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Proper fix for previous RR -cancer_mode fix. 

I "fixed" this once before but instead of testing with unit tests I used integration tests.
Bad decision.

The proper fix is in now, with a bonafide unit test included.
This commit is contained in:
Eric Banks 2013-06-26 14:48:09 -04:00
parent 28d4c3debc
commit 876e40466a
2 changed files with 28 additions and 1 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
View File

@ -878,7 +878,7 @@ public class SlidingWindow {
int stop = region.getStop() - windowHeaderStart;
// make sure the bitset is complete given the region (it might not be in multi-sample mode)
if ( region.getStop() > markedSites.getStartLocation() + markedSites.getVariantSiteBitSet().length )
if ( region.getStop() > markedSites.getStartLocation() + markedSites.getVariantSiteBitSet().length - 1 )
markSites(region.getStop());
CloseVariantRegionResult closeVariantRegionResult = closeVariantRegion(start, stop, knownSnpPositions);

27
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindowUnitTest.java
View File

@ -253,6 +253,33 @@ public class SlidingWindowUnitTest extends BaseTest {
return count;
}
@Test(enabled = true)
public void testMarkingRegionInCancerMode() {
final int contextSize = 10;
final SlidingWindow slidingWindow = new SlidingWindow("1", 0, contextSize, header, new GATKSAMReadGroupRecord("test"), 0, 0.05, 0.05, 0.05, 20, 20, 100, ReduceReads.DownsampleStrategy.Normal, false);
slidingWindow.addRead(createSimpleRead("1", 0, 34, 75));
slidingWindow.addRead(createSimpleRead("2", 0, 97, 73));
slidingWindow.addRead(createSimpleRead("3", 0, 98, 75));
slidingWindow.addRead(createSimpleRead("4", 0, 98, 75));
slidingWindow.addRead(createSimpleRead("5", 0, 98, 75));
final CompressionStash regions = new CompressionStash();
regions.add(new FinishedGenomeLoc("1", 0, 89, 109, true));
slidingWindow.closeVariantRegions(regions, null, false);
Assert.assertEquals(slidingWindow.getMarkedSitesForTesting().getVariantSiteBitSet().length, 76 + contextSize);
}
private GATKSAMRecord createSimpleRead(final String name, final int refIndex, final int alignmentStart, final int length) {
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, name, refIndex, alignmentStart, length);
read.setReadBases(Utils.dupBytes((byte) 'A', length));
read.setBaseQualities(Utils.dupBytes((byte) 30, length));
read.setMappingQuality(60);
return read;
}
/////////////////////////////////////////////////////////////////
//// This section tests the consensus creation functionality ////