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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
This commit is contained in:
aaron 2009-05-27 22:32:25 +00:00
parent ce6a0f522b
commit d275c18e58
3 changed files with 251 additions and 0 deletions
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101
java/src/org/broadinstitute/sting/utils/glf/LikelihoodObject.java 100755
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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;
}
}

45
java/test/org/broadinstitute/sting/utils/glf/GLFRecordTest.java 100755
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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() {
}
}

105
java/test/org/broadinstitute/sting/utils/glf/LikelihoodObjectTest.java 100755
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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);
}
}
}