本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.setMappingQuality()方法的一些代码示例，展示了GATKSAMRecord.setMappingQuality()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。GATKSAMRecord.setMappingQuality()方法的具体详情如下：
包路径：org.broadinstitute.gatk.utils.sam.GATKSAMRecord
类名称：GATKSAMRecord
方法名：setMappingQuality

GATKSAMRecord.setMappingQuality介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk-protected

@Test
  public void BasicTest() {
    BaseQualitySumPerAlleleBySample a = new BaseQualitySumPerAlleleBySample();

    final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(5, 1, 10000);
    final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 76);

    read.setMappingQuality(60);
    Assert.assertTrue(a.isUsableRead(read));

    read.setMappingQuality(0);
    Assert.assertFalse(a.isUsableRead(read));

    read.setMappingQuality(QualityUtils.MAPPING_QUALITY_UNAVAILABLE);
    Assert.assertFalse(a.isUsableRead(read));

  }
}

代码示例来源：origin: broadgsa/gatk

read.setMappingQuality(Math.min(aRead.getRead().getMappingQuality() + 10, 254));

代码示例来源：origin: broadgsa/gatk

private GATKSAMRecord makeOverlappingRead(final String leftFlank, final int leftQual, final String overlapBases,
                     final byte[] overlapQuals, final String rightFlank, final int rightQual,
                     final int alignmentStart) {
  final String bases = leftFlank + overlapBases + rightFlank;
  final int readLength = bases.length();
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, alignmentStart, readLength);
  final byte[] leftQuals = Utils.dupBytes((byte) leftQual, leftFlank.length());
  final byte[] rightQuals = Utils.dupBytes((byte) rightQual, rightFlank.length());
  final byte[] quals = Utils.concat(leftQuals, overlapQuals, rightQuals);
  read.setCigarString(readLength + "M");
  read.setReadBases(bases.getBytes());
  for ( final EventType type : EventType.values() )
    read.setBaseQualities(quals, type);
  read.setReadGroup(rgForMerged);
  read.setMappingQuality(60);
  return read;
}

代码示例来源：origin: broadgsa/gatk

@Test
  public void testRBPMappingQuals() {

    // create a read with high MQ
    final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, 1, 10);
    read.setReadBases(Utils.dupBytes((byte) 'A', 10));
    read.setBaseQualities(Utils.dupBytes((byte) 30, 10));
    read.setCigarString("10M");
    read.setMappingQuality(200); // set a MQ higher than max signed byte

    // now create the RBP
    final List<PileupElement> elts = new LinkedList<>();
    elts.add(new PileupElement(read, 0, read.getCigar().getCigarElement(0), 0, 0));
    final Map<String, ReadBackedPileupImpl> pileupsBySample = new HashMap<>();
    pileupsBySample.put("foo", new ReadBackedPileupImpl(loc, elts));
    final ReadBackedPileup pileup = new ReadBackedPileupImpl(loc, pileupsBySample);

    Assert.assertEquals(pileup.getMappingQuals()[0], 200);
  }
}

代码示例来源：origin: broadgsa/gatk

private List<PileupElement> makeReads( final int n, final int mapq, final String op ) {
  final int readLength = 3;
  final List<PileupElement> elts = new LinkedList<PileupElement>();
  for ( int i = 0; i < n; i++ ) {
    GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, 1, readLength);
    read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
    read.setBaseQualities(Utils.dupBytes((byte) 30, readLength));
    read.setCigarString("1M1" + op + "1M");
    read.setMappingQuality(mapq);
    final int baseOffset = op.equals("M") ? 1 : 0;
    final CigarElement cigarElement = read.getCigar().getCigarElement(1);
    elts.add(new PileupElement(read, baseOffset, cigarElement, 1, 0));
  }
  return elts;
}

