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

GATKSAMRecord.setCigarString介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

/**
 * Create an artificial read based on the parameters
 *
 * @param header         the SAM header to associate the read with
 * @param name           the name of the read
 * @param refIndex       the reference index, i.e. what chromosome to associate it with
 * @param alignmentStart where to start the alignment
 * @param bases          the sequence of the read
 * @param qual           the qualities of the read
 * @param cigar          the cigar string of the read
 * @return the artificial read
 */
public static GATKSAMRecord createArtificialRead(SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual, String cigar) {
  GATKSAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases, qual);
  rec.setCigarString(cigar);
  return rec;
}

代码示例来源：origin: broadgsa/gatk

private GATKSAMRecord createRead(final boolean useGoodBases) {
  GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 10, readBases.getBytes(),
                                 useGoodBases ? Arrays.copyOf(goodQuals, goodQuals.length) :
                                        Arrays.copyOf(badQuals, badQuals.length));
  read.setCigarString("10M");
  return read;
}

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

@Test(dataProvider = "ClipUpstreamProvider", enabled = true)
public void clipUpstreamTest(final int readStart, final int readLength, final int delLength) {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead", 0, readStart, readLength);
  if ( delLength == 0 )
    read.setCigarString(readLength + "M");
  else
    read.setCigarString((readLength / 2) + "M" + delLength + "D" + (readLength / 2) + "M");
  final boolean result = PairHMMIndelErrorModel.mustClipUpstream(read, refWindowStart);
  Assert.assertEquals(result, read.getSoftStart() < refWindowStart && read.getSoftEnd() > refWindowStart);
}

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

@Test(dataProvider = "ClipDownstreamProvider", enabled = true)
public void clipDownstreamTest(final int readStart, final int readLength, final int delLength) {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead", 0, readStart, readLength);
  if ( delLength == 0 )
    read.setCigarString(readLength + "M");
  else
    read.setCigarString((readLength / 2) + "M" + delLength + "D" + (readLength / 2) + "M");
  final boolean result = PairHMMIndelErrorModel.mustClipDownstream(read, refWindowEnd);
  Assert.assertEquals(result, read.getSoftStart() < refWindowEnd && read.getSoftStart() + readLength > refWindowEnd);
}

代码示例来源：origin: broadgsa/gatk

@Test
public void realignAtContigBorderTest() {
  final int contigEnd = header.getSequence(0).getSequenceLength();
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "goodRead", 0, contigEnd - 1, 2);
  read.setCigarString("2M");
  Assert.assertEquals(IndelRealigner.realignmentProducesBadAlignment(read, contigEnd), false);
  read.setCigarString("1M1D1M");
  Assert.assertEquals(IndelRealigner.realignmentProducesBadAlignment(read, contigEnd), true);
}

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

@Test
public void clipDownstreamAtBorderTest() {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead", 0, 5, 10);
  read.setCigarString("10M");
  Assert.assertEquals(PairHMMIndelErrorModel.mustClipDownstream(read, 13), true);
  Assert.assertEquals(PairHMMIndelErrorModel.mustClipDownstream(read, 14), false);
}

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 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 GATKSAMRecord createReadAndAddToBin(String cigarString, int alignmentStart) {
    final GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
    read.setCigarString(cigarString);
    read.setAlignmentStart(alignmentStart);
    readBin.add(read);
    return read;
  }
}

代码示例来源：origin: broadgsa/gatk

@Test (enabled = true)
public void testReadWithNsRefAfterDeletion() throws FileNotFoundException {
  final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
  final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
  final int readLength = 76;
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
  read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
  read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
  read.setCigarString("3M414N1D73M");
  final int result = ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, 9393, ReadUtils.ClippingTail.LEFT_TAIL);
  Assert.assertEquals(result, 3);
}

代码示例来源：origin: broadgsa/gatk

@Test (enabled = true)
public void testReadWithNsRefIndexInDeletion() throws FileNotFoundException {
  final ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(b37KGReference));
  final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary());
  final int readLength = 76;
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 8975, readLength);
  read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
  read.setBaseQualities(Utils.dupBytes((byte)30, readLength));
  read.setCigarString("3M414N1D73M");
  final int result = ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, 9392, ReadUtils.ClippingTail.LEFT_TAIL);
  Assert.assertEquals(result, 2);
}

