/*
* Copyright (c) 2007-2013 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.tools;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.sam.AlignmentCounts;
import org.broad.igv.sam.DenseAlignmentCounts;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import java.util.Arrays;
import java.util.Collection;
import static junit.framework.Assert.assertEquals;
/**
* @author jacob
* @date 2013-Jun-24
*/
@RunWith(Parameterized.class)
public class CavenerConsensusCalculatorTest extends AbstractHeadlessTest {
private String inputBases;
private char expectedConsensus;
public CavenerConsensusCalculatorTest(String inputBases, char expectedConsensus) {
this.inputBases = inputBases;
this.expectedConsensus = expectedConsensus;
//System.out.println("Input: " + this.inputBases);
}
@Test
public void testCalcCorrectly() throws Exception {
CavenerConsensusCalculator calc = new CavenerConsensusCalculator();
AlignmentCounts counts = createCounts();
assertEquals(this.expectedConsensus, calc.calculateConsensusBase(counts, 0));
}
private AlignmentCounts createCounts() {
MockAlignmentCounts counts = new MockAlignmentCounts(0, 1);
for (char c : this.inputBases.toCharArray()) {
counts.incPositionCount(0, (byte) c);
}
counts.finish();
return counts;
}
@Parameterized.Parameters
public static Collection<Object[]> data() {
Object[][] data = new Object[][]{
{"aaa", 'a'}, {"ccccccg", 'c'}, {"g", 'g'}, {"n", 'n'},
{"aac", 'a'}, {"acgt", 'n'},
{"aacc", 'm'}, {"aacct", 'm'}, {"ggaaactgga", 'r'}, {"ggggccccatat", 'n'}
};
return Arrays.asList(data);
}
private static class MockAlignmentCounts extends DenseAlignmentCounts {
public MockAlignmentCounts(int start, int end) {
super(start, end, null);
}
public void incPositionCount(int pos, byte b) {
super.incPositionCount(pos, b, (byte) 0, false);
}
}
}