support for scala walkers
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1468 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
parent
7cf9a54b64
commit
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49
build.xml
49
build.xml
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@ -175,6 +175,55 @@
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</javac>
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</target>
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<property name="scala.home" value="/home/radon01/depristo/work/local/scala-2.7.5.final"/>
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<property
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name="build.dir"
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value="${base.dir}/build"
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/>
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<target name="init.scala">
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<property
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name="scala-library.jar"
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value="${scala.home}/lib/scala-library.jar"
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/>
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<path id="build.classpath">
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<pathelement location="${scala-library.jar}" />
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<!--<pathelement location="${your.path}" />-->
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<pathelement location="${build.dir}" />
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</path>
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<taskdef name="scalac" classname="scala.tools.ant.Scalac">
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<classpath>
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<pathelement location="${scala.home}/lib/scala-compiler.jar" />
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<pathelement location="${scala-library.jar}" />
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</classpath>
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</taskdef>
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</target>
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<property name="scala.dir" value="scala" />
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<property name="scala.classes" value="scala/classes" />
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<target name="scala" depends="init.scala" description="build the scala code">
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<echo message="Sting: Compiling scala -- omg!"/>
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<mkdir dir="${scala.classes}"/>
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<scalac srcdir="${scala.dir}" destdir="${scala.classes}" force="changed">
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<include name="**/*.scala"/>
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<classpath>
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<path refid="runtime.dependencies" />
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<pathelement location="build"/>
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<pathelement location="lib/junit-4.4.jar"/>
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<pathelement location="${scala.home}/lib/scala-compiler.jar" />
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<pathelement location="${scala-library.jar}" />
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</classpath>
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</scalac>
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<delete file="${dist}/GATKScala.jar"/>
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<jar jarfile="${dist}/GATKScala.jar">
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<fileset dir="${scala.classes}">
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<include name="**/*.class"/>
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</fileset>
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</jar>
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</target>
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<!-- TEST -->
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<target name="test" depends="test.compile,agent" description="Run unit tests">
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<mkdir dir="${report}"/>
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@ -0,0 +1,200 @@
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package org.broadinstitute.sting.scala
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import gatk.walkers.genotyper.{SingleSampleGenotyper, SSGGenotypeCall}
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import java.io.File
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import net.sf.samtools.SAMRecord
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import org.broadinstitute.sting.gatk.walkers.LocusWalker
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext
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import utils._
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import cmdLine.Argument
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class TransitionTable() {
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var table: Array[Array[Double]] = new Array[Array[Double]](4,4)
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def makeKey(b: Char): Int = {
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return BaseUtils.simpleBaseToBaseIndex(b)
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}
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def fromKey(i: Int): Char = {
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return BaseUtils.baseIndexToSimpleBase(i)
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}
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def add(ref: Char, subst: Char) = {
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table(makeKey(ref))(makeKey(subst)) += 1
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}
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def get(i: Int, j: Int): Double = {
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return table(i)(j)
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}
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def set(i: Int, j: Int, d: Double) = {
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//printf("Setting %d / %d => %f%n", i, j, d)
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table(i)(j) = d
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}
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def mapEntries[A](f: ((Int, Int, Double) => A)): List[A] = {
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return for { i <- List.range(0, 4); j <- List.range(0,4) } yield f(i, j, get(i,j))
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}
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def header(): String = {
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return Utils.join("\t", mapEntries((i,j,x) => "P(%c|true=%c)" format (fromKey(j), fromKey(i))).toArray)
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}
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override def toString(): String = {
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return Utils.join("\t", mapEntries((i,j,x) => "%.2f" format x).toArray)
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}
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def sum(): Double = {
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return sumList(table.toList map (x => sumList(x.toList)))
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}
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def sumList(xs: List[Double]): Double = {
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return (0.0 :: xs) reduceLeft {(x, y) => x + y}
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}
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def getRateMatrix(): TransitionTable = {
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var sums = (table.toList map (x => sumList(x.toList))).toArray
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var t = new TransitionTable()
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//println(sums.toList)
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this mapEntries ((i,j,x) => t.set(i, j, x / sums(i)))
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return t
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}
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}
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class BaseTransitionTableCalculator extends LocusWalker[Unit,Int] {
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private var MIN_MAPPING_QUALITY = 30
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private var MIN_BASE_QUALITY = 20
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private var MIN_LOD = 5
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private var PRINT_FREQ = 1000000
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private var CARE_ABOUT_STRAND = true
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private val SSG = new SingleSampleGenotyper()
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private val table1 = new TransitionTable()
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private val tableFWD = new TransitionTable()
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private val tableREV = new TransitionTable()
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private val table2 = new TransitionTable()
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@Argument() { val shortName = "v", val doc = "Print out verbose output", val required = false }
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var VERBOSE: Boolean = false
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override def initialize() {
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SSG.initialize();
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}
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override def map(tracker: RefMetaDataTracker, ref: ReferenceContext, context: AlignmentContext): Unit = {
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val call = SSG.map(tracker, ref, context)
