.
......@@ -36,6 +36,9 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
}
}
@Output
private var outputFiles: List[File] = Nil
def bamstatsSummary: File = new File(outputDir, "bamstats.summary.json")
def flagstatSummaryFile(contig: Option[String] = None): File = getOutputFile("flagstats.summary.json", contig)
def mappingQualityFile(contig: Option[String] = None): File = getOutputFile("mapping_quality.tsv", contig)
......@@ -44,6 +47,10 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
override def beforeGraph() {
super.beforeGraph()
deps :+= new File(bamFile.getAbsolutePath.replaceAll(".bam$", ".bai"))
outputFiles :+= bamstatsSummary
outputFiles :+= flagstatSummaryFile()
outputFiles :+= mappingQualityFile()
outputFiles :+= clipingFile()
jobOutputFile = new File(outputDir, ".bamstats.out")
if (reference == null) reference = referenceFasta()
}
......
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