Commit 598f2b3d authored by Peter van 't Hof's avatar Peter van 't Hof

Fix some comments

parent 3e35c32b
......@@ -149,6 +149,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
/** Adds base recalibration jobs */
def addBaseRecalibrator(inputBam: File, dir: File, isIntermediate: Boolean, usePrintreads: Boolean): File = {
require(bqsrFile.isDefined, "bqsrFile should contain something at this point")
val baseRecalibrator = BaseRecalibrator(qscript, inputBam, bqsrFile.get) // at this point bqsrFile should exist
if (baseRecalibrator.knownSites.isEmpty) return inputBam
......@@ -160,11 +161,10 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
add(baseRecalibratorAfter)
add(AnalyzeCovariates(qscript, baseRecalibrator.out, baseRecalibratorAfter.out, swapExt(dir, inputBam, ".bam", ".baserecal.pdf")))
}
val printReads = PrintReads(qscript, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.bam"))
printReads.BQSR = Some(baseRecalibrator.out)
printReads.isIntermediate = isIntermediate
if (usePrintreads) {
val printReads = PrintReads(qscript, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.bam"))
printReads.BQSR = Some(baseRecalibrator.out)
printReads.isIntermediate = isIntermediate
add(printReads)
printReads.out
} else inputBam
......
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