/*
* Copyright (c) 2007-2012 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.sam;
import htsjdk.samtools.util.CloseableIterator;
import org.broad.igv.Globals;
import org.broad.igv.sam.reader.BAMFileReader;
import org.broad.igv.sam.reader.SAMReader;
import org.broad.igv.util.TestUtils;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.File;
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;
BAMFileReader bamreader = new BAMFileReader(new File(bamfile));
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;
BAMFileReader bamreader = new BAMFileReader(new File(bamfile));
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");
}
}