Examples with GATKRead org.broadinstitute.hellbender.utils.read.GATKRead used on opensource projects

Example 21 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class ReadFilterPluginUnitTest method simpleGoodRead.

private GATKRead simpleGoodRead(final SAMFileHeader header) {
    final String cigarString = "101M";
    final Cigar cigar = TextCigarCodec.decode(cigarString);
    GATKRead read = createRead(header, cigar, 1, 0, 10);
    read.setMappingQuality(50);
    return read;
}

Example 22 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class ReadFilterLibraryUnitTest method testReadLengthFilter.

@Test
public void testReadLengthFilter() {
    final SAMFileHeader header = createHeaderWithReadGroups();
    final GATKRead read = simpleGoodRead(header);
    ReadLengthReadFilter f = new ReadLengthReadFilter();
    f.minReadLength = 10;
    f.maxReadLength = 20;
    read.setBases(new byte[5]);
    //fail
    Assert.assertFalse(f.test(read), read.toString());
    read.setBases(new byte[10]);
    //pass
    Assert.assertTrue(f.test(read), read.toString());
    read.setBases(new byte[15]);
    //pass
    Assert.assertTrue(f.test(read), read.toString());
    read.setBases(new byte[20]);
    //pass
    Assert.assertTrue(f.test(read), read.toString());
    read.setBases(new byte[25]);
    //fail
    Assert.assertFalse(f.test(read), read.toString());
}

Example 23 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class ReadFilterLibraryUnitTest method testPlatformUnitFilter.

@Test
public void testPlatformUnitFilter() {
    final SAMFileHeader header = createHeaderWithReadGroups();
    final PlatformUnitReadFilter f = new PlatformUnitReadFilter(header);
    final GATKRead read = simpleGoodRead(header);
    final String fred = "fred";
    header.getReadGroup(read.getReadGroup()).setPlatformUnit(fred);
    f.blackListedLanes = Collections.emptySet();
    header.getReadGroup(read.getReadGroup()).setPlatformUnit(fred);
    //pass - no blacklist
    Assert.assertTrue(f.test(read), read.toString());
    f.blackListedLanes = Collections.singleton(fred);
    header.getReadGroup(read.getReadGroup()).setPlatformUnit(fred);
    //fail
    Assert.assertFalse(f.test(read), read.toString());
    f.blackListedLanes = Collections.singleton(fred);
    header.getReadGroup(read.getReadGroup()).setPlatformUnit(fred + "suffix");
    //pass - exact matching
    Assert.assertTrue(f.test(read), read.toString());
    f.blackListedLanes = Collections.singleton(fred);
    header.getReadGroup(read.getReadGroup()).setPlatformUnit(fred.toUpperCase());
    //pass - case sensitive matching
    Assert.assertTrue(f.test(read), read.toString());
    f.blackListedLanes = new LinkedHashSet<>(Arrays.asList(fred, "bozo"));
    header.getReadGroup(read.getReadGroup()).setPlatformUnit(fred);
    //fail
    Assert.assertFalse(f.test(read), read.toString());
    f.blackListedLanes = Collections.singleton(fred);
    read.setAttribute(SAMTag.PU.name(), fred);
    //fail - match
    Assert.assertFalse(f.test(read), read.toString());
}

Example 24 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class ReadFilterLibraryUnitTest method testNonZeroFragmentLengthReadFilter.

@Test
public void testNonZeroFragmentLengthReadFilter() {
    final SAMFileHeader header = createHeaderWithReadGroups();
    final GATKRead read = simpleGoodRead(header);
    read.setFragmentLength(0);
    Assert.assertFalse(NONZERO_FRAGMENT_LENGTH_READ_FILTER.test(read), "NONZERO_FRAGMENT_LENGTH_READ_FILTER " + read.toString());
    read.setFragmentLength(9);
    Assert.assertTrue(NONZERO_FRAGMENT_LENGTH_READ_FILTER.test(read), "NONZERO_FRAGMENT_LENGTH_READ_FILTER " + read.toString());
}

Example 25 with GATKRead

use of org.broadinstitute.hellbender.utils.read.GATKRead in project gatk by broadinstitute.

the class ReadFilterLibraryUnitTest method testWonkyCigars.

@Test(dataProvider = "badCigars")
public void testWonkyCigars(String cigarString) {
    GATKRead read = ReadClipperTestUtils.makeReadFromCigar(cigarString);
    Assert.assertFalse(GOOD_CIGAR.test(read), read.getCigar().toString());
}