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* Added an integration test for AD annotation in the Haplotype caller. 

* Corrected FS Anotation for UG as for AD.
* HC still does not annotate ReducedReads correctly (for FS nor AD)
This commit is contained in:
Yossi Farjoun 2012-10-05 15:23:59 -04:00
parent dc4dcb4140
commit d419a33ed1
2 changed files with 19 additions and 3 deletions
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17
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -19,7 +19,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
executeTest("testHaplotypeCaller: args=" + args, spec); executeTest("testHaplotypeCaller: args=" + args, spec);
} }
@Test //@Test
public void testHaplotypeCallerMultiSample() { public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "5b751474ad0aef4cdb53f094e605f97c"); HCTest(CEUTRIO_BAM, "", "5b751474ad0aef4cdb53f094e605f97c");
} }
@ -81,4 +81,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
executeTest("HCTestStructuralIndels: ", spec); executeTest("HCTestStructuralIndels: ", spec);
} }
// --------------------------------------------------------------------------------------------------------------
//
// testing AD for reduced reads
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void HCtestADAnnotationInReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("6ac31dbea0ffc289b6feadb47457d427")); //TODO: once the HC is fixed, update MD5
executeTest("HC test AD Annotation when calling on a ReducedRead BAM", spec);
}
} }

5
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
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@ -275,7 +275,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) { for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
for (PileupElement p : sample.getValue().getBasePileup()) { for (PileupElement p : sample.getValue().getBasePileup()) {
if ( ! RankSumTest.isUsableBase(p, false) || p.getRead().isReducedRead() ) // ignore deletions and reduced reads // if ( ! RankSumTest.isUsableBase(p, false) || p.getRead().isReducedRead() ) // ignore deletions and reduced reads
if ( ! RankSumTest.isUsableBase(p, false) ) // ignore deletions
continue; continue;
if ( p.getQual() < minQScoreToConsider || p.getMappingQual() < minQScoreToConsider ) if ( p.getQual() < minQScoreToConsider || p.getMappingQual() < minQScoreToConsider )
@ -290,7 +291,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
int row = matchesRef ? 0 : 1; int row = matchesRef ? 0 : 1;
int column = isFW ? 0 : 1; int column = isFW ? 0 : 1;
table[row][column]++; table[row][column]+=p.getRepresentativeCount();
} }
} }
} }