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The UnifiedGenotyper now makes use of base insertion and base deletion quality scores if they exist in the reads.

This commit is contained in:
Ryan Poplin 2012-08-07 13:58:22 -04:00
parent 2c76f71a03
commit 15085bf03e
2 changed files with 16 additions and 1 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -351,7 +351,9 @@ public class PairHMMIndelErrorModel {
previousHaplotypeSeen = haplotypeBases.clone();
readLikelihood = pairHMM.computeReadLikelihoodGivenHaplotype(haplotypeBases, readBases, readQuals,
contextLogGapOpenProbabilities, contextLogGapOpenProbabilities, contextLogGapContinuationProbabilities,
(read.hasBaseIndelQualities() ? read.getBaseInsertionQualities() : contextLogGapOpenProbabilities),
(read.hasBaseIndelQualities() ? read.getBaseDeletionQualities() : contextLogGapOpenProbabilities),
contextLogGapContinuationProbabilities,
startIndexInHaplotype, matchMetricArray, XMetricArray, YMetricArray);

13
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -355,6 +355,19 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec);
}
@Test
public void testBaseIndelQualityScores() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommandIndelsb37 +
" -I " + privateTestDir + "NA12878.100kb.BQSRv2.example.bam" +
" -o %s" +
" -L 20:10,000,000-10,100,000",
1,
Arrays.asList("b3c923ed9efa04b85fc18a9b45c8d2a6"));
executeTest(String.format("test UG with base indel quality scores"), spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing SnpEff