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

Fix GSA-535: storing likelihoods in allele map was busted when running HaplotypeCaller, only the last likelihood of a haplotype was being stored, as opposed to the max likelihood of all haplotypes mapping to an allele

This commit is contained in:
Guillermo del Angel 2012-09-11 11:01:26 -04:00
parent 10c720cbba
commit 13831106d5
2 changed files with 12 additions and 11 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
View File

@ -335,14 +335,15 @@ public class LikelihoodCalculationEngine {
final GATKSAMRecord read = readsForThisSample.get(iii); // BUGBUG: assumes read order in this list and haplotype likelihood list are the same!
// only count the read if it overlaps the event, otherwise it is not added to the output read list at all
if( callLoc.overlapsP(parser.createGenomeLoc(read)) ) {
final double likelihoods[] = new double[call.getFirst().getAlleles().size()];
int count = 0;
for( final Allele a : call.getFirst().getAlleles() ) {
double maxLikelihood = Double.NEGATIVE_INFINITY;
for( final Haplotype h : call.getSecond().get(a) ) { // use the max likelihood from all the haplotypes which mapped to this allele (achieved via the haplotype mapper object)
final double likelihood = h.getReadLikelihoods(sample.getKey())[iii];
likelihoodMap.add(read, a, likelihood);
if( likelihood > maxLikelihood ) {
maxLikelihood = likelihood;
}
}
likelihoodMap.add(read, a, maxLikelihood);
}
}
}

14
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -21,17 +21,17 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "e5b4a0627a1d69b9356f8a7cd2260e89");
HCTest(CEUTRIO_BAM, "", "5b751474ad0aef4cdb53f094e605f97c");
}
@Test
public void testHaplotypeCallerSingleSample() {
HCTest(NA12878_BAM, "", "202d5b6edaf74f411c170099749f202f");
HCTest(NA12878_BAM, "", "60efcd2d2722087e900f6365985d18bf");
}
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "561931ba3919808ec471e745cb3148c7");
HCTest(CEUTRIO_BAM, "-gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "71bec55320a2f07af0d54be9d7735322");
}
private void HCTestComplexVariants(String bam, String args, String md5) {
@ -42,7 +42,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(CEUTRIO_BAM, "", "3424b398a9f47c8ac606a5c56eb7d8a7");
HCTestComplexVariants(CEUTRIO_BAM, "", "f5a809e3fbd9998f79b75bb2973209e1");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -53,7 +53,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleSymbolic() {
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "b71cfaea9390136c584c9671b149d573");
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "8043b0451a4384e678a93600b34afce7");
}
private void HCTestIndelQualityScores(String bam, String args, String md5) {
@ -64,13 +64,13 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "e1f88fac91424740c0eaac1de48b3970");
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "ea6539e05faf10ffaf76f2d16907c47a");
}
@Test
public void HCTestProblematicReadsModifiedInActiveRegions() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("000fd36d5cf8090386bb2ac15e3ab0b5"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("8d092b25f40456e618eef91fdce8adf0"));
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
}
}