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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-07-13 13:00:55 -04:00
parent 74aa49e423 ff4e31c554
commit e2f2917bd2
1 changed files with 5 additions and 5 deletions
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10
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
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@ -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),