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

GATKSAMRecord.getReadName介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

@Override
public String toString() {
  return String.format("%s ro=%d go=%d cec=%d %s", read.getReadName(), readOffset, genomeOffset, offsetIntoCurrentCigarElement, currentElement);
}

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

@Override
public boolean equals(Object o) {
  if (this == o) {
    return true;
  }
  if (!(o instanceof GATKSAMRecordHashWrapper)) {
    return false;
  }
  GATKSAMRecord other = ((GATKSAMRecordHashWrapper) o).samRec;
  return samRec.getReadName().equals(other.getReadName()) && samRec.getFlags() == other.getFlags();
}

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

@Override
public boolean equals(Object o) {
  if (o instanceof GATKSAMRecord) {
    return getReadName().equals(((GATKSAMRecord)o).getReadName());
  } else {
    return false;
  }
}

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

public static void logReadInfo(final String readName, final GATKSAMRecord rec, final String message) {
  if (readName != null && rec != null && readName.equals(rec.getReadName())) {
    logger.info("Found " + rec.toString() + " - " + message);
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * Debug method to dump contents of object into string for display
 */
public String toString() {
  final StringBuilder sb = new StringBuilder();
  sb.append("Alelles in map:");
  for (final Allele a:alleles) {
    sb.append(a.getDisplayString()+",");
  }
  sb.append("\n");
  for (final Map.Entry <GATKSAMRecord, Map<Allele, Double>> el : getLikelihoodReadMap().entrySet() ) {
    for (final Map.Entry<Allele,Double> eli : el.getValue().entrySet()) {
      sb.append("Read "+el.getKey().getReadName()+". Allele:"+eli.getKey().getDisplayString()+" has likelihood="+Double.toString(eli.getValue())+"\n");
    }
  }
  return sb.toString();
}

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

@Override
  public int compare(final ReadCost o1, final ReadCost o2) {
    final String s1 = o1.read.getReadName() + (o1.read.getReadPairedFlag() ? (o1.read.getFirstOfPairFlag() ? "/1" : "/2") : "");
    final String s2 = o2.read.getReadName() + (o2.read.getReadPairedFlag() ? (o2.read.getFirstOfPairFlag() ? "/1" : "/2") : "");
    return s1.compareTo(s2);
  }
};

代码示例来源：origin: broadgsa/gatk

public void addAlignment(GATKSAMRecord read) {
  output.println("@" + read.getReadName());
  if (read.getReadNegativeStrandFlag()) {
    output.println(ReadUtils.getBasesReverseComplement(read));
    output.println("+");
    output.println(ReadUtils.convertReadQualToString(invertQuals(read.getBaseQualities())));
  } else {
    output.println(ReadUtils.convertReadBasesToString(read));
    output.println("+");
    output.println(ReadUtils.convertReadQualToString(read));
  }
}

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

public int hashCode() {
    // Use a murmur hash of the flags to distribute the values more uniformly over the full range of int
    return samRec.getReadName().hashCode() +  (31 * murmurHasher.hashLong(samRec.getFlags()).asInt());
  }
}

代码示例来源：origin: broadgsa/gatk

@Override
  public int compare(PileupElement element1, PileupElement element2) {
    final int difference = element1.getRead().getAlignmentStart() - element2.getRead().getAlignmentStart();
    return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName());
  }
});

代码示例来源：origin: broadgsa/gatk

private static String createVerboseOutput(final ReadBackedPileup pileup) {
  final StringBuilder sb = new StringBuilder();
  boolean isFirst = true;
  sb.append(pileup.getNumberOfDeletions());
  sb.append(" ");
  for ( PileupElement p : pileup ) {
    if ( isFirst )
      isFirst = false;
    else
      sb.append(",");
    sb.append(p.getRead().getReadName());
    sb.append(verboseDelimiter);
    sb.append(p.getOffset());
    sb.append(verboseDelimiter);
    sb.append(p.getRead().getReadLength());
    sb.append(verboseDelimiter);
    sb.append(p.getRead().getMappingQuality());
  }
  return sb.toString();
}

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

@Override
public boolean equals(Object o) {
  if (o instanceof GATKSAMRecord) {
    return getReadName().equals(((GATKSAMRecord)o).getReadName());
  } else {
    return false;
  }
}

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

@Ensures("result != null")
public String toString() {
  return String.format("%s @ %d = %c Q%d", getRead().getReadName(), getOffset(), (char) getBase(), getQual());
}

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

public void putReadBase(PileupElement pue) {
  ReadBase rb = new ReadBase(pue.getRead().getReadName(), pue.getBase(), pue.getMappingQual(), pue.getQual());
  bases.add(rb);
}

