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Merge pull request #178 from broadinstitute/md_common_suffix_bugfix 

Bugfix for CommonSuffixSplitter
This commit is contained in:
Ryan Poplin 2013-04-22 06:53:01 -07:00
parent fc29a66a63 be66049a6f
commit ff430c821e
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);
}