gatk-3.8/public/java/test/org/broadinstitute/sting/utils/MRUCachingSAMSequencingDictionaryUnitTest.java

/*
 * Copyright (c) 2012 The Broad Institute
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 * 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
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 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
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package org.broadinstitute.sting.utils;


import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.io.File;
import java.io.FileNotFoundException;
import java.util.LinkedList;
import java.util.List;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;

public class MRUCachingSAMSequencingDictionaryUnitTest extends BaseTest {
    private static ReferenceSequenceFile seq;
    private static SAMSequenceDictionary dict;

    @BeforeClass
    public void init() throws FileNotFoundException {
        // sequence
        seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
        dict = seq.getSequenceDictionary();
    }

    @Test
    public void testBasic() {
        final MRUCachingSAMSequenceDictionary caching = new MRUCachingSAMSequenceDictionary(dict);

        Assert.assertEquals(caching.getDictionary(), dict, "Dictionary not the one I expected");

        for ( final SAMSequenceRecord rec : dict.getSequences() ) {
            Assert.assertFalse(caching.isCached(rec.getSequenceIndex()), "Expected index to not be cached");
            Assert.assertFalse(caching.isCached(rec.getSequenceName()), "Expected contig to not be cached");

            Assert.assertEquals(caching.getSequence(rec.getSequenceName()), rec, "Couldn't query for sequence");
            Assert.assertEquals(caching.getSequence(rec.getSequenceIndex()), rec, "Couldn't query for sequence index");
            Assert.assertEquals(caching.hasContig(rec.getSequenceName()), true, "hasContig query for sequence");
            Assert.assertEquals(caching.hasContigIndex(rec.getSequenceIndex()), true, "hasContigIndex query for sequence");
            Assert.assertEquals(caching.getSequenceIndex(rec.getSequenceName()), rec.getSequenceIndex(), "Couldn't query for sequence");

            Assert.assertEquals(caching.hasContig(rec.getSequenceName() + "asdfadsfa"), false, "hasContig query for unknown sequence");
            Assert.assertEquals(caching.hasContigIndex(dict.getSequences().size()), false, "hasContigIndex query for unknown index");

            Assert.assertTrue(caching.isCached(rec.getSequenceIndex()), "Expected index to be cached");
            Assert.assertTrue(caching.isCached(rec.getSequenceName()), "Expected contig to be cached");
        }
    }

    @Test(expectedExceptions = ReviewedStingException.class)
    public void testBadGetSequence() {
        final MRUCachingSAMSequenceDictionary caching = new MRUCachingSAMSequenceDictionary(dict);
        caching.getSequence("notInDictionary");
    }

    @Test(expectedExceptions = ReviewedStingException.class)
    public void testBadGetSequenceIndex() {
        final MRUCachingSAMSequenceDictionary caching = new MRUCachingSAMSequenceDictionary(dict);
        caching.getSequence(dict.getSequences().size());
    }
}