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

GATKSAMRecord.setAlignmentStart介绍

暂无

代码示例

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

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, dataProvider = "RevertSoftClipsBeforeContig")
public void testRevertSoftClippedBasesBeforeStartOfContig(final int softStart, final int alignmentStart) {
  final int nMatches = 10;
  final int nSoft = -1 * (softStart - alignmentStart);
  final String cigar = nSoft + "S" + nMatches + "M";
  final GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
  read.setAlignmentStart(alignmentStart);
  Assert.assertEquals(read.getSoftStart(), softStart);
  Assert.assertEquals(read.getAlignmentStart(), alignmentStart);
  Assert.assertEquals(read.getCigarString(), cigar);
  final GATKSAMRecord reverted = ReadClipper.revertSoftClippedBases(read);
  final int expectedAlignmentStart = 1;
  final String expectedCigar = (1 - softStart) + "H" + read.getAlignmentEnd() + "M";
  Assert.assertEquals(reverted.getSoftStart(), expectedAlignmentStart);
  Assert.assertEquals(reverted.getAlignmentStart(), expectedAlignmentStart);
  Assert.assertEquals(reverted.getCigarString(), expectedCigar);
}

代码示例来源：origin: broadgsa/gatk

@Test
public void testSecondaryAlignmentsDoNotCauseAccidentalRemovalOfMate() {
  final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 530, 1594, true, false);
  final GATKSAMRecord read1 = properReads.get(0);
  read1.setFlags(99);   // first in proper pair, mate negative strand
  final GATKSAMRecord read2Primary = properReads.get(1);
  read2Primary.setFlags(147);   // second in pair, mate unmapped, not primary alignment
  read2Primary.setAlignmentStart(1596); // move the read
  final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary);
  read2NonPrimary.setReadName("foo");
  read2NonPrimary.setFlags(393);   // second in proper pair, on reverse strand
  read2NonPrimary.setAlignmentStart(451);
  read2NonPrimary.setMateAlignmentStart(451);
  final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 10000, 200, 10000);
  manager.addRead(read2NonPrimary, false, false);
  manager.addRead(read1, false, false);
  for ( int i = 0; i < ConstrainedMateFixingManager.EMIT_FREQUENCY; i++ )
    manager.addRead(ArtificialSAMUtils.createArtificialRead(header, "foo" + i, 0, 1500, 10), false, false);
  Assert.assertTrue(manager.forMateMatching.containsKey("foo"));
}

代码示例来源：origin: broadgsa/gatk

record.setReadName(name);
record.setReferenceIndex(refIndex);
record.setAlignmentStart(alignmentStart);
List<CigarElement> elements = new ArrayList<CigarElement>();
elements.add(new CigarElement(length, CigarOperator.characterToEnum('M')));

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

@Test
public void testSecondaryAlignmentsDoNotInterfere() {
  final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 10, 30, true, false);
  final GATKSAMRecord read1 = properReads.get(0);
  read1.setAlignmentStart(8); // move the read
  read1.setFlags(99);   // first in proper pair, mate negative strand
  final GATKSAMRecord read2Primary = properReads.get(1);
  read2Primary.setFlags(147);   // second in pair, mate unmapped, not primary alignment
  Assert.assertEquals(read1.getInferredInsertSize(), 21);
  final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary);
  read2NonPrimary.setFlags(393);   // second in proper pair, on reverse strand
  final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 1000, 1000, 1000);
  manager.addRead(read1, true, false);
  manager.addRead(read2NonPrimary, false, false);
  manager.addRead(read2Primary, false, false);
  Assert.assertEquals(manager.getNReadsInQueue(), 3);
  for ( final SAMRecord read : manager.getReadsInQueueForTesting() ) {
    if ( read.getFirstOfPairFlag() ) {
      Assert.assertEquals(read.getFlags(), 99);
      Assert.assertEquals(read.getInferredInsertSize(), 23);
    } else if ( read.getNotPrimaryAlignmentFlag() ) {
      Assert.assertEquals(read.getFlags(), 393);
      Assert.assertEquals(read.getInferredInsertSize(), -21);
    } else {
      Assert.assertEquals(read.getFlags(), 147);
      Assert.assertEquals(read.getInferredInsertSize(), -23);
    }
  }
}

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

final int readStartOnHaplotype = calcFirstBaseMatchingReferenceInCigar(extendedHaplotypeCigar, swPairwiseAlignment.getAlignmentStart2wrt1());
final int readStartOnReference = referenceStart + haplotype.getAlignmentStartHapwrtRef() + readStartOnHaplotype;
read.setAlignmentStart(readStartOnReference);
read.resetSoftStartAndEnd();

代码示例来源：origin: broadgsa/gatk

read2Supp.setReadName("foo");
read2Supp.setFlags(2209);   // second in pair, mate negative strand, supplementary
read2Supp.setAlignmentStart(100);
read2Supp.setMateAlignmentStart(1000);

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;
}

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

read.setReadUnmappedFlag(false);
read.setMateUnmappedFlag(false);
read.setAlignmentStart(100);
read.setCigarString("50M");
read.setMateAlignmentStart(130);
  bad.setAlignmentStart(1000);
  tests.add( new Object[]{ "positve read starts after mate end", bad, false });

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

read.setAlignmentStart(readStart);
read.setMappingQuality(artificialMappingQuality);
read.setReferenceName(loc.getContig());

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

final GATKSAMRecord emptyRead = new GATKSAMRecord(read.getHeader());
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

/**
 * 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;
}