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When an interval list specifies overlapping intervals merge them before scattering.

This commit is contained in:
Khalid Shakir 2012-02-08 02:12:16 -05:00
parent 6ec686b877
commit 23e7f1bed9
2 changed files with 19 additions and 3 deletions
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4
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervals.scala
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@ -26,7 +26,7 @@ package org.broadinstitute.sting.queue.extensions.gatk
import java.io.File import java.io.File
import collection.JavaConversions._ import collection.JavaConversions._
import org.broadinstitute.sting.utils.interval.IntervalUtils import org.broadinstitute.sting.utils.interval.{IntervalMergingRule, IntervalUtils}
import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource
import net.sf.samtools.SAMFileHeader import net.sf.samtools.SAMFileHeader
import java.util.Collections import java.util.Collections
@ -51,6 +51,8 @@ case class GATKIntervals(reference: File, intervals: List[String]) {
IntervalUtils.parseIntervalArguments(parser, intervals) IntervalUtils.parseIntervalArguments(parser, intervals)
Collections.sort(parsedLocs) Collections.sort(parsedLocs)
Collections.unmodifiableList(parsedLocs) Collections.unmodifiableList(parsedLocs)
val mergedLocs = IntervalUtils.mergeIntervalLocations(parsedLocs, IntervalMergingRule.OVERLAPPING_ONLY)
Collections.unmodifiableList(mergedLocs)
} }
lazy val contigs = locs.map(_.getContig).distinct.toList lazy val contigs = locs.map(_.getContig).distinct.toList

18
public/scala/test/org/broadinstitute/sting/queue/extensions/gatk/GATKIntervalsUnitTest.scala
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@ -32,6 +32,7 @@ import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile
import org.broadinstitute.sting.utils.{GenomeLocSortedSet, GenomeLocParser} import org.broadinstitute.sting.utils.{GenomeLocSortedSet, GenomeLocParser}
import collection.JavaConversions._ import collection.JavaConversions._
import org.broadinstitute.sting.utils.interval.IntervalUtils
class GATKIntervalsUnitTest { class GATKIntervalsUnitTest {
private final lazy val hg18Reference = new File(BaseTest.hg18Reference) private final lazy val hg18Reference = new File(BaseTest.hg18Reference)
@ -57,7 +58,7 @@ class GATKIntervalsUnitTest {
// Assert.assertEquals(gi.getSplits(3).toList, List(1, 2, 3)) // Assert.assertEquals(gi.getSplits(3).toList, List(1, 2, 3))
} }
@Test(timeOut = 30000) @Test(timeOut = 30000L)
def testIntervalFile() { def testIntervalFile() {
var gi = new GATKIntervals(hg19Reference, List(BaseTest.hg19Intervals)) var gi = new GATKIntervals(hg19Reference, List(BaseTest.hg19Intervals))
Assert.assertEquals(gi.locs.size, 189894) Assert.assertEquals(gi.locs.size, 189894)
@ -65,7 +66,7 @@ class GATKIntervalsUnitTest {
// for(Item item: javaConvertedScalaList) // for(Item item: javaConvertedScalaList)
// This for loop is actually an O(N^2) operation as the iterator calls the // This for loop is actually an O(N^2) operation as the iterator calls the
// O(N) javaConvertedScalaList.size() for each iteration of the loop. // O(N) javaConvertedScalaList.size() for each iteration of the loop.
//Assert.assertEquals(gi.getSplits(gi.locs.size).size, 189894) Assert.assertEquals(IntervalUtils.splitFixedIntervals(gi.locs, 189894).size(), 189894)
Assert.assertEquals(gi.contigs.size, 24) Assert.assertEquals(gi.contigs.size, 24)
} }
@ -84,4 +85,17 @@ class GATKIntervalsUnitTest {
Assert.assertEquals(new GATKIntervals(hg18Reference, List("chr1", "chr2", "chr3")).contigs, List("chr1", "chr2", "chr3")) Assert.assertEquals(new GATKIntervals(hg18Reference, List("chr1", "chr2", "chr3")).contigs, List("chr1", "chr2", "chr3"))
Assert.assertEquals(new GATKIntervals(hg18Reference, List("chr1:1-2", "chr1:4-5", "chr2:1-1", "chr3:2-2")).contigs, List("chr1", "chr2", "chr3")) Assert.assertEquals(new GATKIntervals(hg18Reference, List("chr1:1-2", "chr1:4-5", "chr2:1-1", "chr3:2-2")).contigs, List("chr1", "chr2", "chr3"))
} }
@Test
def testSortAndMergeIntervals() {
testSortAndMergeIntervals(Seq("chr1:1-10", "chr1:1-10", "chr1:1-10"), Seq("chr1:1-10"))
testSortAndMergeIntervals(Seq("chr1:1-10", "chr1:1-11", "chr1:1-12"), Seq("chr1:1-12"))
testSortAndMergeIntervals(Seq("chr1:1-10", "chr1:11-20", "chr1:21-30"), Seq("chr1:1-10", "chr1:11-20", "chr1:21-30"))
testSortAndMergeIntervals(Seq("chr1:1-10", "chr1:10-20", "chr1:21-30"), Seq("chr1:1-20", "chr1:21-30"))
testSortAndMergeIntervals(Seq("chr1:1-10", "chr1:21-30", "chr1:10-20"), Seq("chr1:1-20", "chr1:21-30"))
}
private def testSortAndMergeIntervals(actual: Seq[String], expected: Seq[String]) {
Assert.assertEquals(new GATKIntervals(hg18Reference, actual.toList).locs.toSeq, expected.map(hg18GenomeLocParser.parseGenomeLoc(_)))
}
} }