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Bug fix: if there are multiple records at a given position, it turns out that SelectVariants would drop all variants that follow after one that fails filters (instead of dropping just the failing one). Added an integration test to cover this case.

This commit is contained in:
Eric Banks 2011-12-19 10:04:33 -05:00
parent 728d66cca4
commit 3069a689fe
2 changed files with 25 additions and 8 deletions
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20
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -493,12 +493,12 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
if (DISCORDANCE_ONLY) {
Collection<VariantContext> compVCs = tracker.getValues(discordanceTrack, context.getLocation());
if (!isDiscordant(vc, compVCs))
return 0;
continue;
}
if (CONCORDANCE_ONLY) {
Collection<VariantContext> compVCs = tracker.getValues(concordanceTrack, context.getLocation());
if (!isConcordant(vc, compVCs))
return 0;
continue;
}
if (alleleRestriction.equals(NumberAlleleRestriction.BIALLELIC) && !vc.isBiallelic())
@ -512,16 +512,20 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
VariantContext sub = subsetRecord(vc, samples);
if ( (sub.isPolymorphicInSamples() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) {
boolean failedJexlMatch = false;
for ( VariantContextUtils.JexlVCMatchExp jexl : jexls ) {
if ( !VariantContextUtils.match(sub, jexl) ) {
return 0;
failedJexlMatch = true;
break;
}
}
if (SELECT_RANDOM_NUMBER) {
randomlyAddVariant(++variantNumber, sub);
}
else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
vcfWriter.add(sub);
if ( !failedJexlMatch ) {
if (SELECT_RANDOM_NUMBER) {
randomlyAddVariant(++variantNumber, sub);
}
else if (!SELECT_RANDOM_FRACTION || ( GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
vcfWriter.add(sub);
}
}
}
}

13
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -116,6 +116,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testUsingDbsnpName--" + testFile, spec);
}
@Test
public void testMultipleRecordsAtOnePosition() {
String testFile = validationDataLocation + "selectVariants.onePosition.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
"-T SelectVariants -R " + b36KGReference + " -select 'KG_FREQ < 0.5' --variant " + testFile + " -o %s -NO_HEADER",
1,
Arrays.asList("20b52c96f5c48258494d072752b53693")
);
executeTest("testMultipleRecordsAtOnePositionFirstIsFiltered--" + testFile, spec);
}
@Test
public void testParallelization() {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";