From 1d2b5456083c0387f3d5ff94092c891662d11190 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 20 Jul 2009 02:47:50 +0000
Subject: [PATCH] add FLT toString method (to be used in PrintRODs) and add it
 to ROD list

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1279 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/ReferenceOrderedData.java      |  1 +
 .../org/broadinstitute/sting/gatk/refdata/rodFLT.java | 11 +++++++++++
 2 files changed, 12 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
index bfb6b1711..f15b429b3 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
@@ -65,6 +65,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         addModule("HapMapAlleleFrequencies", HapMapAlleleFrequenciesROD.class);
         addModule("SAMPileup", rodSAMPileup.class);
         addModule("GELI", rodGELI.class);
+        addModule("FLT", rodFLT.class);
         addModule("RefSeq", rodRefSeq.class);
         addModule("Table", TabularROD.class);
         addModule("PooledEM", PooledEMSNPROD.class);
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java
index 11761f58f..c0f963346 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java
@@ -29,6 +29,17 @@ public class rodFLT extends TabularROD implements SNPCallFromGenotypes {
         else
             return bases[1];
     }
+
+    public String toString() {
+        StringBuffer sb = new StringBuffer();
+        sb.append(loc.getContig() + "\t" + loc.getStart() + "\t");
+        sb.append(getRefSnpFWD() + "\t-1\t-1\t" + getAltBasesFWD());
+        for (int i=0; i < 12; i++)
+            sb.append("\t0");
+        sb.append("\n");
+        return sb.toString();
+    }
+
     public boolean isReference()   { return false; }
     public boolean isSNP()         { return true; }
     public boolean isInsertion()   { return false; }