/*
* 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
* 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.
*/
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package org.broad.igv.sam;
import htsjdk.samtools.util.CloseableIterator;
import org.broad.igv.Globals;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.sam.reader.BAMReader;
import org.broad.igv.sam.reader.SAMReader;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import java.util.List;
import static junit.framework.Assert.assertEquals;
import static junit.framework.Assert.assertTrue;
/**
* @author jrobinso
*/
public class BAMFileReaderTest {
public BAMFileReaderTest() {
}
@BeforeClass
public static void setUpClass() throws Exception {
Globals.setHeadless(true);
}
@AfterClass
public static void tearDownClass() throws Exception {
}
/**
* Test of close method, of class BAMQueryReader.
*/
@Test
public void testClose() throws Exception {
String bamfile = TestUtils.LARGE_DATA_DIR + "HG00171.hg18.bam";
String chr = "chr1";
int end = 300000000;
int start = end / 5;
int stopafter = 10;
int counter = 0;
BAMReader bamreader = new BAMReader(new ResourceLocator(bamfile), true);
CloseableIterator<PicardAlignment> bamiter = bamreader.query(chr, start, end, true);
while (bamiter.hasNext()) {
Alignment bamrecord = bamiter.next();
if (counter >= stopafter) {
break;
} else {
counter++;
}
}
bamreader.close();
boolean closeSucceeded = false;
try {
CloseableIterator<PicardAlignment> bamiter2 = bamreader.query(chr, start, end, true);
} catch (NullPointerException npe) {
closeSucceeded = true;
}
assertTrue(closeSucceeded);
}
/**
* Test of query method, of class BAMQueryReader.
*/
@Test
public void testQueryAgainstSam() throws Exception {
String bamfile = TestUtils.LARGE_DATA_DIR + "HG00171.hg18.bam";
String samfile = TestUtils.LARGE_DATA_DIR + "HG00171.hg18.sam";
String chr = "chr1";
int end = 300000000;
int start = end / 5;
BAMReader bamreader = new BAMReader(new ResourceLocator(bamfile), true);
SAMReader samreader = new SAMReader(samfile);
CloseableIterator<PicardAlignment> bamiter = bamreader.query(chr, start, end, true);
CloseableIterator<PicardAlignment> samiter = samreader.iterator();
int count = 0;
while (bamiter.hasNext()) {
Alignment bamrecord = bamiter.next();
Alignment samrecord = samiter.next();
assertTrue(bamrecord.getStart() >= start);
assertTrue(bamrecord.getEnd() <= end);
assertEquals(bamrecord.getReadName(), samrecord.getReadName());
assertEquals(bamrecord.getSample(), samrecord.getSample());
count++;
}
assertTrue("No data retrieved", count > 0);
System.out.println("Retrieved " + count + " rows");
}
public int count(CloseableIterator<PicardAlignment> iter) {
int counter = 0;
while (iter.hasNext()) {
iter.next();
counter++;
}
return counter;
}
}