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