Examples with DataProvider org.testng.annotations.DataProvider used on opensource projects

Example 86 with DataProvider

use of org.testng.annotations.DataProvider in project gatk by broadinstitute.

the class SampleCollectionUnitTest method testSampleIndexByReadWithReadGroupWithoutSample.

@Test(dataProvider = "samFileHeaderData", dependsOnMethods = "testCreation")
public void testSampleIndexByReadWithReadGroupWithoutSample(final SAMFileHeader header) {
    final String readGroup = header.getReadGroups().stream().filter(rg -> rg.getSample() == null).map(SAMReadGroupRecord::getId).findFirst().orElse(null);
    if (readGroup == null)
        return;
    final SampleCollection sampleCollection = new SampleCollection(header);
    final GATKRead read = ArtificialReadUtils.createRandomRead(header, 100);
    if (sampleCollection.sampleCount() > 0) {
        read.setReadGroup(readGroup);
        Assert.assertEquals(sampleCollection.sampleIndexByRead(read), -1);
    }
}

Example 87 with DataProvider

use of org.testng.annotations.DataProvider in project gatk by broadinstitute.

the class SampleCollectionUnitTest method testReadGroupIndexByReadWithReadGroupWithoutSample.

@Test(dataProvider = "samFileHeaderData", dependsOnMethods = "testCreation")
public void testReadGroupIndexByReadWithReadGroupWithoutSample(final SAMFileHeader header) {
    final String readGroup = header.getReadGroups().stream().filter(rg -> rg.getSample() == null).map(SAMReadGroupRecord::getId).findFirst().orElse(null);
    if (readGroup == null)
        return;
    final SampleCollection sampleCollection = new SampleCollection(header);
    final GATKRead read = ArtificialReadUtils.createRandomRead(header, 100);
    read.setReadGroup(readGroup);
    Assert.assertEquals(sampleCollection.readGroupIndexByRead(read), sampleCollection.readGroupIndexById(readGroup));
}

Example 88 with DataProvider

use of org.testng.annotations.DataProvider in project gatk by broadinstitute.

the class GatherBamFilesIntegrationTest method gatherBAMTestData.

@DataProvider(name = "bamgathering")
public Object[][] gatherBAMTestData() {
    final File origBam = new File(TEST_DATA_DIR, "orig.bam");
    final List<File> splitBamsUnmappedLast = Arrays.asList(new File(TEST_DATA_DIR, "indchr1.bam"), new File(TEST_DATA_DIR, "indchr2.bam"), new File(TEST_DATA_DIR, "indchr3.bam"), new File(TEST_DATA_DIR, "indchr4.bam"), new File(TEST_DATA_DIR, "indchr5.bam"), new File(TEST_DATA_DIR, "indchr6.bam"), new File(TEST_DATA_DIR, "indchr7.bam"), new File(TEST_DATA_DIR, "indchr8.bam"), new File(TEST_DATA_DIR, "indUnknownChrom.bam"));
    final List<File> splitBamsUnmappedFirst = Arrays.asList(new File(TEST_DATA_DIR, "indUnknownChrom.bam"), new File(TEST_DATA_DIR, "indchr1.bam"), new File(TEST_DATA_DIR, "indchr2.bam"), new File(TEST_DATA_DIR, "indchr3.bam"), new File(TEST_DATA_DIR, "indchr4.bam"), new File(TEST_DATA_DIR, "indchr5.bam"), new File(TEST_DATA_DIR, "indchr6.bam"), new File(TEST_DATA_DIR, "indchr7.bam"), new File(TEST_DATA_DIR, "indchr8.bam"));
    final List<File> splitBamsUnmappedMissing = Arrays.asList(new File(TEST_DATA_DIR, "indchr1.bam"), new File(TEST_DATA_DIR, "indchr2.bam"), new File(TEST_DATA_DIR, "indchr3.bam"), new File(TEST_DATA_DIR, "indchr4.bam"), new File(TEST_DATA_DIR, "indchr5.bam"), new File(TEST_DATA_DIR, "indchr6.bam"), new File(TEST_DATA_DIR, "indchr7.bam"), new File(TEST_DATA_DIR, "indchr8.bam"));
    return new Object[][] { { splitBamsUnmappedLast, origBam, true, true }, { splitBamsUnmappedFirst, origBam, false, true }, { splitBamsUnmappedMissing, origBam, false, false } };
}

