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Bugfix for indel DP calculations using reduced reads 

-- Adding tests for SNP and indel calling on reduced BAM
This commit is contained in:
Mark DePristo 2012-10-19 14:42:00 -04:00
parent 0fcd358ace
commit 6b6caf8e3a
2 changed files with 19 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -231,7 +231,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
int count = 0;
for (PileupElement p : pileup) {
if (p.isDeletion() || p.isInsertionAtBeginningOfRead() || BaseUtils.isRegularBase(p.getBase()))
count++;
count += p.getRepresentativeCount();
}
return count;

18
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -452,4 +452,22 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
Arrays.asList("bbf16e1873e525ee5975021cfb8988cf"));
executeTest("test calling on a ReducedRead BAM", spec);
}
@Test
public void testReducedBamSNPs() {
testReducedCalling("SNP", "");
}
@Test
public void testReducedBamINDELs() {
testReducedCalling("INDEL", "");
}
private void testReducedCalling(final String model, final String md5) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s -L 20:10,000,000-11,000,000 -glm " + model, 1,
Arrays.asList(md5));
executeTest("test calling on a ReducedRead BAM with " + model, spec);
}
}