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Minor fix for merging intervals which hadn't been necessary when only merging from the left to right. Added integration tests to cover the parallelization of RTC.

This commit is contained in:
Eric Banks 2011-10-06 22:38:44 -04:00
parent c61804a450
commit ca9cd9b688
2 changed files with 31 additions and 6 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
View File

@ -415,6 +415,10 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
eventStartPos = lastPosition;
else
eventStartPos = Math.min(eventStartPos, lastPosition);
} else if ( eventStartPos == -1 && e.eventStartPos != -1 ) {
eventStartPos = e.eventStartPos;
eventStopPos = e.eventStopPos;
furthestStopPos = e.furthestStopPos;
}
}
pointEvents.add(newPosition);

33
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
View File

@ -8,20 +8,41 @@ import java.util.Arrays;
public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
@Test
public void testIntervals() {
public void testIntervals1() {
String md5 = "3f0b63a393104d0c4158c7d1538153b8";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000 -o %s",
1,
Arrays.asList("3f0b63a393104d0c4158c7d1538153b8"));
executeTest("test standard", spec1);
Arrays.asList(md5));
executeTest("test standard nt=1", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
"-nt 4 -T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000 -o %s",
1,
Arrays.asList("5085054c78e256432dc75c85a9ac631c"));
executeTest("test dbsnp", spec2);
Arrays.asList(md5));
executeTest("test standard nt=4", spec2);
}
@Test
public void testIntervals2() {
String md5 = "e0f745b79b679c225314a2abef4919ff";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000 -o %s",
1,
Arrays.asList(md5));
executeTest("test with dbsnp nt=1", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
"-nt 4 -T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,200,000 -o %s",
1,
Arrays.asList(md5));
executeTest("test with dbsnp nt=4", spec2);
}
@Test
public void testKnownsOnly() {
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -R " + b36KGReference + " --known " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI known -o %s",
1,