gatk-3.8/public/java/test/net/sf/picard/reference/FastaSequenceIndexBuilderUnitTest.java

/*
 * Copyright (c) 2010 The Broad Institute
 *
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 * obtaining a copy of this software and associated documentation
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 * copies of the Software, and to permit persons to whom the
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 *
 * 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,
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 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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package net.sf.picard.reference;

import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSourceProgressListener;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;

import java.io.File;
import java.io.FileNotFoundException;

/**
 * Test the fasta sequence index reader.
 */
public class FastaSequenceIndexBuilderUnitTest extends BaseTest {

    private FastaSequenceIndexBuilder builder;
    private ReferenceDataSourceProgressListener progress;
    private File fastaFile;
    private FastaSequenceIndex controlIndex;

    @BeforeMethod
    public void doForEachTest() throws FileNotFoundException {
        controlIndex = new FastaSequenceIndex();
    }

    /**
     * Tests basic unix file with one contig
     * File is the exampleFASTA.fasta shipped with GATK
     */
    @Test
    public void unixFileTest() {
        logger.warn("Executing unixFileTest");

        fastaFile = new File(validationDataLocation + "exampleFASTA.fasta");
        builder = new FastaSequenceIndexBuilder(fastaFile, progress);
        FastaSequenceIndex index = builder.createIndex();
        controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));

        Assert.assertTrue(index.equals(controlIndex));
    }


    /**
     * Tests basic windows file with one contig
     * File is a simple fasta file
     */
    @Test
    public void windowsFileTest() {
        logger.warn("Executing windowsFileTest");

        fastaFile = new File(validationDataLocation + "exampleFASTA-windows.fasta");
        builder = new FastaSequenceIndexBuilder(fastaFile, progress);
        FastaSequenceIndex index = builder.createIndex();
        controlIndex.add(new FastaSequenceIndexEntry("chr2", 7, 29, 7, 9,0));

        Assert.assertTrue(index.equals(controlIndex));
    }

    /**
     * Tests fasta with the two contigs from above combined
     * File is the exampleFASTA.fasta shipped with GATK
     */
    @Test
    public void combinedWindowsUnix() {
        logger.warn("Executing combinedWindowsUnix");

        fastaFile = new File(validationDataLocation + "exampleFASTA-combined.fasta");
        builder = new FastaSequenceIndexBuilder(fastaFile, progress);
        FastaSequenceIndex index = builder.createIndex();
        controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 100000, 60, 61,0));
        controlIndex.add(new FastaSequenceIndexEntry("chr2", 101680, 29, 7, 9,1));

        Assert.assertTrue(index.equals(controlIndex));
    }

    /**
     * Tests fasta with the two contigs from above combined
     * File is the exampleFASTA.fasta shipped with GATK
     */
    @Test
    public void threeVariableLengthContigs() {
        logger.warn("Executing threeVariableLengthContigs");

        fastaFile = new File(validationDataLocation + "exampleFASTA-3contigs.fasta");
        builder = new FastaSequenceIndexBuilder(fastaFile, progress);
        FastaSequenceIndex index = builder.createIndex();
        controlIndex.add(new FastaSequenceIndexEntry("chr1", 6, 17, 5, 6,0));
        controlIndex.add(new FastaSequenceIndexEntry("chr2", 35, 21, 7, 8,1));
        controlIndex.add(new FastaSequenceIndexEntry("chr3", 66, 100, 10, 11,2));

        Assert.assertTrue(index.equals(controlIndex));
    }
}