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

GATKSAMRecord.setCigar介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG, dataProvider = "NumHardClipped")
public void testNumHardClipped(final Cigar cigar, final int expected) {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, cigar == null ? 10 : cigar.getReadLength());
  read.setCigar(cigar);
  Assert.assertEquals(AlignmentUtils.getNumHardClippedBases(read), expected, "Cigar " + cigar + " failed num hard clips");
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG, dataProvider = "NumAlignedBasesCountingSoftClips")
public void testNumAlignedBasesCountingSoftClips(final Cigar cigar, final int expected) {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, cigar == null ? 10 : cigar.getReadLength());
  read.setCigar(cigar);
  Assert.assertEquals(AlignmentUtils.getNumAlignedBasesCountingSoftClips(read), expected, "Cigar " + cigar + " failed NumAlignedBasesCountingSoftClips");
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG, dataProvider = "NumAlignedBlocks")
public void testNumAlignedBlocks(final Cigar cigar, final int expected) {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, cigar == null ? 10 : cigar.getReadLength());
  read.setCigar(cigar);
  Assert.assertEquals(AlignmentUtils.getNumAlignmentBlocks(read), expected, "Cigar " + cigar + " failed NumAlignedBlocks");
}

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

@Override
public GATKSAMRecord apply(final GATKSAMRecord read) {
  if(read == null)
    throw new UserException.BadInput("try to transform a null GATKSAMRecord");
  final Cigar originalCigar = read.getCigar();
  if (originalCigar.isValid(read.getReadName(),-1) != null)
    throw new UserException.BadInput("try to transform a read with non-valid cigar string: readName: "+read.getReadName()+" Cigar String: "+originalCigar);
  read.setCigar(refactorNDNtoN(originalCigar));
  return read;
}

代码示例来源：origin: broadgsa/gatk

List<CigarElement> elements = new ArrayList<CigarElement>();
elements.add(new CigarElement(length, CigarOperator.characterToEnum('M')));
record.setCigar(new Cigar(elements));
record.setProperPairFlag(false);

代码示例来源：origin: broadgsa/gatk

hardClippedRead.setCigar(cigarShift.cigar);
if (start == 0)
  hardClippedRead.setAlignmentStart(read.getAlignmentStart() + calculateAlignmentStartShift(read.getCigar(), cigarShift.cigar));

代码示例来源：origin: broadgsa/gatk

public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
  // we can not deal with screwy records
  if ( read.getReadUnmappedFlag() || read.getCigar().numCigarElements() == 0 ) {
    emit(read);
    return 0;
  }
  // move existing indels (for 1 indel reads only) to leftmost position within identical sequence
  int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read);
  if ( numBlocks == 2 ) {
    Cigar newCigar = AlignmentUtils.leftAlignIndel(IndelRealigner.unclipCigar(read.getCigar()), ref.getBases(), read.getReadBases(), 0, 0, true);
    newCigar = IndelRealigner.reclipCigar(newCigar, read);
    read.setCigar(newCigar);
  }
  emit(read);
  return 1;
}

代码示例来源：origin: broadgsa/gatk

originalRead.getReadBases(), swPairwiseAlignment.getAlignmentStart2wrt1(), 0, true);
read.setCigar(readToRefCigar);

代码示例来源：origin: broadgsa/gatk

read.setCigar(newCigar);

代码示例来源：origin: broadgsa/gatk

final ArrayList<CigarElement> cList = new ArrayList<CigarElement>();
cList.add(c);
returnRead.setCigar( new Cigar( cList ));
returnRead.setMappingQuality( firstRead.getMappingQuality() );

代码示例来源：origin: broadgsa/gatk

protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) {
  SAMFileHeader header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test");
  header.setSequenceDictionary(dictionary);
  header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
  GATKSAMRecord record = new GATKSAMRecord(header);
  record.setReadName(readName);
  record.setReferenceIndex(dictionary.getSequenceIndex(contig));
  record.setAlignmentStart(alignmentStart);
  Cigar cigar = new Cigar();
  int len = alignmentEnd - alignmentStart + 1;
  cigar.add(new CigarElement(len, CigarOperator.M));
  record.setCigar(cigar);
  record.setReadString(new String(new char[len]).replace("\0", "A"));
  record.setBaseQualities(new byte[len]);
  record.setReadGroup(new GATKSAMReadGroupRecord(header.getReadGroup("test")));
  return record;
}

代码示例来源：origin: broadgsa/gatk

private GATKSAMRecord revertSoftClippedBases(GATKSAMRecord read) {
  GATKSAMRecord unclipped = (GATKSAMRecord) read.clone();
  Cigar unclippedCigar = new Cigar();
  int matchesCount = 0;
  for (CigarElement element : read.getCigar().getCigarElements()) {
    if (element.getOperator() == CigarOperator.SOFT_CLIP || element.getOperator() == CigarOperator.MATCH_OR_MISMATCH)
      matchesCount += element.getLength();
    else if (matchesCount > 0) {
      unclippedCigar.add(new CigarElement(matchesCount, CigarOperator.MATCH_OR_MISMATCH));
      matchesCount = 0;
      unclippedCigar.add(element);
    } else
      unclippedCigar.add(element);
  }
  if (matchesCount > 0)
    unclippedCigar.add(new CigarElement(matchesCount, CigarOperator.MATCH_OR_MISMATCH));
  unclipped.setCigar(unclippedCigar);
  final int newStart = read.getAlignmentStart() + calculateAlignmentStartShift(read.getCigar(), unclippedCigar);
  unclipped.setAlignmentStart(newStart);
  if ( newStart <= 0 ) {
    // if the start of the unclipped read occurs before the contig,
    // we must hard clip away the bases since we cannot represent reads with
    // negative or 0 alignment start values in the SAMRecord (e.g., 0 means unaligned)
    return hardClip(unclipped, 0, - newStart);
  } else {
    return unclipped;
  }
}

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

/**
 * Build a SAM record featuring the absolute minimum required dataset.
 *
 * @param contig         Contig to populate.
 * @param alignmentStart start of alignment
 * @param alignmentEnd   end of alignment
 *
 * @return New SAM Record
 */
protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) {
  SAMFileHeader header = new SAMFileHeader();
  header.setSequenceDictionary(sequenceSourceFile.getSequenceDictionary());
  GATKSAMRecord record = new GATKSAMRecord(header);
  record.setReadName(readName);
  record.setReferenceIndex(sequenceSourceFile.getSequenceDictionary().getSequenceIndex(contig));
  record.setAlignmentStart(alignmentStart);
  Cigar cigar = new Cigar();
  int len = alignmentEnd - alignmentStart + 1;
  cigar.add(new CigarElement(len, CigarOperator.M));
  record.setCigar(cigar);
  record.setReadBases(new byte[len]);
  record.setBaseQualities(new byte[len]);
  return 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;
}