From ff4e31c554f65d9d6ba28a08760409d746602d4a Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Wed, 13 Jul 2011 12:59:18 -0400 Subject: [PATCH] Changing the file names as per Kris request. --- .../queue/qscripts/RecalibrateBaseQualities.scala | 10 +++++----- 1 file changed, 5 insertions(+), 5 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 51de3a7ad..dc9ae0f4b 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala @@ -41,11 +41,11 @@ class RecalibrateBaseQualities extends QScript { nContigs = getNumberOfContigs(input) - val recalFile1: File = swapExt(input, ".bam", "recal1.csv") - val recalFile2: File = swapExt(input, ".bam", "recal2.csv") - val recalBam: File = swapExt(input, ".bam", "recal.bam") - val path1: String = "before" - val path2: String = "after" + val recalFile1: File = swapExt(input, ".bam", ".recal1.csv") + val recalFile2: File = swapExt(input, ".bam", ".recal2.csv") + val recalBam: File = swapExt(input, ".bam", ".recal.bam") + val path1: String = input + "before" + val path2: String = input + "after" add(cov(input, recalFile1), recal(input, recalFile1, recalBam),