/*
* 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
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package org.broad.igv.feature.tribble;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.util.TestUtils;
import org.broad.igv.variant.vcf.VCFVariant;
import htsjdk.tribble.AbstractFeatureReader;
import htsjdk.tribble.FeatureCodec;
import org.junit.Before;
import org.junit.Test;
import java.io.IOException;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
import static junit.framework.Assert.assertEquals;
import static junit.framework.Assert.assertTrue;
/**
*
*/
public class CachingFeatureReaderTest {
String path = TestUtils.LARGE_DATA_DIR + "CEU.SRP000032.2010_03.genotypes.vcf.gz";
AbstractFeatureReader baseReader;
CachingFeatureReader cacheReader;
@Before
public void setUp() throws IOException {
Genome genome = null; // <= don't do chromosome alias conversion
FeatureCodec codec = CodecFactory.getCodec(path, null);
baseReader = AbstractFeatureReader.getFeatureReader(path, path + ".tbi", codec, true);
cacheReader = new CachingFeatureReader(baseReader);
}
@Test
/*
1 182773022 182773023
1 182773812 182773813
1 182774171 182774172
1 182774425 182774426
1 182774496 182774497
1 182774630 182774631
1 182774894 182774895
1 182775195 182775196
1 182775253 182775254
1 182776704 182776705
1 182776741 182776742
*/
public void testGetSequenceNames() throws Exception {
List<String> seqNames = cacheReader.getSequenceNames();
assertEquals(23, seqNames.size());
}
@Test
public void testQuery() throws Exception {
Set<String> baseReaderLoci = new HashSet();
final int start = 182773022;
final int end = 182776742;
final String chr = "1";
Iterator<VCFVariant> iter = baseReader.query(chr, start, end);
while (iter.hasNext()) {
VCFVariant var = iter.next();
assertEquals(chr, var.getChr());
assertTrue(var.getEnd() >= start && var.getStart() <= end);
baseReaderLoci.add(getLocusString(var));
}
assertTrue(baseReaderLoci.size() > 0);
// Now use CachingFeatureReader and insure results are the same
Set<String> cacheReaderLoci = new HashSet();
iter = cacheReader.query(chr, start, end);
while (iter.hasNext()) {
VCFVariant var = iter.next();
assertEquals(chr, var.getChr());
assertTrue(var.getEnd() >= start && var.getStart() <= end);
cacheReaderLoci.add(getLocusString(var));
}
assertEquals(baseReaderLoci.size(), cacheReaderLoci.size());
for (String locus : cacheReaderLoci) {
assertTrue(baseReaderLoci.contains(locus));
}
}
String getLocusString(VCFVariant variant) {
return variant.getChr() + ":" + variant.getStart() + "-" + variant.getEnd();
}
}