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We now require at least 10 samples to merge variants into complex events in the HC. Added a new population based bam for the complex event integration test.

This commit is contained in:
Ryan Poplin 2012-10-24 14:07:36 -04:00
parent 6e421a72d6
commit 094db7bf24
3 changed files with 3 additions and 5 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
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@ -217,7 +217,7 @@ public class GenotypingEngine {
} }
cleanUpSymbolicUnassembledEvents( haplotypes ); cleanUpSymbolicUnassembledEvents( haplotypes );
if( activeAllelesToGenotype.isEmpty() && haplotypes.get(0).getSampleKeySet().size() >= 3 ) { // if not in GGA mode and have at least 3 samples try to create MNP and complex events by looking at LD structure if( activeAllelesToGenotype.isEmpty() && haplotypes.get(0).getSampleKeySet().size() >= 10 ) { // if not in GGA mode and have at least 10 samples try to create MNP and complex events by looking at LD structure
mergeConsecutiveEventsBasedOnLD( haplotypes, startPosKeySet, ref, refLoc ); mergeConsecutiveEventsBasedOnLD( haplotypes, startPosKeySet, ref, refLoc );
} }
if( !activeAllelesToGenotype.isEmpty() ) { // we are in GGA mode! if( !activeAllelesToGenotype.isEmpty() ) { // we are in GGA mode!

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
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@ -139,7 +139,7 @@ public class LikelihoodCalculationEngine {
} }
private static int computeFirstDifferingPosition( final byte[] b1, final byte[] b2 ) { private static int computeFirstDifferingPosition( final byte[] b1, final byte[] b2 ) {
for( int iii = 0; iii < b1.length && iii < b2.length; iii++ ){ for( int iii = 0; iii < b1.length && iii < b2.length; iii++ ) {
if( b1[iii] != b2[iii] ) { if( b1[iii] != b2[iii] ) {
return iii; return iii;
} }

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
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@ -42,7 +42,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test @Test
public void testHaplotypeCallerMultiSampleComplex() { public void testHaplotypeCallerMultiSampleComplex() {
HCTestComplexVariants(CEUTRIO_BAM, "", "30598abeeb0b0ae5816ffdbf0c4044fd"); HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "966d338f423c86a390d685aa6336ec69");
} }
private void HCTestSymbolicVariants(String bam, String args, String md5) { private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -94,6 +94,4 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
Arrays.asList("79af83432dc4a1768b3ebffffc4d2b8f")); Arrays.asList("79af83432dc4a1768b3ebffffc4d2b8f"));
executeTest("HC calling on a ReducedRead BAM", spec); executeTest("HC calling on a ReducedRead BAM", spec);
} }
} }