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Updated DoC to work with scatter-gather; and, also manually implemented scatter-gather by sample above the scatter-gather by interval. Thansk to Khalid for his support! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5231 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2011-02-11 19:14:42 +00:00
parent e7d38247bb
commit cdf53188d6
1 changed files with 48 additions and 20 deletions
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68
scala/qscript/oneoffs/fromer/ReadDepthCNVanalysis.scala
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@ -3,8 +3,9 @@ package oneoffs.fromer
import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.QScript
import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.queue.util.BAMutilities
import org.broadinstitute.sting.queue.util.VCF_BAM_utilities
import java.io.PrintWriter
import org.apache.commons.io.IOUtils
class ReadDepthCNVanalysis extends QScript {
qscript =>
@ -39,6 +40,10 @@ class ReadDepthCNVanalysis extends QScript {
@Input(doc = "Starting value of read-depth bins", shortName = "START_BIN", required = false)
var START_BIN = 1
val DOC_OUTPUT_SUFFIX: String = ".sample_interval_summary"
val DOC_MEAN_COVERAGE_OUTPUT: String = ".sample_interval.averageCoverage.txt"
trait CommandLineGATKArgs extends CommandLineGATK {
this.intervalsString = List(qscript.intervals)
this.jarFile = qscript.gatkJarFile
@ -49,13 +54,19 @@ class ReadDepthCNVanalysis extends QScript {
// A target has a list of samples and bam files to use for DoC
class Target(val name: String, val samples: List[String], val bams: List[File]) {
def DoC_output = new File(name + "." + outputDoC)
var prefix: String = outputDoC.getParent()
if (prefix == null)
prefix = ""
else
prefix = prefix + "/"
override def toString(): String = String.format("[Target %s with samples %s against bams %s]", name, samples, bams)
def DoC_output = new File(prefix + name + "." + outputDoC.getName())
override def toString(): String = String.format("[Target %s [%s] with samples %s against bams %s]", name, DoC_output, samples, bams)
}
def script = {
val sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = BAMutilities.getMapOfBamsForSample(BAMutilities.parseBamsInput(bams))
val sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]] = VCF_BAM_utilities.getMapOfBAMsForSample(VCF_BAM_utilities.parseBAMsInput(bams))
val samples: List[String] = sampleToBams.keys.toList
Console.out.printf("Samples are %s%n", samples)
@ -65,6 +76,8 @@ class ReadDepthCNVanalysis extends QScript {
Console.out.printf("Target is %s%n", target)
add(new DoC(target))
}
add(new combineDoC(targets.map(u => new File(u.DoC_output.getPath() + DOC_OUTPUT_SUFFIX))))
}
def buildTargets(samples: List[String], sampleToBams: scala.collection.mutable.Map[String, scala.collection.mutable.Set[File]]): List[Target] = {
@ -73,34 +86,49 @@ class ReadDepthCNVanalysis extends QScript {
case (Nil, y) =>
return Nil
case (subsamples, remaining) =>
return new Target("group" + count, subsamples, BAMutilities.findBamsForSamples(subsamples, sampleToBams)) ::
buildTargetsHelper(remaining, count + 1)
return new Target("group" + count, subsamples, VCF_BAM_utilities.findBAMsForSamples(subsamples, sampleToBams)) ::
buildTargetsHelper(remaining, count + 1)
}
return buildTargetsHelper(samples, 0)
}
class DoC(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.DepthOfCoverage with CommandLineGATKArgs {
this.omitIntervalStatistics = false
this.omitDepthOutputAtEachBase = true
this.omitLocusTable = true
class DoC(t: Target) extends CommandLineGATKArgs with ScatterGatherableFunction {
this.analysis_type = "DepthOfCoverage"
this.minBaseQuality = Some(0)
this.minMappingQuality = Some(0)
this.out = t.DoC_output
this.input_file = t.bams
this.dcov = Some(MAX_DEPTH)
this.downsample_to_coverage = Some(MAX_DEPTH)
this.downsampling_type = Some(DownsampleType.BY_SAMPLE)
this.start = Some(START_BIN)
this.stop = Some(MAX_DEPTH)
this.nBins = Some(NUM_BINS)
this.scatterCount = scatterCountInput
this.scatterClass = classOf[IntervalScatterFunction]
@Output
@Gather(classOf[org.broadinstitute.sting.queue.function.scattergather.SimpleTextGatherFunction])
var intervalSampleOut: File = new File(t.DoC_output.getPath() + DOC_OUTPUT_SUFFIX)
override def commandLine = super.commandLine +
" --omitDepthOutputAtEachBase --omitLocusTable --minBaseQuality 0 --minMappingQuality 0" +
" --start " + START_BIN + " --stop " + MAX_DEPTH + " --nBins " + NUM_BINS +
" -o " + new File(intervalSampleOut.getParentFile(), t.DoC_output.getName())
override def dotString = "DOC: " + t.DoC_output
}
class combineDoC(DoCsToCombine: List[File]) extends CommandLineFunction {
override def description = "Combines DoC outputs for multiple samples (at same loci)"
@Input(doc = "")
var inputDoCfiles: List[File] = DoCsToCombine
@Output
val outputDoCaverageCoverage: File = new File(outputDoC.getPath + DOC_MEAN_COVERAGE_OUTPUT)
var command: String = "~/CNV/wave1+2/scripts/mergeDoC.pl -gatk " + qscript.gatkJarFile.getPath.replaceFirst("dist/GenomeAnalysisTK.jar", "") + " -ref " + qscript.referenceFile + " -out " + outputDoCaverageCoverage
for (input <- inputDoCfiles) {
command += " " + input
}
def commandLine = command
}
}