Unit tests

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4660 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModelUnitTest.java

@@ -0,0 +1,92 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
+
+import org.apache.log4j.Logger;
+import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.text.XReadLines;
+import org.broadinstitute.sting.BaseTest;
+import org.testng.annotations.Test;
+import org.testng.annotations.BeforeTest;
+import org.testng.Assert;
+
+import Jama.*; 
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintStream;
+import java.util.*;
+import java.util.regex.Pattern;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: rpoplin
+ * Date: Feb 26, 2010
+ */
+
+public final class VariantGaussianMixtureModelUnitTest extends BaseTest {
+    private static int N_VARIANTS = 100;
+    VariantDatum[] variantData1 = new VariantDatum[N_VARIANTS];
+
+    @BeforeTest
+    public void beforeTest() {
+        for ( int i = 0; i < N_VARIANTS; i++ ) {
+            variantData1[i].isKnown = i % 2 == 0;      // every other is know
+            variantData1[i].qual = (N_VARIANTS - i) * 1.0;
+        }
+
+        // first 25 are tv, 25-75 are 50/50, and 75+ are all transitions
+        int i = 0;
+        for ( ; i < (N_VARIANTS * 0.25); i++ ) { variantData1[i].isTransition = true; }
+        for ( ; i < (N_VARIANTS * 0.75); i++ ) { variantData1[i].isTransition = i % 2 == 0; }
+        for ( ; i < N_VARIANTS; i++ ) { variantData1[i].isTransition = false; }
+    }
+
+    @Test
+    public final void testFindTranches1() {
+        List<Tranche> tranches = VariantGaussianMixtureModel.findTranches(variantData1, new double[]{0.1, 20}, 2.0);
+        Assert.assertEquals( tranches.size(), 2 );
+
+        Tranche t1 = tranches.get(0);
+        Assert.assertEquals( t1.fdr, 0.1 );
+        Assert.assertEquals( t1.pCut, 26 );
+        Assert.assertEquals( t1.numKnown, 37 );
+        Assert.assertEquals( t1.numNovel, 37 );
+
+        Tranche t2 = tranches.get(1);
+        Assert.assertEquals( t2.fdr, 20 );
+        Assert.assertEquals( t2.pCut, 21 );
+        Assert.assertEquals( t2.numKnown, 37 );
+        Assert.assertEquals( t2.numNovel, 37 );
+    }
+}