From ab2a80f3eaa17f27cddd8f3ab2af73e3a3069d2e Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 17 Jun 2009 21:32:21 +0000
Subject: [PATCH] A new ROD type that allows one to input a geli.calls file
 back into a walker.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1036 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/rodVariants.java       | 78 +++++++++++++++++++
 1 file changed, 78 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java
new file mode 100755
index 000000000..2d458b6af
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java
@@ -0,0 +1,78 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+import java.io.IOException;
+
+public class rodVariants extends BasicReferenceOrderedDatum {
+    private GenomeLoc loc;
+    private char refBase = 'N';
+    private int depth;
+    private int maxMappingQuality;
+    private String bestGenotype = "NN";
+    private float lodBtr;
+    private float lodBtnb;
+    private float[] genotypeLikelihoods = new float[10];
+    
+    public rodVariants(final String name) { super(name); }
+
+    public String delimiterRegex() { return "\\s+"; }
+
+    public boolean parseLine(Object header, String[] parts) throws IOException {
+        if (!parts[0].startsWith("#")) {
+            loc = new GenomeLoc(parts[0], Long.valueOf(parts[1]));
+            refBase = parts[2].charAt(0);
+            depth = Integer.valueOf(parts[3]);
+            maxMappingQuality = Integer.valueOf(parts[4]);
+            bestGenotype = parts[5];
+            lodBtr = Float.valueOf(parts[6]);
+            lodBtnb = Float.valueOf(parts[7]);
+
+            for (int pieceIndex = 8, offset = 0; pieceIndex < 18; pieceIndex++, offset++) {
+                genotypeLikelihoods[offset] = Float.valueOf(parts[pieceIndex]);
+            }
+
+            return true;
+        }
+
+        return false;
+    }
+
+    public String toString() {
+        return String.format("%s %c %d %d %s %4.4f %4.4f %f %f %f %f %f %f %f %f %f %f",
+                loc,
+                refBase,
+                depth,
+                maxMappingQuality,
+                bestGenotype,
+                lodBtr,
+                lodBtnb,
+                genotypeLikelihoods[0],
+                genotypeLikelihoods[1],
+                genotypeLikelihoods[2],
+                genotypeLikelihoods[3],
+                genotypeLikelihoods[4],
+                genotypeLikelihoods[5],
+                genotypeLikelihoods[6],
+                genotypeLikelihoods[7],
+                genotypeLikelihoods[8],
+                genotypeLikelihoods[9]
+        );
+    }
+
+    public GenomeLoc getLocation() { return loc; }
+
+    public char getReferenceBase() { return refBase; }
+
+    public int getPileupDepth() { return depth; }
+
+    public int getMaxMappingQuality() { return maxMappingQuality; }
+
+    public String getBestGenotype() { return bestGenotype; }
+
+    public float getLodBtr() { return lodBtr; }
+
+    public float getLodBtnb() { return lodBtnb; }
+
+    public float[] getGenotypeLikelihoods() { return genotypeLikelihoods; }
+}