/*
* 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.AlignmentIndexer;
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 java.io.IOException;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
/**
* @author jrobinso
*/
public class SamQueryTextReaderTest {
public SamQueryTextReaderTest() {
}
@BeforeClass
public static void setUpClass() throws Exception {
Globals.setHeadless(true);
}
@AfterClass
public static void tearDownClass() throws Exception {
}
private void createSamIndex(String samfile) throws IOException {
AlignmentIndexer.getInstance(new File(samfile), null, null).createSamIndex();
}
/**
* Test of query method, of class SamQueryTextReader.
*/
@Test
public void testQuery() throws Exception {
String testFile = TestUtils.DATA_DIR + "sam/NA12878.muc1.test.sam";
createSamIndex(testFile);
String chr = "chr1";
int start = 153426040;
int end = 153426154;
// Test posA query that includes overlaps (contained == false)
boolean contained = false;
SAMReader reader = new SAMReader(testFile);
CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
int count = 0;
while (iter.hasNext()) {
Alignment record = iter.next();
if (record.isMapped()) {
assertEquals(chr, record.getChr());
assertTrue(record.getEnd() >= start);
assertTrue(record.getStart() <= end);
}
count++;
}
assertEquals(64, count);
iter.close();
reader.close();
}
/**
* Test of query method, of class SamQueryTextReader.
* <p/>
* Regression test for RT 134402.
*/
@Test
public void testQuery2() throws Exception {
String testFile = TestUtils.DATA_DIR + "sam/test_2_plus_one_read.sam";
createSamIndex(testFile);
//chr3:125,963,167-125,972,750
String chr = "chr3";
int start = 125963167;
int end = 125972750;
// Test posA query that includes overlaps (contained == false)
boolean contained = false;
SAMReader reader = new SAMReader(testFile);
CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
int count = 0;
while (iter.hasNext()) {
Alignment record = iter.next();
assertEquals(chr, record.getChr());
assertTrue(record.getEnd() >= start);
assertTrue(record.getStart() <= end);
count++;
}
assertEquals(329, count);
iter.close();
reader.close();
}
/**
* Test of query method, of class SamQueryTextReader.
* <p/>
* Regression test for RT 134339.
*/
@Test
public void testQuery3() throws Exception {
String testFile = TestUtils.DATA_DIR + "sam/test_minus_converted.sam";
createSamIndex(testFile);
//chr3:125,963,167-125,972,750
String chr = "chr1";
int start = 12550532;
int end = 12550610;
// Test posA query that includes overlaps (contained == false)
boolean contained = false;
SAMReader reader = new SAMReader(testFile);
CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
int count = 0;
while (iter.hasNext()) {
Alignment record = iter.next();
assertEquals(chr, record.getChr());
assertTrue(record.getEnd() >= start);
assertTrue(record.getStart() <= end);
count++;
}
assertEquals(2, count);
iter.close();
reader.close();
}
@Test
public void testMoran() throws Exception {
String testFile = TestUtils.LARGE_DATA_DIR + "r2.allProb.sorted.sam";
String chr = "mm9chrY";
int start = 799939;
int end = 800152;
// Test posA query that includes overlaps (contained == false)
boolean contained = false;
SAMReader reader = new SAMReader(testFile);
CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, contained);
int count = 0;
while (iter.hasNext()) {
Alignment record = iter.next();
assertEquals(chr, record.getChr());
assertTrue(record.getEnd() >= start);
assertTrue(record.getStart() <= end);
count++;
}
assertEquals(134, count);
iter.close();
reader.close();
}
}