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Added capability of running multiple bam files in the same directory.

This commit is contained in:
Mauricio Carneiro 2011-07-01 16:02:28 -04:00
parent 11d4af0e75
commit d19351f71a
1 changed files with 4 additions and 4 deletions
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8
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
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@ -41,9 +41,9 @@ class RecalibrateBaseQualities extends QScript {
nContigs = getNumberOfContigs(input)
val recalFile1: File = new File("recal1.csv")
val recalFile2: File = new File("recal2.csv")
val recalBam: File = swapExt(input, ".bam", "recal.bam")
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"
@ -88,4 +88,4 @@ class RecalibrateBaseQualities extends QScript {
this.analysisName = queueLogDir + inRecalFile + ".analyze_covariates"
this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
}
}
}