From d2af26e81f60dfd7dbd9520639643380b32be0f6 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 24 Sep 2009 16:33:11 +0000
Subject: [PATCH] Pooled EM SNP Rod converted over to the Variation interface

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1719 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/PooledEMSNPROD.java    | 104 +++++++++++++++---
 1 file changed, 89 insertions(+), 15 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
index d3f44faa0..77baf3fef 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
@@ -1,19 +1,7 @@
 package org.broadinstitute.sting.gatk.refdata;
 
-import java.util.*;
-import java.util.regex.MatchResult;
-import java.util.regex.Pattern;
-import java.util.regex.Matcher;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.xReadLines;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.apache.log4j.Logger;
+import java.util.ArrayList;
+import java.util.List;
 
 /**
  * loc ref alt EM_alt_freq discovery_likelihood discovery_null discovery_prior discovery_lod EM_N n_ref n_het n_hom
@@ -22,7 +10,7 @@ import org.apache.log4j.Logger;
  * chr1:1104842 A N 0.000000 -84.816002 -84.816002 0.000000 0.000000 324.000000 162 0 0
  *
  */
-public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes {
+public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes, VariationRod {
     public PooledEMSNPROD(final String name) {
         super(name);
     }
@@ -33,10 +21,85 @@ public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public String getAltBasesFWD() { return this.get("alt"); }
     public char getAltSnpFWD() throws IllegalStateException { return getAltBasesFWD().charAt(0); }
     public boolean isReference()   { return getVariationConfidence() < 0.01; }
+
+    /**
+     * gets the alternate base.  Use this method if we're biallelic
+     *
+     * @return
+     */
+    @Override
+    public String getAlternateBase() {
+        return getAltBasesFWD();
+    }
+
+    /**
+     * gets the alternate bases.  Use this method if the allele count is greater then 2
+     *
+     * @return
+     */
+    @Override
+    public List<String> getAlternateBases() {
+        List<String> str = new ArrayList<String>();
+        str.add(this.getAltBasesFWD());
+        return str;
+    }
+
+    /**
+     * get the frequency of this variant
+     *
+     * @return VariantFrequency with the stored frequency
+     */
+    @Override
+    public double getNonRefAlleleFrequency() {
+        return this.getMAF();
+    }
+
+    /** @return the VARIANT_TYPE of the current variant */
+    @Override
+    public VARIANT_TYPE getType() {
+        if (isSNP()) {
+            return VARIANT_TYPE.SNP;
+        }
+        return VARIANT_TYPE.REFERENCE;
+    }
+
     public boolean isSNP()         { return ! isReference(); }
     public boolean isInsertion()   { return false; }
     public boolean isDeletion()    { return false; }
+
+    /**
+     * get the reference base(s) at this position
+     *
+     * @return the reference base or bases, as a string
+     */
+    @Override
+    public String getReference() {
+        return this.get("ref");
+    }
+
     public boolean isIndel()       { return false; }
+
+    /**
+     * gets the alternate base is the case of a SNP.  Throws an IllegalStateException if we're not a SNP
+     * of
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getAlternativeBaseForSNP() {
+        return this.getAltSnpFWD();
+    }
+
+    /**
+     * gets the reference base is the case of a SNP.  Throws an IllegalStateException if we're not a SNP
+     *
+     * @return a char, representing the alternate base
+     */
+    @Override
+    public char getReferenceForSNP() {
+        return this.getRefSnpFWD();
+    }
+
     public double getMAF()         { return Double.parseDouble(this.get("EM_alt_freq")); }
     public double getHeterozygosity() { return 2 * getMAF() * (1 - getMAF()); }
     public boolean isGenotype()    { return false; }
@@ -45,6 +108,17 @@ public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); }
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
+
+    /**
+     * get the -1 * (log 10 of the error value)
+     *
+     * @return the log based error estimate
+     */
+    @Override
+    public double getNegLog10PError() {
+        return this.getVariationConfidence();
+    }
+
     public int length() { return 1; }
 
     // SNPCallFromGenotypes interface