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Fix for PBT bug reported on the forum: the AD is actually output correctly now (rather than with 'null' or some gibberish memory pointer).

This commit is contained in:
Eric Banks 2012-12-13 23:28:30 +00:00
parent aeab932c63
commit 696bf95fba
2 changed files with 25 additions and 13 deletions
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26
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
View File

@ -811,9 +811,9 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
updateTrioMetricsCounters(phasedMother,phasedFather,phasedChild,mvCount,metricsCounters);
mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
vc.getChr(),vc.getStart(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.getFamilyID(),
phasedMother.getExtendedAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getDP(),Arrays.asList(phasedMother.getAD()),
phasedMother.getLikelihoodsString(), phasedFather.getGenotypeString(),phasedFather.getDP(),Arrays.asList(phasedFather.getAD()),phasedFather.getLikelihoodsString(),
phasedChild.getGenotypeString(),Arrays.asList(phasedChild.getDP()),phasedChild.getAD(),phasedChild.getLikelihoodsString());
phasedMother.getExtendedAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getDP(),printAD(phasedMother.getAD()),
phasedMother.getLikelihoodsString(), phasedFather.getGenotypeString(),phasedFather.getDP(),printAD(phasedFather.getAD()),phasedFather.getLikelihoodsString(),
phasedChild.getGenotypeString(),phasedChild.getDP(),printAD(phasedChild.getAD()),phasedChild.getLikelihoodsString());
if(!(phasedMother.getType()==mother.getType() && phasedFather.getType()==father.getType() && phasedChild.getType()==child.getType()))
metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
}
@ -823,8 +823,8 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t%s:%s:%s:%s\t.\t.\t.\t.\t%s\t%s\t%s\t%s",
vc.getChr(),vc.getStart(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.getFamilyID(),
phasedMother.getExtendedAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getDP(),Arrays.asList(phasedMother.getAD()),phasedMother.getLikelihoodsString(),
phasedChild.getGenotypeString(),phasedChild.getDP(),Arrays.asList(phasedChild.getAD()),phasedChild.getLikelihoodsString());
phasedMother.getExtendedAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedMother.getGenotypeString(),phasedMother.getDP(),printAD(phasedMother.getAD()),phasedMother.getLikelihoodsString(),
phasedChild.getGenotypeString(),phasedChild.getDP(),printAD(phasedChild.getAD()),phasedChild.getLikelihoodsString());
}
}
else{
@ -834,8 +834,8 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
metricsCounters.put(NUM_GENOTYPES_MODIFIED,metricsCounters.get(NUM_GENOTYPES_MODIFIED)+1);
mvfLine = String.format("%s\t%d\t%s\t%s\t%s\t.\t.\t.\t.\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
vc.getChr(),vc.getStart(),vc.getAttribute(VCFConstants.ALLELE_COUNT_KEY),sample.getFamilyID(),
phasedFather.getExtendedAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedFather.getGenotypeString(),phasedFather.getDP(),Arrays.asList(phasedFather.getAD()),phasedFather.getLikelihoodsString(),
phasedChild.getGenotypeString(),phasedChild.getDP(),Arrays.asList(phasedChild.getAD()),phasedChild.getLikelihoodsString());
phasedFather.getExtendedAttribute(TRANSMISSION_PROBABILITY_TAG_NAME),phasedFather.getGenotypeString(),phasedFather.getDP(),printAD(phasedFather.getAD()),phasedFather.getLikelihoodsString(),
phasedChild.getGenotypeString(),phasedChild.getDP(),printAD(phasedChild.getAD()),phasedChild.getLikelihoodsString());
}
//Report violation if set so
@ -850,6 +850,18 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
return metricsCounters;
}
private static String printAD(final int[] AD) {
if ( AD == null || AD.length == 0 )
return ".";
final StringBuilder sb = new StringBuilder();
sb.append(AD[0]);
for ( int i = 1; i < AD.length; i++) {
sb.append(",");
sb.append(AD[i]);
}
return sb.toString();
}
/**
* Initializes the reporting counters.
*

12
public/java/test/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmissionIntegrationTest.java
View File

@ -29,7 +29,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("f4b0b5471e03306ee2fad27d88b217b6","f8721f4f5d3bae2848ae15c3f120709b")
Arrays.asList("af979bcb353edda8dee2127605c71daf","1ea9994f937012e8de599ec7bcd62a0e")
);
executeTest("testTrueNegativeMV", spec);
}
@ -48,7 +48,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("dbc64776dcc9e01a468b61e4e0db8277","547fdfef393f3045a96d245ef6af8acb")
Arrays.asList("1dc36ff8d1d5f5d2c1c1bf21517263bf","547fdfef393f3045a96d245ef6af8acb")
);
executeTest("testTruePositiveMV", spec);
}
@ -67,7 +67,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("37793e78861bb0bc070884da67dc10e6","9529e2bf214d72e792d93fbea22a3b91")
Arrays.asList("ae60f2db6102ca1f4e93cd18d0634d7a","9529e2bf214d72e792d93fbea22a3b91")
);
executeTest("testFalsePositiveMV", spec);
}
@ -86,7 +86,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("e4da7639bb542d6440975da12b94973f","8c157d79dd00063d2932f0d2b96f53d8")
Arrays.asList("590ee56e745984296f73e4277277eac7","8c157d79dd00063d2932f0d2b96f53d8")
);
executeTest("testSpecialCases", spec);
}
@ -108,7 +108,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-o %s"
),
2,
Arrays.asList("ab92b714471a000285577d540e1fdc2e","343e418850ae4a687ebef2acd55fcb07")
Arrays.asList("78158d738917b8f0b7a736a1739b2cc5","343e418850ae4a687ebef2acd55fcb07")
);
executeTest("testPriorOption", spec);
}
@ -149,7 +149,7 @@ public class PhaseByTransmissionIntegrationTest extends WalkerTest {
"-fatherAlleleFirst"
),
2,
Arrays.asList("4b937c1b4e96602a7479b07b59254d06","52ffa82428e63ade22ea37b72ae58492")
Arrays.asList("dc6afb769b55e6038677fa590b2b2e89","52ffa82428e63ade22ea37b72ae58492")
);
executeTest("testFatherAlleleFirst", spec);
}