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IndelArtifact filter can now handle filtering false SNPs that occur within the span of an indel but after the first position 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1495 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-01 03:34:39 +00:00
parent 85ca68fab6
commit 0addae967a
2 changed files with 3 additions and 4 deletions
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3
java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
View File

@ -14,7 +14,8 @@ public class SimpleIndelROD extends TabularROD implements Genotype, AllelicVaria
} }
public GenomeLoc getLocation() { 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<String> getFWDAlleles() { public List<String> getFWDAlleles() {

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/variants/VECIndelArtifact.java
View File

@ -25,7 +25,6 @@ public class VECIndelArtifact implements VariantExclusionCriterion {
} }
AllelicVariant indelCall = (AllelicVariant)tracker.lookup("indels", null); AllelicVariant indelCall = (AllelicVariant)tracker.lookup("indels", null);
// TODO - fix indel call capability to span full indel
if ( indelCall != null ) { if ( indelCall != null ) {
exclude = true; exclude = true;
source = "IndelCall"; source = "IndelCall";
@ -33,10 +32,9 @@ public class VECIndelArtifact implements VariantExclusionCriterion {
} }
rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null); rodDbSNP dbsnp = (rodDbSNP)tracker.lookup("dbSNP", null);
// TODO - fix dbsnp capability to span full indel
if ( dbsnp != null && dbsnp.isIndel() ) { if ( dbsnp != null && dbsnp.isIndel() ) {
exclude = true; exclude = true;
source = "dbsnp"; source = "dbSNP";
return; return;
} }