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/*
* 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.
*/
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package org.broad.igv.sam.reader;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.util.CloseableIterator;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.sam.Alignment;
import org.broad.igv.sam.SAMAlignment;
import org.broad.igv.util.ResourceLocator;
import org.junit.*;
import java.io.IOException;
import java.util.List;
import java.util.stream.Collectors;
import org.junit.Ignore;
import static org.junit.Assert.*;
/**
* @author jrobinso
*/
public class BAMHttpReaderTest extends AbstractHeadlessTest {
private static final String BAM_URL_STRING = "http://1000genomes.s3.amazonaws.com/phase3/data/HG01879/exome_alignment/HG01879.mapped.ILLUMINA.bwa.ACB.exome.20120522.bam";
BAMReader reader;
@BeforeClass
public static void setUpClass() throws Exception {
AbstractHeadlessTest.setUpClass();
}
@AfterClass
public static void tearDownClass() throws Exception {
}
@Before
public void setUp() throws Exception {
reader = new BAMReader(new ResourceLocator(BAM_URL_STRING), true);
}
@After
public void tearDown() throws Exception {
reader.close();
reader = null;
}
@Ignore("No network access")
@Test
public void testGetHeader() throws IOException {
SAMFileHeader header = reader.getFileHeader();
assertEquals(86, header.getSequenceDictionary().size());
assertEquals("1.0", header.getVersion());
}
@Ignore("No network access")
@Test
public void testIterator() throws IOException {
CloseableIterator<SAMAlignment> iter = reader.iterator();
//This takes a long time. We just look for a minimum number
int minnum = 10;
int actnum = 0;
while (iter.hasNext()) {
Alignment a = iter.next();
assertNotNull(a);
actnum++;
if (actnum > minnum) {
break;
}
}
iter.close();
assertTrue(actnum > minnum);
}
@Ignore("No network access")
@Test
public void testQuery() throws Exception {
checkNumber("Y", 10000000 - 1, 10004000, 4);
}
private void checkNumber(String chr, int start, int end, int expected_count) throws IOException {
CloseableIterator<SAMAlignment> iter = reader.query(chr, start, end, false);
int counted = 0;
while (iter.hasNext()) {
Alignment a = iter.next();
counted++;
assertNotNull(a);
}
iter.close();
assertEquals(expected_count, counted);
}
}
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