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Fixed bug in PhaseByTransmission where it was completely dropping multi-allelic records. 

Added test to make sure this is no longer happening.
This commit is contained in:
Eric Banks 2013-08-21 15:46:57 -04:00
parent cdfd07f9eb
commit d4dc5ba04a
2 changed files with 54 additions and 2 deletions
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8
protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
View File

@ -56,7 +56,6 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.samples.Sample;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.help.HelpConstants;
@ -830,9 +829,14 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
return metricsCounters;
final VariantContext vc = tracker.getFirstValue(variantCollection.variants, context.getLocation());
if (vc == null || !vc.isBiallelic())
if ( vc == null )
return metricsCounters;
if ( !vc.isBiallelic() ) {
vcfWriter.add(vc);
return metricsCounters;
}
final VariantContextBuilder builder = new VariantContextBuilder(vc);
final GenotypesContext genotypesContext = GenotypesContext.copy(vc.getGenotypes());

48
protected/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
View File

@ -46,9 +46,16 @@
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broad.tribble.readers.LineIterator;
import org.broad.tribble.readers.PositionalBufferedStream;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.variant.vcf.VCFCodec;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Arrays;
public class PhaseByTransmissionIntegrationTest extends WalkerTest {
@ -57,6 +64,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
private static String TNTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.TN.vcf";
private static String TPTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.TP.vcf";
private static String FPTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.FP.vcf";
private static String MultiAllelicsTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.multiAllelics.vcf";
private static String SpecialTest = phaseByTransmissionTestDataRoot + "PhaseByTransmission.IntegrationTest.Special.vcf";
//Tests using PbT on all genotypes with default parameters
@ -200,4 +208,44 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
executeTest("testFatherAlleleFirst", spec);
}
@Test
public void testMultiAllelics() throws IOException {
WalkerTestSpec spec = new WalkerTestSpec(
buildCommandLine(
"-T PhaseByTransmission",
"--no_cmdline_in_header",
"-R " + b37KGReference,
"--variant " + MultiAllelicsTest,
"-ped "+ goodFamilyFile,
"-L 1:10109-10315",
"-o %s"
),
1,
Arrays.asList("") // don't care about the md5, just testing that records aren't being dropped
);
final File outputVCF = executeTest("testMultiAllelics", spec).getFirst().get(0);
final VCFCodec codec = new VCFCodec();
final FileInputStream originalStream = new FileInputStream(MultiAllelicsTest);
final LineIterator originalLineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(originalStream));
codec.readHeader(originalLineIterator);
int numOriginalRecords = 0;
while ( originalLineIterator.hasNext() ) {
originalLineIterator.next();
numOriginalRecords++;
}
final FileInputStream newStream = new FileInputStream(outputVCF);
final LineIterator newLineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(newStream));
codec.readHeader(newLineIterator);
int numNewRecords = 0;
while ( newLineIterator.hasNext() ) {
newLineIterator.next();
numNewRecords++;
}
Assert.assertTrue(numOriginalRecords > 0);
Assert.assertEquals(numNewRecords, numOriginalRecords);
}
}