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Bugfix for CommonSuffixSplitter 

-- The problem is that the common suffix splitter could eliminate the reference source vertex when there's an incoming node that contains all of the reference source vertex bases and then some additional prefix bases.  In this case we'd eliminate the reference source vertex.  Fixed by checking for this condition and aborting the simplification
-- Update MD5s, including minor improvements
This commit is contained in:
Mark DePristo 2013-04-21 15:42:26 -04:00
parent fc29a66a63
commit be66049a6f
3 changed files with 22 additions and 5 deletions
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17
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/graphs/CommonSuffixSplitter.java
View File

@ -100,6 +100,8 @@ public class CommonSuffixSplitter {
final SeqVertex suffixVTemplate = commonSuffix(toSplit);
if ( suffixVTemplate.isEmpty() ) {
return false;
} else if ( wouldEliminateRefSource(graph, suffixVTemplate, toSplit) ) {
return false;
} else if ( allVerticesAreTheCommonSuffix(suffixVTemplate, toSplit) ) {
return false;
} else {
@ -141,6 +143,21 @@ public class CommonSuffixSplitter {
}
}
/**
* Would factoring out this suffix result in elimating the reference source vertex?
* @param graph the graph
* @param commonSuffix the common suffix of all toSplits
* @param toSplits the list of vertices we're are trying to split
* @return true if toSplit contains the reference source and this ref source has all and only the bases of commonSuffix
*/
private boolean wouldEliminateRefSource(final SeqGraph graph, final SeqVertex commonSuffix, final Collection<SeqVertex> toSplits) {
for ( final SeqVertex toSplit : toSplits ) {
if ( graph.isRefSource(toSplit) )
return toSplit.length() == commonSuffix.length();
}
return false;
}
// private static int counter = 0;
/**

6
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java
View File

@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleComplex1() {
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "57e13aed8dc483514ac15fb757aee1d1");
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "fd51f8c7235eb6547b678093c7a01089");
}
private void HCTestSymbolicVariants(String bam, String args, String md5) {
@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
@Test
public void testHaplotypeCallerMultiSampleGGAComplex() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
"d89c8a32e9c54f66e0331382cac86b27");
"ed3b577e6f7d68bba6774a62d9df9cd9");
}
@Test
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
"89a28d4290523dd55117bc4e44212d73");
"a594a28d8053c3e969c39de81a9d03d6");
}
}

4
protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
View File

@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void testHaplotypeCallerMultiSampleGGA() {
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
"3e2e4a62c6c60d432fa1ca32aee2635b");
"28c3b1f276ec8198801aafe880e40fb6");
}
@Test
@ -166,7 +166,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
@Test
public void HCTestStructuralIndels() {
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ab518ae32535714604a4ffc71fe42511"));
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("cac0d88fa4471c7a0ac96533a9a6354b"));
executeTest("HCTestStructuralIndels: ", spec);
}