Example 89 with DataProvider

use of org.testng.annotations.DataProvider in project gatk by broadinstitute.

the class IntervalsSkipListOneContigUnitTest method intervals.

@DataProvider(name = "intervals")
public Object[][] intervals() {
    ArrayList<Locatable> input = Lists.newArrayList(new SimpleInterval("1", 10, 100));
    ArrayList<Locatable> empty = new ArrayList<>();
    ArrayList<Locatable> manyOverlapping = Lists.newArrayList(new SimpleInterval("1", 10, 100), // special case: multiple intervals starting at the same place
    new SimpleInterval("1", 20, 50), new SimpleInterval("1", 20, 50), new SimpleInterval("1", 20, 50));
    ArrayList<Locatable> mixInput = Lists.newArrayList(// ends before query interval
    new SimpleInterval("1", 10, 20), // ends in query interval
    new SimpleInterval("1", 10, 60), // equal to query interval
    new SimpleInterval("1", 30, 50), // covered by query interval
    new SimpleInterval("1", 40, 42), // ends after query interval
    new SimpleInterval("1", 45, 60), // starts after query interval
    new SimpleInterval("1", 60, 100));
    ArrayList<Locatable> mixExpected = Lists.newArrayList(// ends in query interval
    new SimpleInterval("1", 10, 60), // equal to query interval
    new SimpleInterval("1", 30, 50), // covered by query interval
    new SimpleInterval("1", 40, 42), // ends after query interval
    new SimpleInterval("1", 45, 60));
    // returns input single SimpleInterval, query range, expected SimpleInterval
    return new Object[][] { // single-point boundary cases
    new Object[] { input, new SimpleInterval("1", 10, 10), input }, new Object[] { input, new SimpleInterval("1", 100, 100), input }, new Object[] { input, new SimpleInterval("1", 9, 9), empty }, new Object[] { input, new SimpleInterval("1", 11, 11), input }, new Object[] { input, new SimpleInterval("1", 99, 99), input }, new Object[] { input, new SimpleInterval("1", 101, 101), empty }, // empty list boundary case
    new Object[] { empty, new SimpleInterval("1", 101, 101), empty }, // different contig
    new Object[] { empty, new SimpleInterval("2", 101, 101), empty }, // input exactly matches the query interval
    new Object[] { input, new SimpleInterval("1", 10, 100), input }, // multiple intervals in the same place (potential edge case for indexing)
    new Object[] { manyOverlapping, new SimpleInterval("1", 20, 20), manyOverlapping }, // input with multiple intervals
    new Object[] { mixInput, new SimpleInterval("1", 30, 50), mixExpected } };
}

Example 90 with DataProvider

use of org.testng.annotations.DataProvider in project gatk by broadinstitute.

the class HomRefBlockUnitTest method makeContiguousData.

@DataProvider(name = "ContiguousData")
public Object[][] makeContiguousData() {
    final List<Object[]> tests = new ArrayList<>();
    final VariantContext vc = getVariantContext();
    for (final String chrMod : Arrays.asList("", ".mismatch")) {
        for (final int offset : Arrays.asList(-10, -1, 0, 1, 10)) {
            final boolean equals = chrMod.isEmpty() && offset == 0;
            tests.add(new Object[] { vc.getContig() + chrMod, vc.getStart() + offset, equals });
        }
    }
    return tests.toArray(new Object[][] {});
}