From d45c90b1669f9dc0817606154861686196487fc8 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 17 Jul 2009 14:36:12 +0000
Subject: [PATCH] ROD to represent simple output from IndelGenotyper

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1274 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/SimpleIndelROD.java    | 43 +++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
new file mode 100755
index 000000000..6cb8c7cda
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SimpleIndelROD.java
@@ -0,0 +1,43 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+
+import java.util.*;
+
+public class SimpleIndelROD extends TabularROD implements Genotype {
+
+    public SimpleIndelROD(String name) {
+        super(name);
+    }
+
+    public GenomeLoc getLocation() {
+        return GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
+    }
+
+    public List<String> getFWDAlleles() {
+        String str = this.get("3");
+        return Arrays.asList(str.substring(0, str.indexOf(":")));    
+    }
+
+    public String getFWDRefBases() { return ""; }
+    public char getRef() { return 'N'; }
+    public boolean isPointGenotype() { return false; }
+    public boolean isIndelGenotype() { return true; }
+    public boolean isSNP() { return false; }
+    public boolean isReference() { return false; }
+    public boolean isInsertion() { return this.get("3").charAt(0) == '+'; }
+    public boolean isDeletion() { return this.get("3").charAt(0) == '-'; }
+    public boolean isIndel() { return false; }
+    public double getVariantConfidence() { return 0.0; }
+    public double getConsensusConfidence() { return 0.0; }
+    public boolean isBiallelic() { return true; }
+    public boolean isHom() { return false; }
+    public boolean isHet() { return false; }
+
+    public String toString() {
+        StringBuffer sb = new StringBuffer();
+        sb.append(getLocation() + "\t" + getFWDAlleles().get(0));
+        return sb.toString();
+    }
+ }
\ No newline at end of file