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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2011-07-27 16:14:59 -04:00
parent ab69b8e4ee 64aad67b5f
commit 5809a61b20
2 changed files with 9 additions and 3 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -122,14 +122,16 @@ public class VariantContextAdaptors {
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());
if ( DbSNPHelper.isDeletion(dbsnp) ) {
boolean vcIsDeletion = DbSNPHelper.isDeletion(dbsnp) || DbSNPHelper.isComplexIndel(dbsnp);
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() - (DbSNPHelper.isDeletion(dbsnp) ? 1 : 0),dbsnp.getEnd(), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes); VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (vcIsDeletion ? 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

6
public/java/src/org/broadinstitute/sting/gatk/refdata/utils/helpers/DbSNPHelper.java
View File

@ -117,7 +117,11 @@ public class DbSNPHelper {
} }
public static boolean isIndel(DbSNPFeature feature) { public static boolean isIndel(DbSNPFeature feature) {
return DbSNPHelper.isInsertion(feature) || DbSNPHelper.isDeletion(feature) || feature.getVariantType().contains("in-del"); return DbSNPHelper.isInsertion(feature) || DbSNPHelper.isDeletion(feature) || DbSNPHelper.isComplexIndel(feature);
}
public static boolean isComplexIndel(DbSNPFeature feature) {
return feature.getVariantType().contains("in-del");
} }
public static boolean isHapmap(DbSNPFeature feature) { public static boolean isHapmap(DbSNPFeature feature) {