CRAMReaderTest.java

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 * Copyright (c) 2016 University of California San Diego
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package org.broad.igv.sam.cram;

import htsjdk.samtools.util.CloseableIterator;
import org.broad.igv.Globals;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.sam.Alignment;
import org.broad.igv.sam.PicardAlignment;
import org.broad.igv.sam.reader.BAMReader;
import org.broad.igv.sam.reader.SAMReader;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.junit.AfterClass;
import org.junit.BeforeClass;
import org.junit.Test;

import java.util.List;

import static junit.framework.Assert.assertEquals;
import static junit.framework.Assert.assertTrue;

/**
 * @author jrobinso
 */
public class CRAMReaderTest {

    public CRAMReaderTest() {
    }

    @BeforeClass
    public static void setUpClass() throws Exception {
        Globals.setHeadless(true);
    }

    @AfterClass
    public static void tearDownClass() throws Exception {
    }


    @Test
    public void testIterateLocalCraiCram() throws Exception {

        String cramFile = TestUtils.DATA_DIR + "cram/cram_with_crai_index.cram";
        GenomeManager.getInstance().loadGenome(TestUtils.DATA_DIR + "cram/hg19mini.fasta", null);

        BAMReader reader = new BAMReader(new ResourceLocator(cramFile), true);

        List<String> seqNames = reader.getSequenceNames();
        assertEquals(4, seqNames.size());


        CloseableIterator<PicardAlignment> iter = reader.iterator();
        int counter = count(iter);
        assertEquals(11, counter);

    }

    @Test
    public void testQueryLocalCraiCram() throws Exception {

        String cramFile = TestUtils.DATA_DIR + "cram/cram_with_crai_index.cram";
        GenomeManager.getInstance().loadGenome(TestUtils.DATA_DIR + "cram/hg19mini.fasta", null);

        BAMReader reader = new BAMReader(new ResourceLocator(cramFile), true);

        CloseableIterator<PicardAlignment> iter = reader.query("2", 500, 600, false);
        int counter = count(iter);
        assertEquals(2, counter);
    }


    @Test
    public void testQueryLocalBaiCram() throws Exception {

        String cramFile = TestUtils.DATA_DIR + "cram/cram_with_bai_index.cram";
        GenomeManager.getInstance().loadGenome(TestUtils.DATA_DIR + "cram/hg19mini.fasta", null);

        BAMReader reader = new BAMReader(new ResourceLocator(cramFile), true);

        CloseableIterator<PicardAlignment> iter = reader.query("2", 500, 600, false);
        int counter = count(iter);
        assertEquals(2, counter);
    }



    @Test
    public void testRemoteCraiCram() throws Exception {

        String cramFile = "https://s3.amazonaws.com/igv.broadinstitute.org/test/cram/cram_with_crai_index.cram";
        GenomeManager.getInstance().loadGenome(TestUtils.DATA_DIR + "cram/hg19mini.fasta", null);

        BAMReader reader = new BAMReader(new ResourceLocator(cramFile), true);

        CloseableIterator<PicardAlignment> iter = reader.query("2", 500, 600, false);
        int counter = count(iter);
        assertEquals(2, counter);
    }


    @Test
    public void testRemoteBaiCram() throws Exception {

        String cramFile = TestUtils.DATA_DIR + "cram/cram_with_bai_index.cram";
        GenomeManager.getInstance().loadGenome(TestUtils.DATA_DIR + "cram/hg19mini.fasta", null);

        BAMReader reader = new BAMReader(new ResourceLocator(cramFile), true);

        CloseableIterator<PicardAlignment> iter = reader.query("2", 500, 600, false);
        int counter = count(iter);
        assertEquals(2, counter);
    }


    public int count(CloseableIterator<PicardAlignment> iter) {
        int counter = 0;
        while (iter.hasNext()) {
            iter.next();
            counter++;
        }
        return counter;
    }

}