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

Example 1 with NO_MAPPING_QUALITY

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

the class ReadPileupUnitTest method testSimplePileup.

@Test
public void testSimplePileup() {
    final int readlength = 10;
    final byte[] bases1 = Utils.repeatChars('A', readlength);
    final byte[] quals1 = Utils.repeatBytes((byte) 10, readlength);
    final String cigar1 = "10M";
    final byte[] bases2 = Utils.repeatChars('C', readlength);
    final byte[] quals2 = Utils.repeatBytes((byte) 20, readlength);
    final String cigar2 = "5M3I2M";
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
    final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, bases1, quals1, cigar1);
    read1.setName("read1");
    final GATKRead read2 = ArtificialReadUtils.createArtificialRead(header, bases2, quals2, cigar2);
    read1.setName("read2");
    final List<GATKRead> reads = Arrays.asList(read1, read2);
    final ReadPileup pu = new ReadPileup(loc, reads, 1);
    //checking non-blowup. We're not making any claims about the format of toString
    Assert.assertNotNull(pu.toString());
    Assert.assertEquals(pu.getPileupString('N'), String.format("%s %s N %s%s %s%s", // the position
    loc.getContig(), // the position
    loc.getStart(), // the bases
    (char) read1.getBase(0), // the bases
    (char) read2.getBase(0), // base quality in FASTQ format
    SAMUtils.phredToFastq(read1.getBaseQuality(0)), // base quality in FASTQ format
    SAMUtils.phredToFastq(read2.getBaseQuality(0))));
    Assert.assertEquals(pu.getBases(), new byte[] { (byte) 'A', (byte) 'C' });
    Assert.assertFalse(pu.isEmpty());
    Assert.assertEquals(pu.size(), 2, "size");
    Assert.assertEquals(pu.getBaseCounts(), new int[] { 1, 1, 0, 0 });
    Assert.assertEquals(pu.getBaseQuals(), new byte[] { 10, 20 });
    Assert.assertEquals(pu.getLocation(), loc);
    Assert.assertEquals(pu.getMappingQuals(), new int[] { NO_MAPPING_QUALITY, NO_MAPPING_QUALITY });
    Assert.assertEquals(pu.makeFilteredPileup(p -> p.getQual() >= 12).makeFilteredPileup(p -> p.getMappingQual() >= 0).size(), 1, "getBaseAndMappingFilteredPileup");
    Assert.assertEquals(pu.makeFilteredPileup(r -> r.getQual() >= 12).size(), 1, "getBaseFilteredPileup");
    Assert.assertEquals(pu.getNumberOfElements(p -> true), 2);
    Assert.assertEquals(pu.getNumberOfElements(p -> false), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.isDeletion()), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.isBeforeDeletionStart()), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.isBeforeInsertion()), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.getRead().getMappingQuality() == 0), 2);
    Assert.assertEquals(pu.getOffsets(), Arrays.asList(1, 1), "getOffsets");
    Assert.assertEquals(pu.getReadGroupIDs(), Arrays.asList(new SAMReadGroupRecord[] { null }), "getReadGroups");
    Assert.assertEquals(pu.getReads(), Arrays.asList(read1, read2), "getReads");
    Assert.assertEquals(pu.getSamples(header), Arrays.asList(new String[] { null }), "getSamples");
    Assert.assertTrue(pu.getPileupForLane("fred").isEmpty());
    Assert.assertTrue(pu.makeFilteredPileup(r -> r.getMappingQual() >= 10).isEmpty());
}

Example 2 with NO_MAPPING_QUALITY

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

the class ReadPileupUnitTest method testSimplePileupWithOffset.

