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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2011-07-28 13:56:43 -04:00
parent 1865211b6d 1afc49a297
commit 7a2a65155f
2 changed files with 8 additions and 5 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -112,26 +112,29 @@ public class VariantContextAdaptors {
alleles.add(refAllele); alleles.add(refAllele);
// add all of the alt alleles // add all of the alt alleles
boolean sawNullAllele = false;
for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) { for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) {
if ( ! Allele.acceptableAlleleBases(alt) ) { if ( ! Allele.acceptableAlleleBases(alt) ) {
//System.out.printf("Excluding dbsnp record %s%n", dbsnp); //System.out.printf("Excluding dbsnp record %s%n", dbsnp);
return null; return null;
} }
alleles.add(Allele.create(alt, false)); Allele altAllele = Allele.create(alt, false);
alleles.add(altAllele);
if ( altAllele.isNull() )
sawNullAllele = true;
} }
Map<String, Object> attributes = new HashMap<String, Object>(); Map<String, Object> attributes = new HashMap<String, Object>();
attributes.put(VariantContext.ID_KEY, dbsnp.getRsID()); attributes.put(VariantContext.ID_KEY, dbsnp.getRsID());
boolean vcIsDeletion = DbSNPHelper.isDeletion(dbsnp) || DbSNPHelper.isComplexIndel(dbsnp); if ( sawNullAllele ) {
if ( vcIsDeletion ) {
int index = dbsnp.getStart() - ref.getWindow().getStart() - 1; int index = dbsnp.getStart() - ref.getWindow().getStart() - 1;
if ( index < 0 ) if ( index < 0 )
return null; // we weren't given enough reference context to create the VariantContext return null; // we weren't given enough reference context to create the VariantContext
attributes.put(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY, new Byte(ref.getBases()[index])); attributes.put(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY, new Byte(ref.getBases()[index]));
} }
Collection<Genotype> genotypes = null; Collection<Genotype> genotypes = null;
VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (vcIsDeletion ? 1 : 0),dbsnp.getEnd(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes); VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (sawNullAllele ? 1 : 0),dbsnp.getEnd(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes);
return vc; return vc;
} else } else
return null; // can't handle anything else return null; // can't handle anything else

2
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java
View File

@ -58,7 +58,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
// this really just tests that we are seeing the same number of objects over all of chr1 // this really just tests that we are seeing the same number of objects over all of chr1
WalkerTestSpec spec = new WalkerTestSpec( root + " -L 1" + " -o %s", WalkerTestSpec spec = new WalkerTestSpec( root + " -L 1" + " -o %s",
1, // just one output file 1, // just one output file
Arrays.asList("2532234d2c934a5e14849655dd7b5f4f")); Arrays.asList("045a5b02c86aeb9301dc0b724da0c8f7"));
executeTest("testLargeScaleConversion", spec); executeTest("testLargeScaleConversion", spec);
} }
} }