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

GATKSAMRecord.getCigar介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

public Cigar getCigar() {
  return (newCigar != null ? newCigar : read.getCigar());
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG)
public void testRevertSoftClippedBasesWithThreshold() {
  for (Cigar cigar : cigarList) {
    final int leadingSoftClips = leadingCigarElementLength(cigar, CigarOperator.SOFT_CLIP);
    final int tailSoftClips = leadingCigarElementLength(CigarUtils.invertCigar(cigar), CigarOperator.SOFT_CLIP);
    final GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
    final GATKSAMRecord unclipped = ReadClipper.revertSoftClippedBases(read);
    assertUnclippedLimits(read, unclipped);                                                                     // Make sure limits haven't changed
    Assert.assertNull(read.getCigar().isValid(null, -1));
    Assert.assertNull(unclipped.getCigar().isValid(null, -1));
    if (!(leadingSoftClips > 0 || tailSoftClips > 0))
      Assert.assertEquals(read.getCigarString(), unclipped.getCigarString());
  }
}

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

@Override
protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) {
  final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true );
  if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED )
    return null;
  // If the offset inside a deletion, it does not lie on a read.
  if ( AlignmentUtils.isInsideDeletion(read.getCigar(), offset) ) {
    return INVALID_ELEMENT_FROM_READ;
  }
  int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, 0, 0 );
  final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read );
  if (readPos > numAlignedBases / 2)
    readPos = numAlignedBases - (readPos + 1);
  return (double)readPos;
}

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

@Test(dataProvider = "ComplexReadAlignedToRef", enabled = !DEBUG)
  public void testReadAlignedToRefComplexAlignment(final int testIndex, final GATKSAMRecord read, final String reference, final Haplotype haplotype, final int expectedMaxMismatches) throws Exception {
    final HaplotypeBAMWriter writer = new CalledHaplotypeBAMWriter(new MockDestination());
    final GATKSAMRecord alignedRead = AlignmentUtils.createReadAlignedToRef(read, haplotype, new Haplotype(reference.getBytes(),true), 1, true);
    if ( alignedRead != null ) {
      final int mismatches = AlignmentUtils.getMismatchCount(alignedRead, reference.getBytes(), alignedRead.getAlignmentStart() - 1).numMismatches;
      Assert.assertTrue(mismatches <= expectedMaxMismatches,
          "Alignment of read to ref looks broken.  Expected at most " + expectedMaxMismatches + " but saw " + mismatches
              + " for readBases " + new String(read.getReadBases()) + " with cigar " + read.getCigar() + " reference " + reference + " haplotype "
              + haplotype + " with cigar " + haplotype.getCigar() + " aligned read cigar " + alignedRead.getCigarString() + " @ " + alignedRead.getAlignmentStart());
    }
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * Is this read all insertion?
 *
 * @param read
 * @return whether or not the only element in the cigar string is an Insertion
 */
public static boolean readIsEntirelyInsertion(GATKSAMRecord read) {
  for (CigarElement cigarElement : read.getCigar().getCigarElements()) {
    if (cigarElement.getOperator() != CigarOperator.INSERTION)
      return false;
  }
  return true;
}

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

@Override
protected boolean isUsableBase(final PileupElement p) {
  return super.isUsableBase(p) && p.getRead().getCigar() != null;
}

代码示例来源：origin: broadgsa/gatk

public static int getReadCoordinateForReferenceCoordinateUpToEndOfRead(GATKSAMRecord read, int refCoord, ClippingTail tail) {
  final int leftmostSafeVariantPosition = Math.max(read.getSoftStart(), refCoord);
  return getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), leftmostSafeVariantPosition, tail, false);
}

代码示例来源：origin: broadgsa/gatk

@Requires({"read != null", "read.getAlignmentStart() != -1", "read.getCigar() != null"})
public AlignmentStateMachine(final GATKSAMRecord read) {
  this.read = read;
  this.cigar = read.getCigar();
  this.nCigarElements = cigar.numCigarElements();
  initializeAsLeftEdge();
}

代码示例来源：origin: broadgsa/gatk

/**
 * Checks whether or not the read has any cigar element that is not H or S
 *
 * @param read the read
 * @return true if it has any M, I or D, false otherwise
 */
public static boolean readHasNonClippedBases(GATKSAMRecord read) {
  for (CigarElement cigarElement : read.getCigar().getCigarElements())
    if (cigarElement.getOperator() != CigarOperator.SOFT_CLIP && cigarElement.getOperator() != CigarOperator.HARD_CLIP)
      return true;
  return false;
}

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

@Override
  protected boolean isUsableRead(final GATKSAMRecord read, final int refLoc) {
    return super.isUsableRead(read, refLoc) && read.getSoftStart() + read.getCigar().getReadLength() > refLoc;
  }
}

