本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.setAttribute()方法的一些代码示例，展示了GATKSAMRecord.setAttribute()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.setAttribute()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：setAttribute

GATKSAMRecord.setAttribute介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

public void setReadGroup( final GATKSAMReadGroupRecord readGroup ) {
  mReadGroup = readGroup;
  retrievedReadGroup = true;
  setAttribute("RG", mReadGroup.getId()); // todo -- this should be standardized, but we don't have access to SAMTagUtils!
}

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

/**
 * Add reads that have been dropped for the specified reason to the dropped list.
 */
public void addReads(final Reason reason, final Collection<GATKSAMRecord> reads) {
  Set<GATKSAMRecord> readsForReason = droppedReads.get(reason);
  if (null == readsForReason) {
    readsForReason = new HashSet<>(reads.size());
  }
  for (final GATKSAMRecord rec: reads) {
    if (!previouslyDropped(rec)) {
      // tag the original read so we can track the ones we've already seen and
      // only add them to the dropped list once
      rec.setAttribute(SAMTag.FT.name(), reason.reasonName());
      readsForReason.add(rec);
    }
  }
  droppedReads.put(reason, readsForReason);
}

代码示例来源：origin: broadgsa/gatk

/**
 * Setters and Accessors for base insertion and base deletion quality scores
 */
public void setBaseQualities( final byte[] quals, final EventType errorModel ) {
  switch( errorModel ) {
    case BASE_SUBSTITUTION:
      setBaseQualities(quals);
      break;
    case BASE_INSERTION:
      setAttribute( GATKSAMRecord.BQSR_BASE_INSERTION_QUALITIES, quals == null ? null : SAMUtils.phredToFastq(quals) );
      break;
    case BASE_DELETION:
      setAttribute( GATKSAMRecord.BQSR_BASE_DELETION_QUALITIES, quals == null ? null : SAMUtils.phredToFastq(quals) );
      break;
    default:
      throw new ReviewedGATKException("Unrecognized Base Recalibration type: " + errorModel );
  }
}

代码示例来源：origin: broadgsa/gatk

public boolean finalizeUpdate() {
  // if we haven't made any changes, don't do anything
  if ( newCigar == null )
    return false;
  if ( newStart == -1 )
    newStart = read.getAlignmentStart();
  else if ( Math.abs(newStart - read.getAlignmentStart()) > MAX_POS_MOVE_ALLOWED ) {
    logger.debug(String.format("Attempting to realign read %s at %d more than %d bases to %d.", read.getReadName(), read.getAlignmentStart(), MAX_POS_MOVE_ALLOWED, newStart));
    return false;
  }
  // store the old CIGAR and start in case we need to back out
  final Cigar oldCigar = read.getCigar();
  final int oldStart = read.getAlignmentStart();
  // try updating the read with the new CIGAR and start
  read.setCigar(newCigar);
  read.setAlignmentStart(newStart);
  // back out if necessary
  if ( realignmentProducesBadAlignment(read) ) {
    read.setCigar(oldCigar);
    read.setAlignmentStart(oldStart);
    return false;
  }
  // annotate the record with the original cigar and start (if it changed)
  if ( !NO_ORIGINAL_ALIGNMENT_TAGS ) {
    read.setAttribute(ORIGINAL_CIGAR_TAG, oldCigar.toString());
    if ( newStart != oldStart )
      read.setAttribute(ORIGINAL_POSITION_TAG, oldStart);
  }
  return true;
}

代码示例来源：origin: broadgsa/gatk

private GATKSAMRecord makeRead() {
    final SAMReadGroupRecord rg = header.getReadGroups().get(0);
    final String readName = String.format("%s.%d.%s", "read", readI, rg.getId());
    final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, readName, 0, 1, readLength);
    read.setReadGroup(new GATKSAMReadGroupRecord(rg));
    if ( payloadInBytes > 0 )
      // add a payload byte array to push memory use per read even higher
      read.setAttribute("PL", new byte[payloadInBytes]);
    return read;
  }
}

代码示例来源：origin: broadgsa/gatk

read.setAttribute(SAMTag.NM.name(), SequenceUtil.calculateSamNmTag(read, reference, leftmostIndex - 1));
  if ( read.getAttribute(SAMTag.UQ.name()) != null )
    read.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(read, reference, leftmostIndex-1));
} catch (Exception e) {
  read.setAttribute(SAMTag.MD.name(), null);

