diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java index 4a70f23fb..c9b0cd62c 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java @@ -14,7 +14,8 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria } public GenomeLoc getLocation() { - return GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1"))); + long pos = Long.parseLong(this.get("1")); + return GenomeLocParser.createGenomeLoc(this.get("0"), pos, (isDeletion() ? pos+length() : pos+1)); } public List getFWDAlleles() { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECIndelArtifact.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECIndelArtifact.java index 239176a17..0496d0d48 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECIndelArtifact.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECIndelArtifact.java @@ -25,7 +25,6 @@ public class VECIndelArtifact implements VariantExclusionCriterion { } AllelicVariant indelCall = (AllelicVariant)tracker.lookup("indels", null); - // TODO - fix indel call capability to span full indel if ( indelCall != null ) { exclude = true; source = "IndelCall"; @@ -33,10 +32,9 @@ public class VECIndelArtifact implements VariantExclusionCriterion { } rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null); - // TODO - fix dbsnp capability to span full indel if ( dbsnp != null && dbsnp.isIndel() ) { exclude = true; - source = "dbsnp"; + source = "dbSNP"; return; }