Commit 62fef674 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix compile errors

parent b9a543ec
......@@ -104,7 +104,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
indelRealigner.isIntermediate = isIntermediate
add(indelRealigner)
indelRealigner.o
indelRealigner.out
}
/** Adds base recalibration jobs */
......@@ -116,18 +116,18 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
if (config("use_analyze_covariates", default = false).asBoolean) {
val baseRecalibratorAfter = BaseRecalibrator(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.after"))
baseRecalibratorAfter.BQSR = baseRecalibrator.o
baseRecalibratorAfter.BQSR = baseRecalibrator.out
add(baseRecalibratorAfter)
add(AnalyzeCovariates(this, baseRecalibrator.o, baseRecalibratorAfter.o, swapExt(dir, inputBam, ".bam", ".baserecal.pdf")))
add(AnalyzeCovariates(this, baseRecalibrator.out, baseRecalibratorAfter.out, swapExt(dir, inputBam, ".bam", ".baserecal.pdf")))
}
val printReads = PrintReads(this, inputBam, swapExt(dir, inputBam, ".bam", ".baserecal.bam"))
printReads.BQSR = baseRecalibrator.o
printReads.BQSR = baseRecalibrator.out
printReads.isIntermediate = isIntermediate
add(printReads)
printReads.o
printReads.out
}
}
......
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