代码示例来源：origin: broadgsa/gatk-protected

/**
 * Creates and writes an artificial read given the appropriate data
 *
 * @param readBases   the bases
 * @param contig      the contig
 * @param start       the read start
 * @param cigar       the cigar string
 * @param sample      the sample name (used to get the right read group)
 * @param isNegStrand should this read be on the negative strand?
 */
private void writeRead(final byte[] readBases, final String contig, final int start,
      final String cigar, final String sample, final boolean isNegStrand) {
  final GATKSAMRecord read = new GATKSAMRecord(header);
  read.setBaseQualities(readQuals);
  read.setReadBases(readBases);
  read.setReadName("" + readNameCounter++);
  read.setCigarString(cigar);
  read.setReadPairedFlag(false);
  read.setAlignmentStart(start);
  read.setMappingQuality(60);
  read.setReferenceName(contig);
  read.setReadNegativeStrandFlag(isNegStrand);
  read.setAttribute("RG", sampleRG(sample).getReadGroupId());
  readWriter.addAlignment(read);
}

代码示例来源：origin: broadgsa/gatk-protected

read.setMappingQuality(artificialMappingQuality);
read.setReferenceName(loc.getContig());
read.setReadNegativeStrandFlag(false);

代码示例来源：origin: broadgsa/gatk

cList.add(c);
returnRead.setCigar( new Cigar( cList ));
returnRead.setMappingQuality( firstRead.getMappingQuality() );

代码示例来源：origin: broadgsa/gatk-protected

rec.setMappingQuality(60);

代码示例来源：origin: broadgsa/gatk

emptyRead.setReferenceIndex(read.getReferenceIndex());
emptyRead.setAlignmentStart(0);
emptyRead.setMappingQuality(0);

代码示例来源：origin: broadgsa/gatk-protected

/**
 * Write out a representation of this haplotype as a read
 *
 * @param haplotype a haplotype to write out.  Cannot be null
 * @param paddedRefLoc the reference location.  Cannot be null
 * @param isAmongBestHaplotypes true if among the best haplotypes, false if it was just one possible but not so good
 */
private void writeHaplotype(final Haplotype haplotype,
              final GenomeLoc paddedRefLoc,
              final boolean isAmongBestHaplotypes) {
  final GATKSAMRecord record = new GATKSAMRecord(output.getHeader());
  record.setReadBases(haplotype.getBases());
  record.setAlignmentStart(paddedRefLoc.getStart() + haplotype.getAlignmentStartHapwrtRef());
  record.setBaseQualities(Utils.dupBytes((byte) '!', haplotype.getBases().length));
  record.setCigar(AlignmentUtils.consolidateCigar(haplotype.getCigar()));
  record.setMappingQuality(isAmongBestHaplotypes ? 60 : 0);
  record.setReadName("HC" + uniqueNameCounter++);
  record.setAttribute(AlignmentUtils.HAPLOTYPE_TAG,haplotype.hashCode());
  record.setReadUnmappedFlag(false);
  record.setReferenceIndex(paddedRefLoc.getContigIndex());
  record.setAttribute(SAMTag.RG.toString(), READ_GROUP_ID);
  record.setFlags(16);
  output.add(record);
}

代码示例来源：origin: broadgsa/gatk

private GATKSAMRecord createReadOffContig(final SAMFileHeader header, final boolean negStrand, final int pre, final int post) {
  final int contigLen = header.getSequence(0).getSequenceLength();
  final int readLen = pre + contigLen + post;
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read1", 0, 1, readLen);
  read.setAlignmentStart(1);
  read.setCigar(TextCigarCodec.decode(pre + "S" + contigLen + "M" + post + "S"));
  read.setBaseQualities(Utils.dupBytes((byte) 30, readLen));
  read.setReadBases(Utils.dupBytes((byte)'A', readLen));
  read.setMappingQuality(60);
  read.setMateAlignmentStart(1);
  read.setProperPairFlag(true);
  read.setReadPairedFlag(true);
  read.setInferredInsertSize(30);
  read.setReadNegativeStrandFlag(negStrand);
  read.setMateNegativeStrandFlag(! negStrand);
  read.setReadGroup(new GATKSAMReadGroupRecord("foo"));
  return read;
}