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Merged bug fix from Stable into Unstable

This commit is contained in:
Khalid Shakir 2012-02-08 02:14:26 -05:00
parent f30731f19b 23e7f1bed9
commit ef74363b1b
2 changed files with 18 additions and 2 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
@ -50,6 +50,8 @@ case class GATKIntervals(reference: File, intervals: Seq[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.toSeq lazy val contigs = locs.map(_.getContig).distinct.toSeq

16
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)
@ -60,7 +61,7 @@ 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)
} }
@ -77,4 +78,17 @@ class GATKIntervalsUnitTest {
Assert.assertEquals(new GATKIntervals(hg18Reference, Seq("chr1", "chr2", "chr3")).contigs, Seq("chr1", "chr2", "chr3")) Assert.assertEquals(new GATKIntervals(hg18Reference, Seq("chr1", "chr2", "chr3")).contigs, Seq("chr1", "chr2", "chr3"))
Assert.assertEquals(new GATKIntervals(hg18Reference, Seq("chr1:1-2", "chr1:4-5", "chr2:1-1", "chr3:2-2")).contigs, Seq("chr1", "chr2", "chr3")) Assert.assertEquals(new GATKIntervals(hg18Reference, Seq("chr1:1-2", "chr1:4-5", "chr2:1-1", "chr3:2-2")).contigs, Seq("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(_)))
}
} }