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Merge branch 'master' of ssh://gsa2/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2012-10-05 16:15:07 -04:00
parent 04853252a0 d419a33ed1
commit 52326942cf
4 changed files with 34 additions and 4 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);
}
@Test
//@Test
public void testHaplotypeCallerMultiSample() {
HCTest(CEUTRIO_BAM, "", "5b751474ad0aef4cdb53f094e605f97c");
}
@ -81,4 +81,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
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);
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -73,7 +73,7 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
ReadBackedPileup pileup = stratifiedContext.getBasePileup();
for ( PileupElement p : pileup ) {
if ( alleleCounts.containsKey(p.getBase()) )
alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase())+1);
alleleCounts.put(p.getBase(), alleleCounts.get(p.getBase())+p.getRepresentativeCount());
}
// we need to add counts in the correct order

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 (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;
if ( p.getQual() < minQScoreToConsider || p.getMappingQual() < minQScoreToConsider )
@ -290,7 +291,7 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
int row = matchesRef ? 0 : 1;
int column = isFW ? 0 : 1;
table[row][column]++;
table[row][column]+=p.getRepresentativeCount();
}
}
}

14
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -438,4 +438,18 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
Arrays.asList("22c9fd65ce3298bd7fbf400c9c209f29"));
executeTest("test calling on reads with Ns in CIGAR", spec);
}
// --------------------------------------------------------------------------------------------------------------
//
// testing AD for reduced reads
//
// --------------------------------------------------------------------------------------------------------------
@Test
public void testADAnnotationInReducedBam() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
Arrays.asList("84486c88a0fd1ae996a6402490db8492"));
executeTest("test AD Annotation when calling on a ReducedRead BAM", spec);
}
}