@Test
public void testSimplePileupWithOffset() {
    final int readlength = 10;
    final byte[] bases1 = Utils.repeatChars('A', readlength);
    final byte[] quals1 = Utils.repeatBytes((byte) 10, readlength);
    final String cigar1 = "10M";
    final byte[] bases2 = Utils.repeatChars('C', readlength);
    final byte[] quals2 = Utils.repeatBytes((byte) 20, readlength);
    final String cigar2 = "10M";
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
    final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, bases1, quals1, cigar1);
    read1.setName("read1");
    final GATKRead read2 = ArtificialReadUtils.createArtificialRead(header, bases2, quals2, cigar2);
    read1.setName("read2");
    final List<GATKRead> reads = Arrays.asList(read1, read2);
    final int off = 6;
    final ReadPileup pu = new ReadPileup(loc, reads, off);
    Assert.assertEquals(pu.getBases(), new byte[] { (byte) 'A', (byte) 'C' });
    //checking non-blowup. We're not making any claims about the format of toString
    Assert.assertNotNull(pu.toString());
    Assert.assertEquals(pu.getPileupString('N'), String.format("%s %s N %s%s %s%s", // the position
    loc.getContig(), // the position
    loc.getStart(), // the bases
    (char) read1.getBase(off), // the bases
    (char) read2.getBase(off), // base quality in FASTQ format
    SAMUtils.phredToFastq(read1.getBaseQuality(off)), // base quality in FASTQ format
    SAMUtils.phredToFastq(read2.getBaseQuality(off))));
    Assert.assertFalse(pu.isEmpty());
    Assert.assertEquals(pu.size(), 2, "size");
    Assert.assertEquals(pu.getBaseCounts(), new int[] { 1, 1, 0, 0 });
    Assert.assertEquals(pu.getBaseQuals(), new byte[] { 10, 20 });
    Assert.assertEquals(pu.getLocation(), loc);
    Assert.assertEquals(pu.getMappingQuals(), new int[] { NO_MAPPING_QUALITY, NO_MAPPING_QUALITY });
    Assert.assertTrue(pu.makeFilteredPileup(r -> r.getRead().isReverseStrand()).isEmpty(), "getReverseStrandPileup");
    Assert.assertEquals(pu.makeFilteredPileup(r -> !r.getRead().isReverseStrand()).size(), 2, "getForwardStrandPileup");
    Assert.assertEquals(pu.makeFilteredPileup(p -> p.getQual() >= 12).makeFilteredPileup(p -> p.getMappingQual() >= 0).size(), 1, "getBaseAndMappingFilteredPileup");
    Assert.assertEquals(pu.makeFilteredPileup(p -> p.getQual() >= 12).size(), 1, "getBaseFilteredPileup");
    Assert.assertEquals(pu.getNumberOfElements(p -> true), 2);
    Assert.assertEquals(pu.getNumberOfElements(p -> false), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.isDeletion()), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.isBeforeDeletionStart()), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.isBeforeInsertion()), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.getRead().getMappingQuality() == 0), 2);
    Assert.assertEquals(pu.getOffsets(), Arrays.asList(off, off), "getOffsets");
    Assert.assertEquals(pu.getReadGroupIDs(), Arrays.asList(new SAMReadGroupRecord[] { null }), "getReadGroups");
    Assert.assertEquals(pu.getReads(), Arrays.asList(read1, read2), "getReads");
    Assert.assertEquals(pu.getSamples(header), Arrays.asList(new String[] { null }), "getSamples");
    Assert.assertTrue(pu.getPileupForLane("fred").isEmpty());
    Assert.assertTrue(pu.makeFilteredPileup(p -> p.getMappingQual() >= 10).isEmpty());
}

Example 3 with NO_MAPPING_QUALITY

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

the class ReadPileupUnitTest method testSimplePileupWithIndelsOffset.

