QualityEncodingDetectorTest.java

package htsjdk.samtools.util;

import htsjdk.samtools.SAMException;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMRecordSetBuilder;
import htsjdk.samtools.fastq.FastqReader;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import java.io.File;
import java.util.Arrays;
import java.util.List;

public class QualityEncodingDetectorTest {

    private static class Testcase {
        private final File f;
        private final FastqQualityFormat q;

        Testcase(final File file, final FastqQualityFormat qualityFormat) {
            this.f = file;
            this.q = qualityFormat;
        }
    }

    final static List<Testcase> FASTQ_TESTCASES = Arrays.asList(
            // Need to use full-range quality here, as Solexa and Illumina are near indistinguishable
            new Testcase(new File("./testdata/htsjdk/samtools/util/QualityEncodingDetectorTest/solexa_full_range_as_solexa.fastq"), FastqQualityFormat.Solexa),
            new Testcase(new File("./testdata/htsjdk/samtools/util/QualityEncodingDetectorTest/s_1_sequence.txt"), FastqQualityFormat.Illumina),
            new Testcase(new File("./testdata/htsjdk/samtools/util/QualityEncodingDetectorTest/5k-30BB2AAXX.3.aligned.sam.fastq"), FastqQualityFormat.Standard)
    );
    final static List<Testcase> BAM_TESTCASES = Arrays.asList(
            new Testcase(new File("./testdata/htsjdk/samtools/util/QualityEncodingDetectorTest/unmapped.sam"), FastqQualityFormat.Standard),
            new Testcase(new File("./testdata/htsjdk/samtools/BAMFileIndexTest/index_test.bam"), FastqQualityFormat.Standard),
            new Testcase(new File("./testdata/htsjdk/samtools/util/QualityEncodingDetectorTest/solexa-as-standard.bam"), FastqQualityFormat.Solexa),
            new Testcase(new File("./testdata/htsjdk/samtools/util/QualityEncodingDetectorTest/illumina-as-standard.bam"), FastqQualityFormat.Illumina)

    );

    Object[][] renderObjectArrayArray(final List<Testcase> testcaseList) {
        final Object[][] data = new Object[testcaseList.size()][];
        for (int i = 0; i < data.length; i++) {
            final Testcase testcase = testcaseList.get(i);
            data[i] = new Object[]{testcase.f, testcase.q};
        }
        return data;
    }

    @DataProvider(name = "BAM_TESTCASES")
    Object[][] bamTestcases() {
        return renderObjectArrayArray(BAM_TESTCASES);
    }

    @DataProvider(name = "FASTQ_TESTCASES")
    Object[][] fastqTestcases() {
        return renderObjectArrayArray(FASTQ_TESTCASES);
    }

    @Test(dataProvider = "FASTQ_TESTCASES", groups = {"unix"})
    public void testFastqQualityInference(final File input, final FastqQualityFormat expectedQualityFormat) {
        final FastqReader reader = new FastqReader(input);
        Assert.assertEquals(QualityEncodingDetector.detect(reader), expectedQualityFormat);
        reader.close();
    }

    @Test(dataProvider = "BAM_TESTCASES", groups = {"unix"})
    public void testBamQualityInference(final File input, final FastqQualityFormat expectedQualityFormat) {
        final SAMFileReader reader = new SAMFileReader(input);
        Assert.assertEquals(QualityEncodingDetector.detect(reader), expectedQualityFormat);
        reader.close();
    }

    @Test
    public void testSmallBamForDetectorFailure() {
        final SAMRecordSetBuilder samRecordSetBuilder = createSmallUnmappedSam();
        Assert.assertNotSame(QualityEncodingDetector.detect(samRecordSetBuilder.getSamReader(),
                null), FastqQualityFormat.Standard);
    }

    @Test
    public void testSmallBamWithExpectedQuality() {
        final SAMRecordSetBuilder samRecordSetBuilder = createSmallUnmappedSam();
        Assert.assertEquals(QualityEncodingDetector.detect(samRecordSetBuilder.getSamReader(),
                FastqQualityFormat.Standard), FastqQualityFormat.Standard);
    }

    @Test (expectedExceptions = SAMException.class)
    public void testQualitySanity() {
        final SAMRecordSetBuilder samRecordSetBuilder = createSmallUnmappedSam();
        QualityEncodingDetector.detect(samRecordSetBuilder.getSamReader(),
                FastqQualityFormat.Illumina);
    }

    private SAMRecordSetBuilder createSmallUnmappedSam() {
        final SAMRecordSetBuilder samRecordSetBuilder = new SAMRecordSetBuilder();
        samRecordSetBuilder.setReadLength(25);
        samRecordSetBuilder.addFrag("READ0", -1, -1, false, true, null, "@@@FFFFFHHHHHJIJIIJIIJJJJ", -1);
        samRecordSetBuilder.addFrag("READ1", -1, -1, false, true, null, "@@@FFFFFHHHHHJIJIIJIIJJJJ", -1);
        samRecordSetBuilder.addFrag("READ2", -1, -1, false, true, null, "@CCFDFEDHHHFFHIIII@GH<FFH", -1);
        samRecordSetBuilder.addFrag("READ3", -1, -1, false, true, null, "@@?DFFDFHFFHDHIIHIIEIIJGG", -1);
        samRecordSetBuilder.addFrag("READ4", -1, -1, false, true, null, "@CCFFDDFHHHHHIIJJHFJJJJJH", -1);
        samRecordSetBuilder.addFrag("READ5", -1, -1, false, true, null, "BCCFFFFFHHHHHJJJJJIJJJJJJ", -1);
        samRecordSetBuilder.addFrag("READ6", -1, -1, false, true, null, "@@CDFFFFHHHFHHIJJJJJJJIJJ", -1);
        samRecordSetBuilder.addFrag("READ7", -1, -1, false, true, null, "CCCFFFFFHHHHHJJJJIJJJJHII", -1);
        samRecordSetBuilder.addFrag("READ8", -1, -1, false, true, null, "CCCFFFFFHHHHHJJJJJJJJJJJJ", -1);
        return samRecordSetBuilder;
    }
}