118 lines
5.4 KiB
Plaintext
Executable File
118 lines
5.4 KiB
Plaintext
Executable File
import org.broadinstitute.sting.commandline.{Argument, Output, Input}
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import org.broadinstitute.sting.queue.extensions.gatk.{IntervalScatterFunction, CommandLineGATK}
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.utils.text.XReadLines
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import collection.JavaConversions._
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class ScatterGatherAssociation extends QScript {
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@Argument(fullName="gatkJar",shortName="gatk",doc="Path to the GATK jarfile",required=true)
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var gatkJar : File = _
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@Argument(fullName="metaData",shortName="SM",doc="Sample meta data",required=true)
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var metaData : File = _
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@Argument(fullName="bamList",shortName="I",doc="list of bam files (single .list file)",required=true)
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var bamList : File = _
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@Argument(fullName="outputBase",shortName="o",doc="Base for output files",required=true)
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var outBase : String = _
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@Argument(fullName="noBedGraph",shortName="nbg",doc="Don't use bedgraph format",required=false)
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var dontUseBedGraph : Boolean = false
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@Argument(fullName="reference",shortName="R",doc="Reference file, if not hg19",required=false)
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var referenceFile : File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
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@Argument(fullName="intervals",shortName="L",doc="Interval list, if not whole-exome 1.1",required=false)
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var intervalsFile : File = new File("/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list")
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@Argument(fullName="memoryLimit",shortName="M",doc="Memory limit for SG jobs",required=false)
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var memLimit : Int = 4
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@Argument(fullName="scatterJobs",shortName="SJ",doc="Number of scatter jobs",required=false)
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var scatterJobs : Int = 125
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val ASSOCIATION_TESTS = List("BaseQualityScore","InsertSizeDistribution","MappingQuality0",
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"MateMappingQuality","MateOtherContig","MateSameStrand","MateUnmapped","MismatchRate",
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"ProperPairs","ReadClipping","ReadIndels","ReadMappingQuality","ReferenceMismatches",
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"SampleDepth")
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class RegionalAssociationSG(base : String, ext : String) extends CommandLineGATK with ScatterGatherableFunction{
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this.analysis_type = "RegionalAssociation"
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@Argument(doc="useBed")
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var useBed : Boolean = true
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// the rest are output files implicitly constructed by the multiplexer
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@Output(doc="bqs")
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@Gather(classOf[SimpleTextGatherFunction])
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var bqs : File = new File(String.format("%s.%s.%s", base, "BaseQualityScore", ext))
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@Output(doc="isd")
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@Gather(classOf[SimpleTextGatherFunction])
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var isd : File = new File(String.format("%s.%s.%s",base,"InsertSizeDistribution",ext))
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@Output(doc="mq0")
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@Gather(classOf[SimpleTextGatherFunction])
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var mq0 : File = new File(String.format("%s.%s.%s",base,"MappingQuality0",ext))
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@Output(doc="mmq")
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@Gather(classOf[SimpleTextGatherFunction])
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var mmq : File = new File(String.format("%s.%s.%s",base,"MateMappingQuality",ext))
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@Output(doc="moc")
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@Gather(classOf[SimpleTextGatherFunction])
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var moc : File = new File(String.format("%s.%s.%s",base,"MateOtherContig",ext))
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@Output(doc="mss")
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@Gather(classOf[SimpleTextGatherFunction])
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var mss : File = new File(String.format("%s.%s.%s",base,"MateSameStrand",ext))
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@Output(doc="mu")
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@Gather(classOf[SimpleTextGatherFunction])
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var mu : File = new File(String.format("%s.%s.%s",base,"MateUnmapped",ext))
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@Output(doc="mmr")
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@Gather(classOf[SimpleTextGatherFunction])
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var mmr : File = new File(String.format("%s.%s.%s",base,"MismatchRate",ext))
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@Output(doc="pp")
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@Gather(classOf[SimpleTextGatherFunction])
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var pp : File = new File(String.format("%s.%s.%s",base,"ProperPairs",ext))
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@Output(doc="rc")
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@Gather(classOf[SimpleTextGatherFunction])
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var rc : File = new File(String.format("%s.%s.%s",base,"ReadClipping",ext))
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@Output(doc="ri")
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@Gather(classOf[SimpleTextGatherFunction])
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var ri : File = new File(String.format("%s.%s.%s",base,"ReadIndels",ext))
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@Output(doc="rmq")
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@Gather(classOf[SimpleTextGatherFunction])
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var rmq : File = new File(String.format("%s.%s.%s",base,"ReadMappingQuality",ext))
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@Output(doc="rm")
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@Gather(classOf[SimpleTextGatherFunction])
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var rm : File = new File(String.format("%s.%s.%s",base,"ReferenceMismatches",ext))
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@Output(doc="sd")
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@Gather(classOf[SimpleTextGatherFunction])
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var sd : File = new File(String.format("%s.%s.%s",base,"SampleDepth",ext))
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@Output(doc="rli")
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@Gather(classOf[SimpleTextGatherFunction])
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var rli : File = new File(String.format("%s.%s.%s",base,"ReadsLargeInsertSize",ext))
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override def commandLine = {
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var bedStr : String = ""
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if ( useBed ) {
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bedStr = " -bg "
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}
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super.commandLine + " -AT ALL -o %s%s".format(base,bedStr)
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}
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}
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def script = {
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var ext : String = ""
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if ( dontUseBedGraph ) {
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ext = "tdf"
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} else {
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ext = "bedgraph"
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}
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var association = new RegionalAssociationSG(outBase,ext)
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association.useBed = ! dontUseBedGraph
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association.sample_metadata :+= metaData
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association.intervals :+= intervalsFile
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association.reference_sequence = referenceFile
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association.jarFile = gatkJar
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association.input_file ++= asScalaIterable((new XReadLines(bamList)).readLines).map(u => new File(u)).toList
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association.scatterCount = scatterJobs
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association.memoryLimit = Some(memLimit)
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association.scatterClass = classOf[IntervalScatterFunction]
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add(association)
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}
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} |