代码示例来源：origin: broadgsa/gatk

@Test( )
public void testCreationFromSAMRecordUnmappedButOnGenome() {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5);
  read.setReadUnmappedFlag(true);
  read.setCigarString("*");
  final GenomeLoc loc = genomeLocParser.createGenomeLoc(read);
  Assert.assertEquals(loc.getContig(), read.getReferenceName());
  Assert.assertEquals(loc.getContigIndex(), (int)read.getReferenceIndex());
  Assert.assertEquals(loc.getStart(), read.getAlignmentStart());
  Assert.assertEquals(loc.getStop(), read.getAlignmentStart());
}

代码示例来源：origin: broadgsa/gatk

public GATKSAMRecord makeRead() {
    GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, locus, readLength);
    read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
    final byte[] quals = new byte[readLength];
    for ( int i = 0; i < readLength; i++ )
      quals[i] = (byte)(i % QualityUtils.MAX_SAM_QUAL_SCORE);
    read.setBaseQualities(quals);
    read.setCigarString(cigarString);
    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

@Test(enabled = false && ! DEBUG)
public void testWholeIndelReadInIsolation() {
  final int firstLocus = 44367789;
  GATKSAMRecord indelOnlyRead = ArtificialSAMUtils.createArtificialRead(header, "indelOnly", 0, firstLocus, 76);
  indelOnlyRead.setReadBases(Utils.dupBytes((byte)'A',76));
  indelOnlyRead.setBaseQualities(Utils.dupBytes((byte) '@', 76));
  indelOnlyRead.setCigarString("76I");
  List<GATKSAMRecord> reads = Arrays.asList(indelOnlyRead);
  // create the iterator by state with the fake reads and fake records
  li = makeLTBS(reads);
  // Traditionally, reads that end with indels bleed into the pileup at the following locus.  Verify that the next pileup contains this read
  // and considers it to be an indel-containing read.
  Assert.assertTrue(li.hasNext(),"Should have found a whole-indel read in the normal base pileup without extended events enabled");
  AlignmentContext alignmentContext = li.next();
  Assert.assertEquals(alignmentContext.getLocation().getStart(), firstLocus, "Base pileup is at incorrect location.");
  ReadBackedPileup basePileup = alignmentContext.getBasePileup();
  Assert.assertEquals(basePileup.getReads().size(),1,"Pileup is of incorrect size");
  Assert.assertSame(basePileup.getReads().get(0), indelOnlyRead, "Read in pileup is incorrect");
}

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

@Test
  public void testUnmappedReadsDoNotFail() {
    // create an unmapped read
    final GATKSAMRecord read = new GATKSAMRecord(ArtificialSAMUtils.createArtificialSamHeader());
    read.setReadName("foo");
    read.setReferenceName("*");
    read.setAlignmentStart(100);
    read.setCigarString("*");
    read.setReadUnmappedFlag(true);

    // try to add it to the manager
    final OverhangFixingManager manager = new OverhangFixingManager(null, null, null, 100, 1, 30, false);
    manager.addRead(read); // we just want to make sure that the following call does not fail
    Assert.assertTrue(true);
  }
}

代码示例来源：origin: broadgsa/gatk

@Override protected void setUp() {
  header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 1000);
  genomeLocParser = new GenomeLocParser(header.getSequenceDictionary());
  for ( int j = 0; j < nReads; j++ ) {
    GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read", 0, locus, readLength);
    read.setReadBases(Utils.dupBytes((byte) 'A', readLength));
    final byte[] quals = new byte[readLength];
    for ( int i = 0; i < readLength; i++ )
      quals[i] = (byte)(i % QualityUtils.MAX_SAM_QUAL_SCORE);
    read.setBaseQualities(quals);
    read.setCigarString(cigar);
    reads.add(read);
  }
}

代码示例来源：origin: broadgsa/gatk

protected GATKSAMRecord buildSAMRecord(final String readName, final String contig, final int alignmentStart) {
  GATKSAMRecord record = new GATKSAMRecord(header);
  record.setReadName(readName);
  record.setReferenceIndex(dictionary.getSequenceIndex(contig));
  record.setAlignmentStart(alignmentStart);
  record.setCigarString("1M");
  record.setReadString("A");
  record.setBaseQualityString("A");
  record.setReadGroup(readGroup);
  return record;
}