/*
* 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.AbstractHeadlessTest;
import org.broad.igv.sam.reader.AlignmentReader;
import org.broad.igv.sam.reader.AlignmentReaderFactory;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.Test;
import java.util.*;
import static junit.framework.Assert.assertEquals;
import static junit.framework.Assert.assertTrue;
/**
* @author jrobinso
*/
public class AlignmentPackerTest extends AbstractHeadlessTest {
String path = TestUtils.LARGE_DATA_DIR + "HG00171.hg18.bam";
String chr = "chr1";
int start = 151666494;
int end = start + 1000;
boolean contained = false;
private AlignmentInterval getAlignmentInterval() throws Exception {
ResourceLocator rl = new ResourceLocator(path);
AlignmentReader samReader = AlignmentReaderFactory.getReader(rl);
CloseableIterator<Alignment> iter = samReader.query(chr, start, end, contained);
List<Alignment> list = new ArrayList<Alignment>();
while(iter.hasNext()){
list.add(iter.next());
}
AlignmentInterval interval = new AlignmentInterval(chr, start, end, list, null, null, null);
return interval;
}
/**
* Test of packAlignments method, of class AlignmentPacker.
*/
@Test
public void testPackAlignments() throws Exception {
///////////////////////////
/*
boolean showDuplicates = false;
int qualityThreshold = 0;
int maxLevels = 1000;
*/
AlignmentInterval interval = getAlignmentInterval();
Map<String, List<Row>> result = (new AlignmentPacker()).packAlignments(interval, new AlignmentTrack.RenderOptions());
assertEquals(1, result.size());
for (List<Row> alignmentrows : result.values()) {
for (Row alignmentrow : alignmentrows) {
List<Alignment> alignments = alignmentrow.alignments;
for (int ii = 1; ii < alignments.size(); ii++) {
assertTrue(alignments.get(ii).getAlignmentStart() > alignments.get(ii - 1).getAlignmentStart());
assertTrue(alignments.get(ii).getAlignmentStart() - alignments.get(ii - 1).getAlignmentEnd() >= AlignmentPacker.MIN_ALIGNMENT_SPACING);
}
}
}
}
@Test
public void testGroupAlignmentsPairOrientation() throws Exception {
int expSize = 3; //AlignmentTrack.OrientationType.values().length;
Map<String, List<Row>> result = tstGroupAlignments(AlignmentTrack.GroupOption.PAIR_ORIENTATION, expSize);
}
public Map<String, List<Row>> tstGroupAlignments(AlignmentTrack.GroupOption groupOption, int expSize) throws Exception {
AlignmentTrack.RenderOptions renderOptions = new AlignmentTrack.RenderOptions();
renderOptions.groupByOption = groupOption;
AlignmentInterval interval = getAlignmentInterval();
Map<String, List<Row>> result = (new AlignmentPacker()).packAlignments(interval, renderOptions);
Set<String> names = result.keySet();
//names.removeAll(Arrays.asList("", null));
assertEquals(expSize, names.size());
return result;
}
}