From fd1df31ef0ab60ec735ff5692132441224a02659 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 15 Jul 2011 19:39:42 -0400 Subject: [PATCH] changing the output directory names for Analyze Covariates --- .../sting/queue/qscripts/RecalibrateBaseQualities.scala | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala index 56ca36925..fca420816 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala @@ -42,8 +42,8 @@ class RecalibrateBaseQualities extends QScript { val recalFile1: File = swapExt(bam, ".bam", ".recal1.csv") val recalFile2: File = swapExt(bam, ".bam", ".recal2.csv") val recalBam: File = swapExt(bam, ".bam", ".recal.bam") - val path1: String = bam + "before" - val path2: String = bam + "after" + val path1: String = bam + ".before" + val path2: String = bam + ".after" add(cov(bam, recalFile1), recal(bam, recalFile1, recalBam), @@ -83,7 +83,7 @@ class RecalibrateBaseQualities extends QScript { case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates { this.resources = R this.recal_file = inRecalFile - this.output_dir = outPath.toString + this.output_dir = outPath this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates" this.jobName = queueLogDir + inRecalFile + ".analyze_covariates" }