From 678ddd914f5e700234c299e4082772d63d1621f9 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 10 Jun 2009 21:38:57 +0000
Subject: [PATCH] Stopgap fixes GFF, DbSNP being half-open rather than
 half-closed.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@980 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java | 6 +++---
 java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java  | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
index f238596dd..e1ab70119 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
@@ -132,7 +132,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
     // ----------------------------------------------------------------------
     public String toString() {
         return String.format("%s\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%f\t%f\t%s\t%s\t%d",
-                getLocation().getContig(), getLocation().getStart(), getLocation().getStop(),
+                getLocation().getContig(), getLocation().getStart(), getLocation().getStop()+1,
                 name, strand, refBases, observed, molType,
                 varType, validationStatus, avHet, avHetSE, func, locType, weight );
     }
@@ -152,7 +152,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
 
     public String repl() {
         return String.format("%d\t%s\t%d\t%d\t%s\t0\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%f\t%f\t%s\t%s\t%d",
-                585, getLocation().getContig(), getLocation().getStart()-1, getLocation().getStop()-1,
+                585, getLocation().getContig(), getLocation().getStart()-1, getLocation().getStop(),
                 name, strand, refBases, refBases, observed, molType,
                 varType, validationStatus, avHet, avHetSE, func, locType, weight );
     }
@@ -162,7 +162,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
             String contig = parts[1];
             long start = Long.parseLong(parts[2]) + 1; // The final is 0 based
             long stop = Long.parseLong(parts[3]) + 1;  // The final is 0 based
-            loc = GenomeLoc.parseGenomeLoc(contig, start, stop);
+            loc = GenomeLoc.parseGenomeLoc(contig, start, stop-1);
 
             name = parts[4];
             refBases = parts[5];
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java
index b8729aea7..fb701b6fb 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java
@@ -104,7 +104,7 @@ public class rodGFF extends BasicReferenceOrderedDatum {
     //
     // ----------------------------------------------------------------------
     public String toString() {
-        return String.format("%s\t%s\t%s\t%d\t%d\t%f\t%s\t%s\t%s", contig, source, feature, start, stop, score, strand, frame, getAttributeString());
+        return String.format("%s\t%s\t%s\t%d\t%d\t%f\t%s\t%s\t%s", contig, source, feature, start, stop+1, score, strand, frame, getAttributeString());
     }
 
     public String repl() {
@@ -141,7 +141,7 @@ public class rodGFF extends BasicReferenceOrderedDatum {
         final String source = parts[1];
         final String feature = parts[2];
         final long start = Long.parseLong(parts[3]);
-        final long stop = Long.parseLong(parts[4]);
+        final long stop = Long.parseLong(parts[4])-1;
 
         double score = Double.NaN;
         if ( ! parts[5].equals(".") )