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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-07-15 19:40:02 -04:00
parent 0cac5e9ebe fd1df31ef0
commit 43bd45fcad
1 changed files with 3 additions and 3 deletions
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6
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
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@ -42,8 +42,8 @@ class RecalibrateBaseQualities extends QScript {
val recalFile1: File = swapExt(bam, ".bam", ".recal1.csv") val recalFile1: File = swapExt(bam, ".bam", ".recal1.csv")
val recalFile2: File = swapExt(bam, ".bam", ".recal2.csv") val recalFile2: File = swapExt(bam, ".bam", ".recal2.csv")
val recalBam: File = swapExt(bam, ".bam", ".recal.bam") val recalBam: File = swapExt(bam, ".bam", ".recal.bam")
val path1: String = bam + "before" val path1: String = bam + ".before"
val path2: String = bam + "after" val path2: String = bam + ".after"
add(cov(bam, recalFile1), add(cov(bam, recalFile1),
recal(bam, recalFile1, recalBam), recal(bam, recalFile1, recalBam),
@ -83,7 +83,7 @@ class RecalibrateBaseQualities extends QScript {
case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates { case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates {
this.resources = R this.resources = R
this.recal_file = inRecalFile this.recal_file = inRecalFile
this.output_dir = outPath.toString this.output_dir = outPath
this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates" this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
this.jobName = queueLogDir + inRecalFile + ".analyze_covariates" this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
} }