adding some objects we need for the GLF format.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@846 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 22:32:25 +00:00 · 2009-05-27 22:32:25 +00:00 · d275c18e58
parent ce6a0f522b
commit d275c18e58
3 changed files with 251 additions and 0 deletions
--- a/java/src/org/broadinstitute/sting/utils/glf/LikelihoodObject.java
+++ b/java/src/org/broadinstitute/sting/utils/glf/LikelihoodObject.java
@ -0,0 +1,101 @@
+package org.broadinstitute.sting.utils.glf;
+
+import java.util.HashMap;
+
+
+/*
+ * Copyright (c) 2009 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.
+ */
+
+/**
+ * @author aaron
+ *
+ * <p/>
+ * Class LikelyhoodObject
+ * <p/>
+ * An object used to store likelyhood information for genotypes.  Genotype
+ * likelihoods are assumed to be zero, unless set.  This allows the consumer
+ * to make an empty LikelihoodObject, and just set those values which have
+ * associated likelihood values.
+ */
+public class LikelihoodObject {
+
+    // our possible genotypes, in order according to GLFv3
+    public enum GENOTYPE {
+        AA, AT, AC, AG, CC, CT, CG, GG, GT, TT
+    }
+
+    // the associated probabilities for each genotype
+    final protected HashMap<GENOTYPE, Integer> likelihood = new HashMap<GENOTYPE, Integer>();
+
+    /** create a blank likelihood object */
+    public LikelihoodObject() {
+        for (GENOTYPE type : GENOTYPE.values()) {
+            likelihood.put(type, 0);
+        }
+    }
+
+    /**
+     * create a likelyhood object, given an array of genotype scores in GLFv3 ordering
+     * @param values
+     */
+    public LikelihoodObject(int[] values) {
+        if (values.length != GENOTYPE.values().length) {
+            throw new IllegalArgumentException("invalid array passed to LikelihoodObject, should be size " + GENOTYPE.values().length);
+        }
+        int index = 0;
+        for (GENOTYPE type : GENOTYPE.values()) {
+            if (values[index] < 0 || values[index] > 255) {
+                throw new IllegalArgumentException("likelihood values must be greater or equal 0, and less then 256, value given: " + values[index]);
+            }
+            likelihood.put(type, values[index]);
+            ++index;
+        }
+    }
+
+    /**
+     * set the likelihood, given it's probability and the genotype
+     * @param type the genotype
+     * @param likelyhood the likelihood as a float between 0 and 1, which is converted to a byte
+     */
+    public void setLikelihood(GENOTYPE type, float likelyhood) {
+        likelihood.put(type,(int)Math.round(likelyhood*255.0));
+    }
+
+    /**
+     * return a byte array representation of the likelihood object, in GLFv3 specified order
+     * @return a byte array of the genotype values
+     */
+    public int[] toByteArray() {
+        int ret[] = new int[GENOTYPE.values().length];
+        int index = 0;
+        for (GENOTYPE type : GENOTYPE.values()) {
+            ret[index] = likelihood.get(type);
+            ++index;
+        }
+        return ret;
+    }
+
+
+}
--- a/java/test/org/broadinstitute/sting/utils/glf/GLFRecordTest.java
+++ b/java/test/org/broadinstitute/sting/utils/glf/GLFRecordTest.java
@ -0,0 +1,45 @@
+package org.broadinstitute.sting.utils.glf;
+
+import org.junit.Test;
+
+
+/*
+ * Copyright (c) 2009 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.
+ */
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Class GLFRecordTest
+ *         <p/>
+ *         Tests for the GLFRecord class
+ */
+public class GLFRecordTest {
+
+    @Test
+    public void basicWrite() {
+        
+    }
+
+}
--- a/java/test/org/broadinstitute/sting/utils/glf/LikelihoodObjectTest.java
+++ b/java/test/org/broadinstitute/sting/utils/glf/LikelihoodObjectTest.java
@ -0,0 +1,105 @@
+package org.broadinstitute.sting.utils.glf;
+
+import org.junit.Before;
+import org.junit.Test;
+import static org.junit.Assert.assertEquals;
+import org.broadinstitute.sting.BaseTest;
+import static junit.framework.Assert.assertTrue;
+
+
+/*
+ * Copyright (c) 2009 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.
+ */
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Class LikelihoodObjectTest
+ *         <p/>
+ *         Tests the Likelihood object.
+ */
+public class LikelihoodObjectTest extends BaseTest {
+
+    private LikelihoodObject mLO = null;
+
+    @Before
+    public void before() {
+        mLO = new LikelihoodObject();
+    }
+
+    @Test
+    public void testBlankConstruction() {
+        mLO = new LikelihoodObject();
+        assertTrue(mLO.likelihood.size() == LikelihoodObject.GENOTYPE.values().length);
+    }
+
+    @Test
+    public void testConstructionFromArray() {
+        int[] ray = new int[10];
+        for (int x = 0; x < 10; x++) {
+            ray[x] = ( x * 25 );
+        }
+        mLO = new LikelihoodObject(ray);
+        assertTrue(mLO.likelihood.size() == LikelihoodObject.GENOTYPE.values().length);
+
+        int index = 0;
+        for (LikelihoodObject.GENOTYPE t : LikelihoodObject.GENOTYPE.values()) {
+            assertTrue(ray[index] == mLO.likelihood.get(t));
+            ++index;
+        }
+    }
+
+    @Test
+    public void testByteArrayReturn() {
+        int[] ray = new int[10];
+        for (int x = 0; x < 10; x++) {
+            ray[x] = ( x * 25 );
+        }
+        mLO = new LikelihoodObject(ray);
+        assertTrue(mLO.likelihood.size() == LikelihoodObject.GENOTYPE.values().length);
+
+        int index = 0;
+        int[] ret = mLO.toByteArray();
+        for (index = 0; index < ret.length; index++) {
+            assertTrue(ray[index] == ret[index]);
+        }
+    }
+
+    @Test
+    public void testSetLikelihood() {
+        mLO = new LikelihoodObject();
+        for (LikelihoodObject.GENOTYPE t : LikelihoodObject.GENOTYPE.values()) {
+            mLO.setLikelihood(t,0.5f);
+        }
+        assertTrue(mLO.likelihood.size() == LikelihoodObject.GENOTYPE.values().length);
+
+        int index = 0;
+        int[] ret = mLO.toByteArray();
+        for (index = 0; index < ret.length; index++) {
+            assertTrue(ret[index] == 128);
+        }
+    }
+
+
+}