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
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)
def clipingFile(contig: Option[String] = None): File = getOutputFile("clipping.tsv", contig)
override def 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()
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment