/*
* 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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* THE SOFTWARE.
*/
package org.broad.igv.feature;
import org.broad.igv.feature.tribble.IGVBEDCodec;
import org.broad.igv.util.TestUtils;
import htsjdk.tribble.AbstractFeatureReader;
import org.junit.AfterClass;
import static org.junit.Assert.*;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import java.util.Iterator;
/**
* @author Jim Robinson
* @date 4/26/12
*/
public class JunctionsBedTest {
/**
* Purpose of this test is to insure that a cufflinks "junctions.bed" file is parsed as a junction file, as
* opposed to a plain bed file.
*
* @throws Exception
*/
@Test
public void testJunctionFile() throws Exception {
String bedFile = TestUtils.DATA_DIR + "bed/mini.junctions.bed";
AbstractFeatureReader bfr = AbstractFeatureReader.getFeatureReader(bedFile, new IGVBEDCodec(), false);
Iterator<BasicFeature> iter = bfr.iterator();
while (iter.hasNext()) {
BasicFeature feature = iter.next();
assertTrue( feature instanceof SpliceJunctionFeature);
SpliceJunctionFeature sjf = (SpliceJunctionFeature) feature;
assertTrue(sjf.getJunctionDepth() > 0);
}
}
}