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Merge pull request #529 from broadinstitute/eb_fix_gvcf_writer_missing_blocks 

Fixing a bug in the GVCF writer.
This commit is contained in:
Eric Banks 2014-02-20 02:37:32 -05:00
parent 235f0c6fa0 53a7d5cbae
commit 132e2429c8
2 changed files with 43 additions and 3 deletions
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15
protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/gvcf/GVCFWriter.java
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@ -84,6 +84,7 @@ public class GVCFWriter implements VariantContextWriter {
/** fields updated on the fly during GVCFWriter operation */ /** fields updated on the fly during GVCFWriter operation */
int nextAvailableStart = -1; int nextAvailableStart = -1;
String contigOfNextAvailableStart = null;
private String sampleName = null; private String sampleName = null;
private HomRefBlock currentBlock = null; private HomRefBlock currentBlock = null;
@ -187,10 +188,17 @@ public class GVCFWriter implements VariantContextWriter {
* @return a VariantContext to be emitted, or null if non is appropriate * @return a VariantContext to be emitted, or null if non is appropriate
*/ */
protected VariantContext addHomRefSite(final VariantContext vc, final Genotype g) { protected VariantContext addHomRefSite(final VariantContext vc, final Genotype g) {
if ( nextAvailableStart != -1 && vc.getStart() <= nextAvailableStart ) { if ( nextAvailableStart != -1 ) {
// don't create blocks while the hom-ref site falls before nextAvailableStart (for deletions) // don't create blocks while the hom-ref site falls before nextAvailableStart (for deletions)
return null; if ( vc.getStart() <= nextAvailableStart && vc.getChr().equals(contigOfNextAvailableStart) ) {
} else if ( currentBlock == null ) { return null;
}
// otherwise, reset to non-relevant
nextAvailableStart = -1;
contigOfNextAvailableStart = null;
}
if ( currentBlock == null ) {
currentBlock = createNewBlock(vc, g); currentBlock = createNewBlock(vc, g);
return null; return null;
} else if ( currentBlock.withinBounds(g.getGQ()) ) { } else if ( currentBlock.withinBounds(g.getGQ()) ) {
@ -302,6 +310,7 @@ public class GVCFWriter implements VariantContextWriter {
// g is variant, so flush the bands and emit vc // g is variant, so flush the bands and emit vc
emitCurrentBlock(); emitCurrentBlock();
nextAvailableStart = vc.getEnd(); nextAvailableStart = vc.getEnd();
contigOfNextAvailableStart = vc.getChr();
underlyingWriter.add(vc); underlyingWriter.add(vc);
} }
} }

31
protected/gatk-protected/src/test/java/org/broadinstitute/sting/utils/gvcf/GVCFWriterUnitTest.java
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@ -202,6 +202,37 @@ public class GVCFWriterUnitTest extends BaseTest {
assertGoodVC(mockWriter.emitted.get(1), "21", 3, 3, false); assertGoodVC(mockWriter.emitted.get(1), "21", 3, 3, false);
} }
@Test
public void testCrossingContigBoundaryToLowerPositionsRef() {
final GVCFWriter writer = new GVCFWriter(mockWriter, standardPartition);
writer.add(makeHomRef("20", 30, 30));
writer.add(makeHomRef("20", 31, 30));
Assert.assertEquals(mockWriter.emitted.size(), 0);
writer.add(makeHomRef("21", 10, 30));
Assert.assertEquals(mockWriter.emitted.size(), 1);
assertGoodVC(mockWriter.emitted.get(0), "20", 30, 31, false);
writer.add(makeNonRef("21", 11, 30));
Assert.assertEquals(mockWriter.emitted.size(), 3);
assertGoodVC(mockWriter.emitted.get(1), "21", 10, 10, false);
assertGoodVC(mockWriter.emitted.get(2), "21", 11, 11, true);
}
@Test
public void testCrossingContigBoundaryFromNonRefToLowerPositionsRef() {
final GVCFWriter writer = new GVCFWriter(mockWriter, standardPartition);
writer.add(makeNonRef("20", 20, 30));
Assert.assertEquals(mockWriter.emitted.size(), 1);
writer.add(makeHomRef("21", 10, 30));
Assert.assertEquals(mockWriter.emitted.size(), 1);
assertGoodVC(mockWriter.emitted.get(0), "20", 20, 20, true);
writer.add(makeNonRef("21", 11, 30));
Assert.assertEquals(mockWriter.emitted.size(), 3);
assertGoodVC(mockWriter.emitted.get(1), "21", 10, 10, false);
assertGoodVC(mockWriter.emitted.get(2), "21", 11, 11, true);
}
@Test @Test
public void testCrossingContigBoundaryNonRef() { public void testCrossingContigBoundaryNonRef() {
final GVCFWriter writer = new GVCFWriter(mockWriter, standardPartition); final GVCFWriter writer = new GVCFWriter(mockWriter, standardPartition);