/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
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* 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
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*
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* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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package org.broad.igv.cli_plugin;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.track.TrackLoader;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.broad.igv.variant.VariantTrack;
import org.broad.igv.variant.vcf.VCFVariant;
import org.broad.igv.variant.vcf.VCFWriterTest;
import htsjdk.tribble.Feature;
import htsjdk.variant.vcf.VCFHeader;
import org.junit.Test;
import java.io.FileOutputStream;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import static junit.framework.Assert.assertEquals;
/**
* @author jacob
* @date 2013-Jul-02
*/
public class VCFEncoderTest extends AbstractHeadlessTest {
@Test
public void basicIOTest() throws Exception {
String inputPath = TestUtils.DATA_DIR + "vcf/hc_mod.vcf";
TestUtils.createIndex(inputPath);
VariantTrack inputTrack = (VariantTrack) (new TrackLoader()).load(new ResourceLocator(inputPath), genome).get(0);
VCFEncoder encoder = new VCFEncoder();
Argument arg = new Argument(null, Argument.InputType.VARIANT_TRACK, null, null, null, null, false, null);
Map<Argument, Object> arguments = new HashMap(1);
arguments.put(arg, inputTrack);
encoder.setInputs(null, arguments, arg);
String chr = "chr20";
int start = 10499005;
int end = 10499500;
String outpath = TestUtils.TMP_OUTPUT_DIR + "hc_mod_out.vcf";
OutputStream outputStream = new FileOutputStream(outpath);
List<VCFVariant> infeatures = new ArrayList<VCFVariant>();
for (Feature feat : inputTrack.getFeatures(chr, start, end)) {
infeatures.add((VCFVariant) feat);
}
encoder.encodeAll(outputStream, infeatures.iterator());
TestUtils.createIndex(outpath);
VariantTrack outputTrack = (VariantTrack) (new TrackLoader()).load(new ResourceLocator(inputPath), genome).get(0);
VCFWriterTest.assertHeadersEquals((VCFHeader) inputTrack.getHeader(), (VCFHeader) outputTrack.getHeader());
int n = 0;
for (Feature var1 : inputTrack.getFeatures(chr, start, end)) {
VCFVariant var0 = infeatures.get(n++);
VCFWriterTest.assertVCFVariantsEqual(var0, (VCFVariant) var1);
}
assertEquals("Different number of features from input", infeatures.size(), n);
}
}