From 0addae967ac2d5cbf337a86eac975809f5655c61 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 1 Sep 2009 03:34:39 +0000
Subject: [PATCH] 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
---
 .../org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java | 3 ++-
 .../playground/gatk/walkers/variants/VECIndelArtifact.java    | 4 +---
 2 files changed, 3 insertions(+), 4 deletions(-)

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<String> 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;
         }