From 3dfc77dc896d70c49b06ce121a49b61790179359 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 2 Sep 2009 19:32:29 +0000
Subject: [PATCH] Add an indel rod which represents the initial point of the
 indel only (useful for alternate reference making)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1507 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/PointIndelROD.java         | 15 +++++++++++++++
 .../sting/gatk/refdata/ReferenceOrderedData.java  |  1 +
 2 files changed, 16 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/refdata/PointIndelROD.java

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PointIndelROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/PointIndelROD.java
new file mode 100755
index 000000000..c214b0c35
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/PointIndelROD.java
@@ -0,0 +1,15 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+
+public class PointIndelROD extends SimpleIndelROD {
+
+    public PointIndelROD(String name) {
+        super(name);
+    }
+
+    public GenomeLoc getLocation() {
+        return GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
+    }
+}
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
index e198bf0c2..7bb4ea379 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
@@ -75,6 +75,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         addModule("CleanedOutSNP", CleanedOutSNPROD.class);
         addModule("SangerSNP", SangerSNPROD.class);
         addModule("SimpleIndel", SimpleIndelROD.class);
+        addModule("PointIndel", PointIndelROD.class);
         addModule("HapMapGenotype", HapMapGenotypeROD.class);
         addModule("Intervals", IntervalRod.class);
         addModule("Variants", rodVariants.class);