@Test
public void testSimplePileupWithIndelsOffset() {
    final int readlength = 10;
    final byte[] bases1 = Utils.repeatChars('A', readlength);
    final byte[] quals1 = Utils.repeatBytes((byte) 10, readlength);
    final String cigar1 = "10M";
    final byte[] bases2 = Utils.repeatChars('C', readlength);
    final byte[] quals2 = Utils.repeatBytes((byte) 20, readlength);
    final String cigar2 = "5M3I2M";
    final SAMFileHeader header = ArtificialReadUtils.createArtificialSamHeader();
    final GATKRead read1 = ArtificialReadUtils.createArtificialRead(header, bases1, quals1, cigar1);
    read1.setName("read1");
    final GATKRead read2 = ArtificialReadUtils.createArtificialRead(header, bases2, quals2, cigar2);
    read1.setName("read2");
    final List<GATKRead> reads = Arrays.asList(read1, read2);
    final int offset = 4;
    final ReadPileup pu = new ReadPileup(loc, reads, offset);
    final PileupElement firstElem = pu.getElementForRead(read1);
    Assert.assertNull(firstElem.getAdjacentOperator(PileupElement.Direction.NEXT));
    Assert.assertNull(firstElem.getAdjacentOperator(PileupElement.Direction.PREV));
    final PileupElement secondElem = pu.getElementForRead(read2);
    Assert.assertEquals(secondElem.getAdjacentOperator(PileupElement.Direction.NEXT), CigarOperator.I);
    Assert.assertNull(secondElem.getAdjacentOperator(PileupElement.Direction.PREV));
    //checking non-blowup. We're not making any claims about the format of toString
    Assert.assertNotNull(pu.toString());
    Assert.assertEquals(pu.getPileupString('N'), String.format("%s %s N %s%s %s%s", // the position
    loc.getContig(), // the position
    loc.getStart(), // the bases
    (char) read1.getBase(0), // the bases
    (char) read2.getBase(0), // base quality in FASTQ format
    SAMUtils.phredToFastq(read1.getBaseQuality(0)), // base quality in FASTQ format
    SAMUtils.phredToFastq(read2.getBaseQuality(0))));
    Assert.assertEquals(pu.getBases(), new byte[] { (byte) 'A', (byte) 'C' });
    Assert.assertFalse(pu.isEmpty());
    Assert.assertEquals(pu.size(), 2, "size");
    Assert.assertEquals(pu.getBaseCounts(), new int[] { 1, 1, 0, 0 });
    Assert.assertEquals(pu.getBaseQuals(), new byte[] { 10, 20 });
    Assert.assertEquals(pu.getLocation(), loc);
    Assert.assertEquals(pu.getMappingQuals(), new int[] { NO_MAPPING_QUALITY, NO_MAPPING_QUALITY });
    Assert.assertEquals(pu.makeFilteredPileup(p -> p.getQual() >= 12).makeFilteredPileup(p -> p.getMappingQual() >= 0).size(), 1, "getBaseAndMappingFilteredPileup");
    Assert.assertEquals(pu.makeFilteredPileup(r -> r.getQual() >= 12).size(), 1, "getBaseFilteredPileup");
    Assert.assertEquals(pu.getNumberOfElements(p -> true), 2);
    Assert.assertEquals(pu.getNumberOfElements(p -> false), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.isDeletion()), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.isBeforeDeletionStart()), 0);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.isBeforeInsertion()), 1);
    Assert.assertEquals(pu.getNumberOfElements(p -> p.getRead().getMappingQuality() == 0), 2);
    Assert.assertEquals(pu.getOffsets(), Arrays.asList(offset, offset), "getOffsets");
    Assert.assertEquals(pu.getReadGroupIDs(), Arrays.asList(new SAMReadGroupRecord[] { null }), "getReadGroups");
    Assert.assertEquals(pu.getReads(), Arrays.asList(read1, read2), "getReads");
    Assert.assertEquals(pu.getSamples(header), Arrays.asList(new String[] { null }), "getSamples");
    Assert.assertTrue(pu.getPileupForLane("fred").isEmpty());
    Assert.assertTrue(pu.makeFilteredPileup(r -> r.getMappingQual() >= 10).isEmpty());
}