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val pileup = new ReadBackedPileup(ref.getBase(), context)
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def hasNoNs(): Boolean = {
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return ! (pileup.getBases() exists ('N' ==))
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}
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if ( isDefinitelyHomRef(call) && hasNoNs() ) {
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var (refBases, nonRefBases) = splitBases(ref.getBase, pileup.getBases)
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//printf("nonRefBases %s%n", nonRefBases)
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if ( nonRefBases.length > 0 ) {
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var (nonRefReads, offsets) = getNonRefReads(ref.getBase, pileup)
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var nonRefRead: SAMRecord = nonRefReads.head
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nonRefBases.length match {
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case 1 =>
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addRead(nonRefRead, offsets.head, nonRefBases.head, ref, table1)
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addRead(nonRefRead, offsets.head, nonRefBases.head, ref, if ( nonRefRead.getReadNegativeStrandFlag ) tableREV else tableFWD )
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case 2 =>
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addRead(nonRefRead, offsets.head, nonRefBases.head, ref, table2)
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addRead(nonRefReads.tail.head, offsets.tail.head, nonRefBases.tail.head, ref, table2)
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case x =>
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}
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if ( VERBOSE && pileup.size > 30 && nonRefReads.length < 4 )
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printNonRefBases(ref, nonRefReads, offsets, context.getReads.size())
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}
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}
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}
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implicit def listToJavaList[T](l: List[T]) = java.util.Arrays.asList(l.toArray: _*)
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def printNonRefBases(ref: ReferenceContext, nonRefReads: List[SAMRecord], offsets: List[Integer], depth: Integer): Unit = {
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out.println(new ReadBackedPileup(ref.getLocus(), ref.getBase(), listToJavaList(nonRefReads), offsets) + " " + depth)
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}
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def addRead(nonRefRead: SAMRecord, offset: Integer, nonRefBase: Char, ref: ReferenceContext, table: TransitionTable): Unit = {
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if ( goodRead(nonRefRead, offset) ) {
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//printf("Including site:%n call=%s%n nonRefBases=%s%n refBases=%s%n nonRefRead=%s%n offset=%s%n", call, nonRefBases, refBases, nonRefRead.format, offsets.head)
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//println(call.getReadDepth, call.getReferencebase, nonRefBases, refBases, nonRefRead.getMappingQuality)
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if ( CARE_ABOUT_STRAND && nonRefRead.getReadNegativeStrandFlag() ) {
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// it's on the reverse strand
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val refComp: Char = BaseUtils.simpleComplement(ref.getBase)
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val nonRefComp: Char = BaseUtils.simpleComplement(nonRefBase)
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//printf("Negative: %c/%c is actually %c/%c%n", ref.getBase, nonRefBases.head, refComp, nonRefComp)
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table.add(refComp, nonRefComp)
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} else {
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table.add(ref.getBase, nonRefBase)
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}
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}
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}
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def getNonRefReads(ref: Char, pileup: ReadBackedPileup): (List[SAMRecord], List[Integer]) = {
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def getBase(i: Int): Char = {
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var offset = pileup.getOffsets().get(i)
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return pileup.getReads().get(i).getReadString().charAt(offset.asInstanceOf[Int])
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}
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var subset = for { i <- List.range(0, pileup.size) if getBase(i) != ref } yield i
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var reads = subset map (i => pileup.getReads().get(i))
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var offsets = subset map (i => pileup.getOffsets().get(i))
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//println(reads, offsets, subset)
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return (reads, offsets)
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}
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def hasFewNonRefBases(refBase: Char, pileup: String): List[Char] = {
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splitBases(refBase, pileup) match {
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case (refs, nonRefs) =>
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//printf("nrf=%s, rb=%s%n", nonRefs.mkString, refs.mkString)
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return nonRefs
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}
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}
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def goodRead( read: SAMRecord, offset: Integer ): Boolean = {
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return read.getMappingQuality() > MIN_MAPPING_QUALITY && read.getBaseQualities()(offset.intValue) > MIN_BASE_QUALITY
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}
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def splitBases(refBase: Char, pileup: String): (List[Char], List[Char]) = {
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val refBases = pileup.toList filter (refBase ==)
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val nonRefBases = pileup.toList filter (refBase !=)
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return (refBases, nonRefBases)
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}
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def isDefinitelyHomRef(call: SSGGenotypeCall): Boolean = {
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return ! call.isVariation() && call.getBestNext() > MIN_LOD
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}
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def reduceInit(): Int = {
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return 0;
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}
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def reduce(m: Unit, r: Int): Int = {
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return r;
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}
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override def onTraversalDone(r: Int) = {
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out.println("-------------------- FINAL RESULT --------------------")
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out.println("type\t" + table1.header)
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def print1(t: String, x: TransitionTable) = {
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out.println(t + "\t" + x)
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}
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print1("1-mismatch", table1)
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print1("2-mismatch", table2)
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print1("1-mismatch-fwd", tableFWD)
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print1("1-mismatch-rev", tableREV)
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}
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}
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@ -0,0 +1,5 @@
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object HelloWorld {
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def main(args: Array[String]) {
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println("Hello, world!")
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}
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}
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@ -0,0 +1,25 @@
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package org.broadinstitute.sting.scala
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import org.broadinstitute.sting.gatk.walkers.LocusWalker
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext
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class PrintReadsScala extends LocusWalker[Int,Int] {
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override def map(tracker: RefMetaDataTracker, ref: ReferenceContext, context: AlignmentContext): Int = {
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//println(context.getReads().size())
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return 1
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}
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def reduceInit(): Int = {
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return 0;
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}
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def reduce(m: Int, r: Int): Int = {
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return m + r;
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}
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def main(args: Array[String]) {
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println("Hello, world!")
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}
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}
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