Commit 332551f8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Removed output files

parent 98c67be4
...@@ -40,17 +40,11 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc ...@@ -40,17 +40,11 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
private var outputFiles: List[File] = Nil private var outputFiles: List[File] = Nil
def bamstatsSummary: File = new File(outputDir, "bamstats.summary.json") 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)
def clipingFile(contig: Option[String] = None): File = getOutputFile("clipping.tsv", contig)
override def beforeGraph() { override def beforeGraph() {
super.beforeGraph() super.beforeGraph()
deps :+= new File(bamFile.getAbsolutePath.replaceAll(".bam$", ".bai")) deps :+= new File(bamFile.getAbsolutePath.replaceAll(".bam$", ".bai"))
outputFiles :+= bamstatsSummary outputFiles :+= bamstatsSummary
outputFiles :+= flagstatSummaryFile()
outputFiles :+= mappingQualityFile()
outputFiles :+= clipingFile()
jobOutputFile = new File(outputDir, ".bamstats.out") jobOutputFile = new File(outputDir, ".bamstats.out")
if (reference == null) reference = referenceFasta() if (reference == null) reference = referenceFasta()
} }
......
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