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functional recalibrate script 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4034 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-08-14 16:01:37 +00:00
parent 4710015c17
commit c85ab9db37
1 changed files with 17 additions and 8 deletions
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19
scala/qscript/recalibrate.scala
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@ -12,6 +12,14 @@ class recalibrate extends QScript {
@Argument(doc="gatk jar file") @Argument(doc="gatk jar file")
var gatkJarFile: File = _ var gatkJarFile: File = _
@Argument(doc="Assume initial count covariates has completed", required=false)
var skipInitialCountCovariates: Boolean = false
@Argument(shortName = "R", doc="ref")
var referenceFile: File = _
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; reference_sequence = referenceFile; }
def script = { def script = {
for (bamIn <- bamIns) { for (bamIn <- bamIns) {
val root = bamIn.getPath() val root = bamIn.getPath()
@ -19,7 +27,8 @@ def script = {
val recalData = new File(bamRoot + ".recal_data.csv") val recalData = new File(bamRoot + ".recal_data.csv")
val recalBam = new File(bamRoot + ".recal.bam") val recalBam = new File(bamRoot + ".recal.bam")
val recalRecalData = new File(bamRoot + ".recal.recal_data.csv") val recalRecalData = new File(bamRoot + ".recal.recal_data.csv")
//add(new CountCovariates(bamIn, recalData, "-OQ")) if ( ! skipInitialCountCovariates )
add(new CountCovariates(bamIn, recalData) { useOriginalQualities = true } )
val tableRecal = new TableRecalibrate(bamIn, recalData, recalBam) { useOriginalQualities = true } val tableRecal = new TableRecalibrate(bamIn, recalData, recalBam) { useOriginalQualities = true }
if ( scatter ) { if ( scatter ) {
tableRecal.intervals = new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list") tableRecal.intervals = new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list")
@ -39,7 +48,7 @@ class Index(bamIn: File) extends BamIndexFunction {
bamFile = bamIn bamFile = bamIn
} }
class CountCovariates(bamIn: File, recalDataIn: File) extends org.broadinstitute.sting.queue.extensions.gatk.CountCovariates { class CountCovariates(bamIn: File, recalDataIn: File) extends org.broadinstitute.sting.queue.extensions.gatk.CountCovariates with UNIVERSAL_GATK_ARGS {
this.jarFile = gatkJarFile this.jarFile = gatkJarFile
this.input_file :+= bamIn this.input_file :+= bamIn
this.recal_file = recalDataIn this.recal_file = recalDataIn
@ -47,12 +56,12 @@ class CountCovariates(bamIn: File, recalDataIn: File) extends org.broadinstitute
this.logging_level = "INFO" this.logging_level = "INFO"
this.max_reads_at_locus = Some(20000) this.max_reads_at_locus = Some(20000)
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate") this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
this.memoryLimit = Some(4) this.memoryLimit = Some(3)
override def dotString = "CountCovariates: %s [args %s]".format(bamIn.getName, if (this.num_threads.isDefined) "-nt " + this.num_threads else "") override def dotString = "CountCovariates: %s [args %s]".format(bamIn.getName, if (this.num_threads.isDefined) "-nt " + this.num_threads else "")
} }
class TableRecalibrate(bamInArg: File, recalDataIn: File, bamOutArg: File) extends org.broadinstitute.sting.queue.extensions.gatk.TableRecalibration { class TableRecalibrate(bamInArg: File, recalDataIn: File, bamOutArg: File) extends org.broadinstitute.sting.queue.extensions.gatk.TableRecalibration with UNIVERSAL_GATK_ARGS {
this.jarFile = gatkJarFile this.jarFile = gatkJarFile
this.input_file :+= bamInArg this.input_file :+= bamInArg
this.recal_file = recalDataIn this.recal_file = recalDataIn
@ -70,7 +79,7 @@ class AnalyzeCovariates(recalDataIn: File, outputDir: File) extends org.broadin
this.path_to_resources = "/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/R/" this.path_to_resources = "/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/R/"
this.ignoreQ = Some(5) this.ignoreQ = Some(5)
this.path_to_Rscript = "/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.7.2/bin/Rscript" this.path_to_Rscript = "/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.7.2/bin/Rscript"
this.memoryLimit = Some(4) this.memoryLimit = Some(2)
override def dotString = "AnalyzeCovariates: %s".format(recalDataIn.getName) override def dotString = "AnalyzeCovariates: %s".format(recalDataIn.getName)
} }