From 19d5213d5aa51095b9ef5850e83b3e0580b67c20 Mon Sep 17 00:00:00 2001
From: Laurent Francioli <laurent.francioli@gmail.com>
Date: Wed, 25 Apr 2012 16:27:38 +0200
Subject: [PATCH] Added function to get founders IDs in SampleDB

Signed-off-by: Eric Banks <ebanks@broadinstitute.org>
---
 .../broadinstitute/sting/gatk/samples/SampleDB.java    | 10 ++++++++++
 .../sting/gatk/samples/SampleDBUnitTest.java           |  7 +++++++
 2 files changed, 17 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
index a6f6b3481..31149cd8a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
@@ -235,4 +235,14 @@ public class SampleDB {
         }
         return children;
     }
+
+    public Set<String> getFounderIds(){
+        Set<String> founders = new HashSet<String>();
+        for(Sample sample : getSamples()){
+            if(sample.getParents().size()<1)
+                founders.add(sample.getID());
+
+        }
+        return founders;
+    }
 }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
index 7f21da4f4..85aa28a98 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/samples/SampleDBUnitTest.java
@@ -200,6 +200,13 @@ public class SampleDBUnitTest extends BaseTest {
         Assert.assertEquals(db.getChildrenWithParents(true), new HashSet<Sample>(Arrays.asList(new Sample("kid", "fam1", "dad", "mom", Gender.MALE,   Affection.AFFECTED))));
     }
 
+    @Test()
+    public void testGetFounderIds(){
+        builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies2));
+        SampleDB db = builder.getFinalSampleDB();
+        Assert.assertEquals(db.getFounderIds(), new HashSet<String>(Arrays.asList("dad","mom","dad2","mom2","dad4")));
+    }
+
     @Test()
     public void loadFamilyIDs() {
         builder.addSamplesFromPedigreeStrings(Arrays.asList(testPEDMultipleFamilies));