/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 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
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*/
package org.broad.igv.bbfile;
import org.broad.igv.util.TestUtils;
import org.junit.Test;
import java.io.IOException;
import static org.junit.Assert.*;
/**
* @author jrobinso
* @date Jun 19, 2011
*/
public class BBFileReaderTest {
@Test
public void testBigBed() throws IOException {
String path = TestUtils.DATA_DIR + "bb/chr21.refseq.bb";
BBFileReader bbReader = new BBFileReader(path);
BBFileHeader bbFileHdr = bbReader.getBBFileHeader();
assertTrue(bbFileHdr.isBigBed());
String chr = "chr21";
int start = 26490012;
int end = 42182827;
for (BBZoomLevelHeader header : bbReader.getZoomLevels().getZoomLevelHeaders()) {
assertNotNull(header);
ZoomLevelIterator zlIter = bbReader.getZoomLevelIterator(header.getZoomLevel(), chr, start, chr, end, false);
while (zlIter.hasNext()) {
ZoomDataRecord rec = zlIter.next();
int n = rec.getBasesCovered();
if (n > 0) {
assertEquals(chr, rec.getChromName());
assertTrue(rec.getChromEnd() >= start && rec.getChromStart() <= end);
}
}
}
}
}