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* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
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* copies of the Software, and to permit persons to whom the Software is
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*
* The above copyright notice and this permission notice shall be included in
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*
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package org.broad.igv.sam;
import org.broad.igv.AbstractHeadlessTest;
import org.junit.Test;
/**
* @author jacob
* @date 2013-Oct-31
*/
public class DenseAlignmentCountsTest extends AbstractHeadlessTest {
/**
* Test for IGV-2047, make sure we guard against the boundaries properly
* @throws Exception
*/
@Test
public void testGetMaxCount_smallInterval() throws Exception {
int fullIntervals = 0;
int extraLength = DenseAlignmentCounts.MAX_COUNT_INTERVAL / 4 + 2;
tstGetMaxCount(0, fullIntervals, extraLength);
}
/**
* More normal case of largish interval
* @throws Exception
*/
@Test
public void testGetMaxCount_LargeInterval() throws Exception {
int fullIntervals = 10;
int extraLength = DenseAlignmentCounts.MAX_COUNT_INTERVAL / 4 + 2;
tstGetMaxCount(0, fullIntervals, extraLength);
}
private void tstGetMaxCount(int start, int fullIntervals, int extraLength){
int mci = DenseAlignmentCounts.MAX_COUNT_INTERVAL;
int end = start + fullIntervals*mci + extraLength;
DenseAlignmentCounts daCounts = new DenseAlignmentCounts(start, end, null);
int[] queryStarts = {start, start + 50, start + mci, start + mci + 50, start, start, start, start + 10};
int[] queryLengths ={50, 50, 50, 50, (int) (mci*1.5), 2*mci, (int)(2.5*mci), end-start + 10};
for(int ii=0; ii < queryStarts.length; ii++){
int queryStart = queryStarts[ii];
int queryEnd = queryStart + queryLengths[ii];
daCounts.getMaxCount(start, queryEnd);
}
}
}