From 9445326c6cbcc68fc46f8109d2e173824197706c Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Sun, 20 Nov 2011 18:26:27 -0500
Subject: [PATCH] Genotype is Comparable via sampleName

---
 build.xml                                            |  4 ++--
 .../sting/utils/variantcontext/Genotype.java         | 12 +++++++++++-
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/build.xml b/build.xml
index 232b074f6..66d99ac67 100644
--- a/build.xml
+++ b/build.xml
@@ -927,8 +927,8 @@
                 <jvmarg value="-Dpipeline.run=${pipeline.run}" />
                 <jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
                 <jvmarg line="${cofoja.jvm.args}"/>
-<!--                 <jvmarg value="-Xdebug"/> -->
-<!--                 <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
+                <jvmarg value="-Xdebug"/>
+                <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/>
 
                 <classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
                 <classfileset dir="${java.private.test.classes}" erroronmissingdir="false">
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
index b100d6da5..1691129c9 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
@@ -12,7 +12,7 @@ import java.util.*;
  *
  * @author Mark DePristo
  */
-public class Genotype {
+public class Genotype implements Comparable<Genotype> {
 
     public final static String PHASED_ALLELE_SEPARATOR = "|";
     public final static String UNPHASED_ALLELE_SEPARATOR = "/";
@@ -351,4 +351,14 @@ public class Genotype {
     public int getAttributeAsInt(String key, int defaultValue)            { return commonInfo.getAttributeAsInt(key, defaultValue); }
     public double getAttributeAsDouble(String key, double  defaultValue)  { return commonInfo.getAttributeAsDouble(key, defaultValue); }
     public boolean getAttributeAsBoolean(String key, boolean  defaultValue)  { return commonInfo.getAttributeAsBoolean(key, defaultValue); }
+
+    /**
+     * comparable genotypes -> compareTo on the sample names
+     * @param genotype
+     * @return
+     */
+    @Override
+    public int compareTo(final Genotype genotype) {
+        return getSampleName().compareTo(genotype.getSampleName());
+    }
 }
\ No newline at end of file