代码示例来源：origin: broadgsa/gatk

@Test()
public void testPLFromReadWithRGButNoPL() {
  final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
  final String rgID = "ID";
  final SAMReadGroupRecord rg = new SAMReadGroupRecord(rgID);
  header.addReadGroup(rg);
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10);
  read.setAttribute("RG", rgID);
  Assert.assertEquals(NGSPlatform.fromRead(read), NGSPlatform.UNKNOWN);
}

代码示例来源：origin: broadgsa/gatk

read1.setAttribute("RG",readGroupOne.getId());
GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
read2.setAttribute("RG",readGroupTwo.getId());
GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
read3.setAttribute("RG",readGroupOne.getId());
GATKSAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10);
read4.setAttribute("RG",readGroupTwo.getId());
GATKSAMRecord read5 = ArtificialSAMUtils.createArtificialRead(header,"read5",0,1,10);
read5.setAttribute("RG",readGroupTwo.getId());
GATKSAMRecord read6 = ArtificialSAMUtils.createArtificialRead(header,"read6",0,1,10);
read6.setAttribute("RG",readGroupOne.getId());
GATKSAMRecord read7 = ArtificialSAMUtils.createArtificialRead(header,"read7",0,1,10);
read7.setAttribute("RG",readGroupOne.getId());

代码示例来源：origin: broadgsa/gatk

/**
 * A unit test that creates an artificial read for testing some code that uses reads
 */
@Test(dataProvider = "TestMappings")
public void testPLFromReadWithRG(final String plField, final NGSPlatform expected) {
  final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
  final String rgID = "ID";
  final SAMReadGroupRecord rg = new SAMReadGroupRecord(rgID);
  if ( plField != null )
    rg.setPlatform(plField);
  header.addReadGroup(rg);
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10);
  read.setAttribute("RG", rgID);
  Assert.assertEquals(NGSPlatform.fromRead(read), expected);
}

代码示例来源：origin: broadgsa/gatk

@Test
public void testGetPileupForSample() {
  String sample1 = "sample1";
  String sample2 = "sample2";
  SAMReadGroupRecord readGroupOne = new SAMReadGroupRecord("rg1");
  readGroupOne.setSample(sample1);
  SAMReadGroupRecord readGroupTwo = new SAMReadGroupRecord("rg2");
  readGroupTwo.setSample(sample2);
  SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
  header.addReadGroup(readGroupOne);
  header.addReadGroup(readGroupTwo);
  GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
  read1.setAttribute("RG",readGroupOne.getId());
  GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
  read2.setAttribute("RG",readGroupTwo.getId());
  Map<String,ReadBackedPileupImpl> sampleToPileupMap = new HashMap<String,ReadBackedPileupImpl>();
  sampleToPileupMap.put(sample1,new ReadBackedPileupImpl(null,Collections.singletonList(read1),0));
  sampleToPileupMap.put(sample2,new ReadBackedPileupImpl(null,Collections.singletonList(read2),0));
  ReadBackedPileup pileup = new ReadBackedPileupImpl(null,sampleToPileupMap);
  ReadBackedPileup sample2Pileup = pileup.getPileupForSample(sample2);
  Assert.assertEquals(sample2Pileup.getNumberOfElements(),1,"Sample 2 pileup has wrong number of elements");
  Assert.assertEquals(sample2Pileup.getReads().get(0),read2,"Sample 2 pileup has incorrect read");
  ReadBackedPileup missingSamplePileup = pileup.getPileupForSample("missing");
  Assert.assertNull(missingSamplePileup,"Pileup for sample 'missing' should be null but isn't");
  missingSamplePileup = pileup.getPileupForSample("not here");
  Assert.assertNull(missingSamplePileup,"Pileup for sample 'not here' should be null but isn't");
}

代码示例来源：origin: broadgsa/gatk

read1.setAttribute("RG",readGroupOne.getId());
GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
read2.setAttribute("RG",readGroupTwo.getId());
GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
read3.setAttribute("RG",readGroupOne.getId());
GATKSAMRecord read4 = ArtificialSAMUtils.createArtificialRead(header,"read4",0,1,10);
read4.setAttribute("RG",readGroupTwo.getId());

代码示例来源：origin: broadgsa/gatk

prevBase = readBases[i];
read.setAttribute(RecalUtils.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency);

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

read.setAttribute(HAPLOTYPE_TAG, haplotype.hashCode());

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

if (emitOriginalQuals && read.getAttribute(SAMTag.OQ.name()) == null) { // Save the old qualities if the tag isn't already taken in the read
  try {
    read.setAttribute(SAMTag.OQ.name(), SAMUtils.phredToFastq(read.getBaseQualities()));
  } catch (IllegalArgumentException e) {
    throw new UserException.MalformedBAM(read, "illegal base quality encountered; " + e.getMessage());