64 lines
1.9 KiB
Scala
64 lines
1.9 KiB
Scala
package oneoffs.fromer
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.gatk.DownsampleType
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class ReadDepthCNVanalysis extends QScript {
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qscript =>
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@Input(doc = "bam input, as .bam or as a list of files", shortName = "I", required = true)
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var bams: File = _
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@Argument(doc = "gatk jar file", shortName = "J", required = true)
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var gatkJarFile: File = _
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@Argument(shortName = "R", doc = "ref", required = true)
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var referenceFile: File = _
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@Argument(shortName = "L", doc = "Intervals", required = false)
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var intervals: String = _
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@Input(doc = "level of parallelism for BAM DoC. By default is set to 0 [no scattering].", shortName = "scatter", required = false)
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var scatterCountInput = 0
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@Output(doc = "DoC file to output", shortName = "o", required = true)
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var outputDoC: File = _
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@Input(doc = "Maximum depth (before GATK down-sampling kicks in...)", shortName = "MAX_DEPTH", required = false)
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var MAX_DEPTH = 20000
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trait CommandLineGATKArgs extends CommandLineGATK {
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this.intervalsString = List(qscript.intervals)
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this.jarFile = qscript.gatkJarFile
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this.reference_sequence = qscript.referenceFile
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//this.memoryLimit = Some(3)
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this.logging_level = "INFO"
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}
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def script = {
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add(new DepthOfCoverage(bams, outputDoC))
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}
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class DepthOfCoverage(bam: File, docOutPath: File) extends org.broadinstitute.sting.queue.extensions.gatk.DepthOfCoverage with CommandLineGATKArgs {
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this.omitIntervalStatistics = false
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this.omitDepthOutputAtEachBase = true
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this.omitLocusTable = true
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this.minBaseQuality = Some(0)
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this.minMappingQuality = Some(0)
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this.out = docOutPath
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this.input_file :+= bam
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this.dcov = Some(MAX_DEPTH)
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this.downsampling_type = Some(DownsampleType.BY_SAMPLE)
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this.scatterCount = scatterCountInput
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override def dotString = "DOC: " + bam.getName
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}
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} |