From 423a3ee894d41c3efeb7269ae187bb3eaa959d98 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 23 Sep 2009 20:22:09 +0000
Subject: [PATCH] Added a sequenom rod to empower Carrie to convert 1KG
 validation SNPs to sequenom format

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1706 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/refdata/ReferenceOrderedData.java    |  1 +
 .../sting/gatk/refdata/SequenomROD.java       | 54 +++++++++++++++++++
 2 files changed, 55 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/refdata/SequenomROD.java

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
index 9bec6e50f..c6454e91b 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
@@ -67,6 +67,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         addModule("Table", TabularROD.class);
         addModule("PooledEM", PooledEMSNPROD.class);
         addModule("CleanedOutSNP", CleanedOutSNPROD.class);
+        addModule("Sequenom", SequenomROD.class);
         addModule("SangerSNP", SangerSNPROD.class);
         addModule("SimpleIndel", SimpleIndelROD.class);
         addModule("PointIndel", PointIndelROD.class);
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SequenomROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SequenomROD.java
new file mode 100755
index 000000000..693889d45
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SequenomROD.java
@@ -0,0 +1,54 @@
+package org.broadinstitute.sting.gatk.refdata;
+
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+
+import java.util.*;
+
+public class SequenomROD extends TabularROD implements AllelicVariant {
+
+    public SequenomROD(String name) {
+        super(name);
+    }
+
+    public GenomeLoc getLocation() {
+        long pos = Long.parseLong(this.get("1"));
+        return GenomeLocParser.createGenomeLoc(this.get("0"), pos);
+    }
+
+    public List<String> getFWDAlleles() {
+        return Arrays.asList(this.get("2"));
+    }
+
+    public String getFWDRefBases() { return ""; }
+    public String getAltBasesFWD() { return getFWDAlleles().get(0); }
+    public String getRefBasesFWD() { return ""; }
+    public char getRefSnpFWD() { return 'N'; }
+    public char getAltSnpFWD() { return getAltBasesFWD().charAt(0); }
+    public char getRef() { return 'N'; }
+    public List<String> getGenotype() { return getFWDAlleles(); }
+    public boolean isGenotype() { return false; }
+    public boolean isPointGenotype() { return true; }
+    public boolean isIndelGenotype() { return false; }
+    public boolean isSNP() { return true; }
+    public boolean isReference() { return false; }
+    public boolean isInsertion() { return false; }
+    public boolean isDeletion() { return false; }
+    public boolean isIndel() { return false; }
+    public double getVariantConfidence() { return 0.0; }
+    public double getVariationConfidence() { 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 double getHeterozygosity() { return 0.0; }
+    public double getMAF() { return 0.0; }
+    public int getPloidy() { return 2; }
+    public int length() { return 1; }
+
+    public String toString() {
+        StringBuffer sb = new StringBuffer();
+        sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t" + getFWDAlleles().get(0));
+        return sb.toString();
+    }
+ }
\ No newline at end of file