zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added respectPhaseInInput flag to RBP and integration tests

This commit is contained in:
Menachem Fromer 2012-03-22 17:40:21 -04:00
parent 1dfaacfeb5
commit b9b9219ac7
2 changed files with 40 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

22
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
View File

@ -129,6 +129,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
@Argument(fullName = "permitNoSampleOverlap", shortName = "permitNoSampleOverlap", doc = "Don't exit (just WARN) when the VCF and BAMs do not overlap in samples", required = false)
private boolean permitNoSampleOverlap = false;
@Argument(fullName = "respectPhaseInInput", shortName = "respectPhaseInInput", doc = "Will only phase genotypes in cases where the resulting output will necessarily be consistent with any existing phase (for example, from trios)", required = false)
private boolean respectPhaseInInput = false;
private GenomeLoc mostDownstreamLocusReached = null;
private LinkedList<VariantAndReads> unphasedSiteQueue = null;
@ -487,6 +490,13 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
private int phasingSiteIndex = -1;
private Map<String, PhasingRead> readsAtHetSites = null;
private void clearFields() {
hetGenotypes = null;
prevHetAndInteriorIt = null;
phasingSiteIndex = -1;
readsAtHetSites = null;
}
public boolean hasPreviousHets() {
return phasingSiteIndex > 0;
}
@ -513,12 +523,20 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
}
phasingSiteIndex = listHetGenotypes.size();
if (phasingSiteIndex == 0) { // no previous sites against which to phase
hetGenotypes = null;
prevHetAndInteriorIt = null;
clearFields();
return;
}
prevHetAndInteriorIt.previous(); // so that it points to the previous het site [and NOT one after it, due to the last call to next()]
if (respectPhaseInInput) {
Genotype prevHetGenotype = prevHetAndInteriorIt.clone().next().unfinishedVariant.getGenotype(sample);
if (!prevHetGenotype.isPhased()) {
// Make this genotype unphaseable, since its previous het is not already phased [as required by respectPhaseInInput]:
clearFields();
return;
}
}
// Add the (het) position to be phased:
GenomeLoc phaseLocus = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vr.variant);
GenotypeAndReadBases grbPhase = new GenotypeAndReadBases(vr.variant.getGenotype(sample), vr.sampleReadBases.get(sample), phaseLocus);

20
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
View File

@ -80,4 +80,24 @@ public class ReadBackedPhasingIntegrationTest extends WalkerTest {
executeTest("MAX 10 het sites [TEST SIX]; require PQ >= 10; cacheWindow = 20000; has inconsistent sites", spec);
}
@Test
public void test7() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "CEU.trio.2010_03.genotypes.hg18.vcf", 20000, 10, 10)
+ " -L chr20:332341-802503",
1,
Arrays.asList("c37548b333b65f58d0edfc5c2a62a28a"));
executeTest("Use trio-phased VCF, but ignore its phasing [TEST SEVEN]", spec);
}
@Test
public void test8() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "CEU.trio.2010_03.genotypes.hg18.vcf", 20000, 10, 10)
+ " -L chr20:332341-802503" + " -respectPhaseInInput",
1,
Arrays.asList("dfc7cdddd702e63d46d04f61a3ecd720"));
executeTest("Use trio-phased VCF, and respect its phasing [TEST EIGHT]", spec);
}
}