gatk-3.8/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsTest.java

package org.broadinstitute.sting.utils.sam;

import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.iterators.PeekingStingIterator;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
import static junit.framework.Assert.assertTrue;
import net.sf.samtools.SAMRecord;

/**
 * Created by IntelliJ IDEA.
 * User: aaronmckenna
 * Date: Jun 3, 2009
 * Time: 3:09:34 AM
 * To change this template use File | Settings | File Templates.
 */
public class ArtificialSAMUtilsTest extends BaseTest {


    @Test
    public void basicReadIteratorTest() {
        StingSAMIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 100);
        int count = 0;
        while (iter.hasNext()) {
            SAMRecord rec = iter.next();
            count++;
        }
        assertEquals(100 * 100, count);
    }

    @Test
    public void tenPerChromosome() {
        StingSAMIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 10);
        int count = 0;
        while (iter.hasNext()) {
            SAMRecord rec = iter.next();

            assertEquals(Integer.valueOf(Math.round(count / 10)), rec.getReferenceIndex());
            count++;
        }
        assertEquals(100 * 10, count);
    }

    @Test
    public void onePerChromosome() {
        StingSAMIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 1);
        int count = 0;
        while (iter.hasNext()) {
            SAMRecord rec = iter.next();

            assertEquals(Integer.valueOf(count), rec.getReferenceIndex());
            count++;
        }
        assertEquals(100 * 1, count);
    }

    @Test
    public void basicUnmappedIteratorTest() {
        StingSAMIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 100, 1000);
        int count = 0;
        for (int x = 0; x < (100* 100); x++ ) {
            if (!iter.hasNext()) {
                fail ("we didn't get the expected number of reads");
            }
            SAMRecord rec = iter.next();
            assertTrue(rec.getReferenceIndex() >= 0);
            count++;
        }
        assertEquals(count, 100 * 100);

        // now we should have 1000 unmapped reads
        count = 0;
        while (iter.hasNext()) {
            SAMRecord rec = iter.next();
            assertTrue(rec.getReferenceIndex() < 0);
            count++;
        }
        assertEquals(1000, count);
    }

    @Test
    public void testPeeking() {
        PeekingStingIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 100);
        int count = 0;
        while (iter.hasNext()) {
            int readCnt = ((ArtificialSAMIterator)(iter)).readsTaken();

            // peek the record
            SAMRecord rec = iter.peek();
            assertTrue(rec.getReferenceIndex() >= 0);

            // next the record
            SAMRecord rec2 = iter.next();
            assertTrue(rec2.getReadName() == rec.getReadName());
            assertTrue(rec2.getAlignmentStart() == rec.getAlignmentStart());

            // find out how many reads we've taken now
             int readCnt2 = ((ArtificialSAMIterator)(iter)).readsTaken();

            count++;
            if (count < 100*100) assertEquals(readCnt + 1, readCnt2);
            else assertEquals(readCnt, readCnt2);
        }
        assertEquals(100 * 100, count );

    }
}