Commit 4f24e9f3 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove old functions

parent 3decab94
......@@ -228,36 +228,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
outputFiles += ("finalBamFile" -> bamFile)
}
// def addSortSam(inputSam: List[File], outputFile: File, dir: String): File = {
// val sortSam = new SortSam
// sortSam.input = inputSam
// sortSam.createIndex = true
// sortSam.output = outputFile
// sortSam.memoryLimit = 2
// sortSam.nCoresRequest = 2
// sortSam.jobResourceRequests :+= "h_vmem=4G"
// if (!skipMarkduplicates) sortSam.isIntermediate = true
// add(sortSam)
//
// return sortSam.output
// }
// def addMergeBam(inputSam: List[File], outputFile: File, dir: String): File = {
// val mergeSam = new MergeSamFiles
// mergeSam.input = inputSam
// mergeSam.createIndex = true
// mergeSam.output = outputFile
// mergeSam.memoryLimit = 2
// mergeSam.nCoresRequest = 2
// mergeSam.assumeSorted = true
// mergeSam.USE_THREADING = true
// mergeSam.jobResourceRequests :+= "h_vmem=4G"
// if (!skipMarkduplicates) mergeSam.isIntermediate = true
// add(mergeSam)
//
// return mergeSam.output
// }
def addAddOrReplaceReadGroups(inputSam: File, outputDir: String): File = {
val addOrReplaceReadGroups = AddOrReplaceReadGroups(this, inputSam, outputDir)
addOrReplaceReadGroups.createIndex = true
......
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