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Merged bug fix from Stable into Unstable

This commit is contained in:
Mauricio Carneiro 2011-07-14 16:44:57 -04:00
parent c0bbeb23ba 9f5180ab05
commit 4f8230c750
1 changed files with 27 additions and 12 deletions
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37
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
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@ -3,6 +3,7 @@ package org.broadinstitute.sting.queue.qscripts
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import net.sf.samtools.SAMFileReader import net.sf.samtools.SAMFileReader
import io.Source._
/** /**
* Created by IntelliJ IDEA. * Created by IntelliJ IDEA.
@ -37,21 +38,35 @@ class RecalibrateBaseQualities extends QScript {
return samReader.getFileHeader.getSequenceDictionary.getSequences.size() return samReader.getFileHeader.getSequenceDictionary.getSequences.size()
} }
// Reads a BAM LIST file and creates a scala list with all the files
def createListFromFile(in: File):List[File] = {
if (in.toString.endsWith("bam"))
return List(in)
var l: List[File] = List()
for (bam <- fromFile(in).getLines)
l :+= new File(bam)
return l
}
def script = { def script = {
nContigs = getNumberOfContigs(input) val bamList = createListFromFile(input)
nContigs = getNumberOfContigs(bamList(0))
val recalFile1: File = swapExt(input, ".bam", ".recal1.csv") for (bam <- bamList) {
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), val recalFile1: File = swapExt(bam, ".bam", ".recal1.csv")
recal(input, recalFile1, recalBam), val recalFile2: File = swapExt(bam, ".bam", ".recal2.csv")
cov(recalBam, recalFile2), val recalBam: File = swapExt(bam, ".bam", ".recal.bam")
analyzeCovariates(recalFile1, path1), val path1: String = bam + "before"
analyzeCovariates(recalFile2, path2)) val path2: String = bam + "after"
add(cov(bam, recalFile1),
recal(bam, recalFile1, recalBam),
cov(recalBam, recalFile2),
analyzeCovariates(recalFile1, path1),
analyzeCovariates(recalFile2, path2))
}
} }
trait CommandLineGATKArgs extends CommandLineGATK { trait CommandLineGATKArgs extends CommandLineGATK {