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

@Override
protected Double getElementForPileupElement(final PileupElement p) {
  final int offset = AlignmentUtils.calcAlignmentByteArrayOffset(p.getRead().getCigar(), p, 0, 0);
  return (double)AnnotationUtils.getFinalVariantReadPosition(p.getRead(), offset);
}

代码示例来源：origin: broadgsa/gatk

@Test(dataProvider = "ClippedReadLengthData", enabled = !DEBUG)
public void testHardClipReadLengthIsRight(final int originalReadLength, final int nToClip) {
  GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(originalReadLength + "M", 0);
  read.getReadLength(); // provoke the caching of the read length
  final int expectedReadLength = originalReadLength - nToClip;
  GATKSAMRecord clipped = ReadClipper.hardClipByReadCoordinates(read, 0, nToClip - 1);
  Assert.assertEquals(clipped.getReadLength(), expectedReadLength,
      String.format("Clipped read length %d with cigar %s not equal to the expected read length %d after clipping %d bases from the left from a %d bp read with cigar %s",
          clipped.getReadLength(), clipped.getCigar(), expectedReadLength, nToClip, read.getReadLength(), read.getCigar()));
}

代码示例来源：origin: broadgsa/gatk

public CigarCounter(GATKSAMRecord read) {
  CigarOperator[] operators = CigarOperator.values();
  counter = new HashMap<CigarOperator, Integer>(operators.length);
  for (CigarOperator op : operators)
    counter.put(op, 0);
  for (CigarElement cigarElement : read.getCigar().getCigarElements())
    counter.put(cigarElement.getOperator(), counter.get(cigarElement.getOperator()) + cigarElement.getLength());
}

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

@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

private Cigar makeExpectedCigar1(final Cigar originalCigar, final char indelOp, final int indelStart, final int indelSize, final int readLength) {
  if ( indelSize == 0 || indelStart < 17 || indelStart > (26 - (indelOp == 'D' ? indelSize : 0)) )
    return originalCigar;
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, readLength);
  read.setCigarString(buildTestCigarString(indelOp, 0, 16, indelSize, readLength));
  return read.getCigar();
}

代码示例来源：origin: broadgsa/gatk

public Pair<Long, Long> map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
  List<CigarElement> cigarElements = read.getCigar().getCigarElements();
  CigarElement lastElement = null;
  for (CigarElement element : cigarElements) {
    if (element.getOperator() != CigarOperator.HARD_CLIP)
      lastElement = element;
  }
  if (lastElement == null)
    throw new UserException.MalformedBAM(read, "read does not have any bases, it's all hard clips");
  long endsInIndel = lastElement.getOperator() == CigarOperator.INSERTION || lastElement.getOperator() == CigarOperator.DELETION? 1 : 0;
  long endsInSC = lastElement.getOperator() == CigarOperator.SOFT_CLIP ? 1 : 0;
  return new Pair<Long, Long>(endsInIndel, endsInSC);
}

代码示例来源：origin: broadgsa/gatk

private Cigar makeExpectedCigar2(final Cigar originalCigar, final char indelOp, final int indelStart, final int indelSize, final int readLength) {
  if ( indelStart < 17 || indelStart > (26 - (indelOp == 'D' ? indelSize : 0)) )
    return originalCigar;
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, readLength);
  if ( indelOp == 'I' && (indelSize == 1 || indelSize == 3) && indelStart % 2 == 1 )
    read.setCigarString(buildTestCigarString(indelOp, 0, Math.max(indelStart - indelSize, 16), indelSize, readLength));
  else if ( (indelSize == 2 || indelSize == 4) && (indelOp == 'D' || indelStart % 2 == 0) )
    read.setCigarString(buildTestCigarString(indelOp, 0, 16, indelSize, readLength));
  else
    return originalCigar;
  return read.getCigar();
}

代码示例来源：origin: broadgsa/gatk

private Cigar makeExpectedCigar3(final Cigar originalCigar, final char indelOp, final int indelStart, final int indelSize, final int readLength) {
  if ( indelStart < 17 || indelStart > (28 - (indelOp == 'D' ? indelSize : 0)) )
    return originalCigar;
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, readLength);
  if ( indelSize == 3 && (indelOp == 'D' || indelStart % 3 == 1) )
    read.setCigarString(buildTestCigarString(indelOp, 0, 16, indelSize, readLength));
  else if ( (indelOp == 'I' && indelSize == 4 && indelStart % 3 == 2) ||
      (indelOp == 'I' && indelSize == 2 && indelStart % 3 == 0) ||
      (indelOp == 'I' && indelSize == 1 && indelStart < 28 && indelStart % 3 == 2) )
    read.setCigarString(buildTestCigarString(indelOp, 0, Math.max(indelStart - indelSize, 16), indelSize, readLength));
  else
    return originalCigar;
  return read.getCigar();
}

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;
}