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just recalibrates now recalibrates one sample, fully, not splitting intervals (naming makes more sense) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5746 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-05-03 21:42:23 +00:00
parent c2f8536e02
commit 9f2a8033ff
1 changed files with 15 additions and 41 deletions
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56
scala/qscript/oneoffs/carneiro/justRecalibrate.scala
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@ -25,9 +25,6 @@ class justRecalibrate extends QScript {
@Input(doc="path to R resources folder inside the Sting repository", fullName="path_to_r", shortName="r", required=false)
var R: String = new File("/humgen/gsa-scr1/carneiro/stable/R")
@Input(doc="bad regions interval", shortName="bad", required=false)
var badInterval: File = new File("/humgen/gsa-hpprojects/dev/carneiro/goodbad/data/bad_regions.hg19.intervals")
@Input(doc="Reference fasta file", shortName="R", required=false)
var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
@ -35,36 +32,23 @@ class justRecalibrate extends QScript {
var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
val queueLogDir: String = ".qlog/"
val nContigs: Int = 85 // Take it from the BAM file if you want to be more sophisticated!
def script = {
val first: Boolean = true
val bad: Boolean = true
val badRecalFile1: File = new File("bad_recal1.csv");
val badRecalFile2: File = new File("bad_recal2.csv");
val badBam: File = new File("bad.bam");
val badPath1: String = "bad1";
val badPath2: String = "bad2";
val recalFile1: File = new File("recal1.csv")
val recalFile2: File = new File("recal2.csv")
val bam: File = new File("recal.bam")
val path1: String = "before"
val path2: String = "after"
val goodRecalFile1: File = new File("good_recal1.csv")
val goodRecalFile2: File = new File("good_recal2.csv")
val goodBam: File = new File("good.bam")
val goodPath1: String = "good1"
val goodPath2: String = "good2"
add(cov(input, badRecalFile1, first, bad),
recal(input, badRecalFile1, badBam, bad),
cov(badBam, badRecalFile2, !first, bad),
analyzeCovariates(badRecalFile1, badPath1),
analyzeCovariates(badRecalFile2, badPath2))
add(cov(input, goodRecalFile1, first, !bad),
recal(input, goodRecalFile1, goodBam, !bad),
cov(goodBam, goodRecalFile2, !first, !bad),
analyzeCovariates(goodRecalFile1, goodPath1),
analyzeCovariates(goodRecalFile2, goodPath2))
add(cov(input, recalFile1, first),
recal(input, recalFile1, bam),
cov(bam, recalFile2, !first),
analyzeCovariates(recalFile1, path1),
analyzeCovariates(recalFile2, path2))
}
trait CommandLineGATKArgs extends CommandLineGATK {
@ -74,7 +58,7 @@ class justRecalibrate extends QScript {
this.isIntermediate = true
}
case class cov (inBam: File, outRecalFile: File, FIRST: Boolean, BAD: Boolean) extends CountCovariates with CommandLineGATKArgs {
case class cov (inBam: File, outRecalFile: File, FIRST: Boolean) extends CountCovariates with CommandLineGATKArgs {
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
this.input_file :+= inBam
@ -82,27 +66,17 @@ class justRecalibrate extends QScript {
this.useOriginalQualities = FIRST
this.analysisName = queueLogDir + outRecalFile + ".covariates"
this.jobName = queueLogDir + outRecalFile + ".covariates"
if (BAD) {
this.intervals :+= badInterval
this.scatterCount = 85
}
else
this.excludeIntervals :+= badInterval
this.scatterCount = nContigs
}
case class recal (inBam: File, inRecalFile: File, outBam: File, BAD: Boolean) extends TableRecalibration with CommandLineGATKArgs {
case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
this.input_file :+= inBam
this.recal_file = inRecalFile
this.out = outBam
this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration"
this.jobName = queueLogDir + outBam + ".recalibration"
if (BAD) {
this.intervals :+= badInterval
this.scatterCount = 85
}
else
this.excludeIntervals :+= badInterval
this.scatterCount = nContigs
}
case class analyzeCovariates (inRecalFile: File, outPath: String) extends AnalyzeCovariates {