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

GATKSAMRecord.setReadName介绍

暂无

代码示例

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

@Test(dataProvider = "MostLikelyAlleleData")
  public void testMostLikelyAllele(final List<Allele> alleles, final List<List<Double>> perReadlikelihoods, final Allele best, final Allele second) {
    final PerReadAlleleLikelihoodMap map = new PerReadAlleleLikelihoodMap();

    for ( int readI = 0; readI < perReadlikelihoods.size(); readI++ ) {
      final List<Double> likelihoods = perReadlikelihoods.get(readI);

      final byte[] bases = Utils.dupBytes((byte)'A', 10);
      final byte[] quals = Utils.dupBytes((byte) 30, 10);
      final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, "10M");
      read.setReadName("readName" + readI);

      for ( int i = 0; i < alleles.size(); i++ ) {
        final Allele allele = alleles.get(i);
        final double likelihood = likelihoods.get(i);
        map.add(read, allele, likelihood);
      }
    }

    final MostLikelyAllele mla = map.getMostLikelyDiploidAlleles();
    Assert.assertEquals(mla.getMostLikelyAllele(), best);
    Assert.assertEquals(mla.getSecondMostLikelyAllele(), second);
  }
}

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

@Test(dataProvider = "RemovingPoorlyModelledReadData")
public void testRemovingPoorlyModelledReads(final int readLen, final int nReads, final int nBad, final int nGood) {
  final PerReadAlleleLikelihoodMap map = new PerReadAlleleLikelihoodMap();
  final Set<GATKSAMRecord> goodReads = new HashSet<GATKSAMRecord>();
  final Set<GATKSAMRecord> badReads = new HashSet<GATKSAMRecord>();
  for ( int readI = 0; readI < nReads; readI++ ) {
    final boolean bad = readI < nBad;
    final double likelihood = bad ? -100.0 : 0.0;
    final byte[] bases = Utils.dupBytes((byte)'A', readLen);
    final byte[] quals = Utils.dupBytes((byte) 40, readLen);
    final Allele allele = Allele.create(Utils.dupString("A", readI+1));
    final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, readLen + "M");
    read.setReadName("readName" + readI);
    map.add(read, allele, likelihood);
    (bad ? badReads : goodReads).add(read);
  }
  final List<GATKSAMRecord> removedReads = map.filterPoorlyModelledReads(0.01);
  Assert.assertEquals(removedReads.size(), nBad, "nBad " + nBad + " nGood " + nGood);
  Assert.assertEquals(new HashSet<GATKSAMRecord>(removedReads), badReads, "nBad " + nBad + " nGood " + nGood);
  Assert.assertEquals(map.size(), nGood, "nBad " + nBad + " nGood " + nGood);
  Assert.assertTrue(map.getStoredElements().containsAll(goodReads), "nBad " + nBad + " nGood " + nGood);
  Assert.assertEquals(map.getStoredElements().size(), nGood, "nBad " + nBad + " nGood " + nGood);
}

代码示例来源：origin: broadgsa/gatk

throw new ReviewedGATKException("Invalid alignment start for artificial read, start = " + alignmentStart);
GATKSAMRecord record = new GATKSAMRecord(header);
record.setReadName(name);
record.setReferenceIndex(refIndex);
record.setAlignmentStart(alignmentStart);

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

read2.setReadName(read.getReadName() + ".clone");

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-protected

/**
 * Creates a hard-clipped view on a existing read record.
 * @param read the underlying unclipped read.
 * @param start inclusive first position in {@code read} included in the clipped view.
 * @param end inclusive last position in {@code read} included in the clipped view.
 */
public ClippedGATKSAMRecord(final GATKSAMRecord read, int start, int end) {
  super(read.getHeader());
  this.setReferenceIndex(read.getReferenceIndex());
  this.setAlignmentStart(read.getAlignmentStart() + start);
  this.setMappingQuality(100);
  // setting read indexing bin below
  this.setFlags(read.getFlags());
  this.setMateReferenceIndex(read.getMateReferenceIndex());
  this.setMateAlignmentStart(read.getMateAlignmentStart());
  this.setInferredInsertSize(read.getInferredInsertSize());
  this.setReadBases(Arrays.copyOfRange(read.getReadBases(), start, end));
  this.setBaseQualities(Arrays.copyOfRange(read.getBaseQualities(),start,end));
  this.setReadName(read.getReadName());
  insertionQuals = Arrays.copyOfRange(read.getBaseInsertionQualities(),start,end);
  deletionQuals = Arrays.copyOfRange(read.getBaseDeletionQualities(),start,end);
  // Set these to null in order to mark them as being candidates for lazy initialization.
  // If this is not done, they will have non-null defaults.
  super.setReadName(null);
  super.setCigarString(null);
  super.setReadBases(null);
  super.setBaseQualities(null);
  // Do this after the above because setCigarString will clear it.
  GATKBin.setReadIndexingBin(this, -1);
}

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);

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-protected

read.setBaseQualities(readQuals);
read.setReadBases(readBases);
read.setReadName(artificialReadName+readCounter++);

代码示例来源：origin: broadgsa/gatk

returnRead.setReadGroup( firstRead.getReadGroup() );
returnRead.setReferenceName( firstRead.getReferenceName() );
returnRead.setReadName( firstRead.getReadName() );
final CigarElement c = new CigarElement(bases.length, CigarOperator.M);
final ArrayList<CigarElement> cList = new ArrayList<CigarElement>();

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-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;
}