代码示例来源：origin: broadgsa/gatk

/** tes that we get the read we put into the map function */
  @Test
  public void testReturnRead() {
    SAMFileHeader head = ArtificialSAMUtils.createArtificialSamHeader(3,1,1000);
    GATKSAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
    SAMRecord ret = walker.map(bases, rec, null);
    assertTrue(ret == rec);
    assertTrue(ret.getReadName().equals(rec.getReadName()));
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * The reads map function.
 *
 *
 * @param ref  the reference bases that correspond to our read, if a reference was provided
 * @param read the read itself, as a GATKSAMRecord
 * @return the ReadClipper object describing what should be done to clip this read
 */
public ReadClipperWithData map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
  if ( onlyDoRead == null || read.getReadName().equals(onlyDoRead) ) {
    if ( clippingRepresentation == ClippingRepresentation.HARDCLIP_BASES || clippingRepresentation == ClippingRepresentation.REVERT_SOFTCLIPPED_BASES )
      read = ReadClipper.revertSoftClippedBases(read);
    ReadClipperWithData clipper = new ReadClipperWithData(read, sequencesToClip);
    //
    // run all three clipping modules
    //
    clipBadQualityScores(clipper);
    clipCycles(clipper);
    clipSequences(clipper);
    return clipper;
  }
  return null;
}

代码示例来源：origin: broadgsa/gatk

public void setCigar(Cigar cigar, boolean fixClippedCigar) {
  if ( cigar == null ) {
    newCigar = null;
    return;
  }
  if ( fixClippedCigar && getReadBases().length < read.getReadLength() )
    cigar = reclipCigar(cigar);
  // no change?
  if ( read.getCigar().equals(cigar) ) {
    newCigar = null;
    return;
  }
  // no indel?
  String str = cigar.toString();
  if ( !str.contains("D") && !str.contains("I") ) {
    logger.debug("Modifying a read with no associated indel; although this is possible, it is highly unlikely.  Perhaps this region should be double-checked: " + read.getReadName() + " near " + read.getReferenceName() + ":" + read.getAlignmentStart());
    //    newCigar = null;
    //    return;
  }
  newCigar = cigar;
}

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

/**
 * Helper function that returns the phred-scaled base quality score we should use for calculating
 * likelihoods for a pileup element.  May return 0 to indicate that the observation is bad, and may
 * cap the quality score by the mapping quality of the read itself.
 *
 * @param p                            Pileup element
 * @param ignoreBadBases               Flag to ignore bad bases
 * @param capBaseQualsAtMappingQual    Whether to cap base Q at mapping quality
 * @param minBaseQual                  Min qual to use
 * @return                             New phred-scaled base quality
 */
private static byte qualToUse(PileupElement p, boolean ignoreBadBases, boolean capBaseQualsAtMappingQual, int minBaseQual) {
  if ( ignoreBadBases && !BaseUtils.isRegularBase( p.getBase() ) )
    return 0;
  byte qual = p.getQual();
  if ( qual > SAMUtils.MAX_PHRED_SCORE )
    throw new UserException.MalformedBAM(p.getRead(), String.format("the maximum allowed quality score is %d, but a quality of %d was observed in read %s.  Perhaps your BAM incorrectly encodes the quality scores in Sanger format; see http://en.wikipedia.org/wiki/FASTQ_format for more details", SAMUtils.MAX_PHRED_SCORE, qual, p.getRead().getReadName()));
  if ( capBaseQualsAtMappingQual )
    qual = (byte)Math.min((int)qual, p.getMappingQual());
  if ( (int)qual < minBaseQual )
    qual = (byte)0;
  return qual;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Ensure that splitting read groups still works when dealing with null read groups.
 */
@Test
public void testSplitByNullReadGroups() {
  SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1,1,1000);
  GATKSAMRecord read1 = ArtificialSAMUtils.createArtificialRead(header,"read1",0,1,10);
  GATKSAMRecord read2 = ArtificialSAMUtils.createArtificialRead(header,"read2",0,1,10);
  GATKSAMRecord read3 = ArtificialSAMUtils.createArtificialRead(header,"read3",0,1,10);
  ReadBackedPileup pileup = new ReadBackedPileupImpl(null,
                            Arrays.asList(read1,read2,read3),
                            Arrays.asList(1,1,1));
  ReadBackedPileup nullRgPileup = pileup.getPileupForReadGroup(null);
  List<GATKSAMRecord> nullRgReads = nullRgPileup.getReads();
  Assert.assertEquals(nullRgPileup.getNumberOfElements(), 3, "Wrong number of reads in null read group");
  Assert.assertEquals(nullRgReads.get(0), read1, "Read " + read1.getReadName() + " should be in null rg but isn't");
  Assert.assertEquals(nullRgReads.get(1), read2, "Read " + read2.getReadName() + " should be in null rg but isn't");
  Assert.assertEquals(nullRgReads.get(2), read3, "Read " + read3.getReadName() + " should be in null rg but isn't");
  ReadBackedPileup rg1Pileup = pileup.getPileupForReadGroup("rg1");
  Assert.assertNull(rg1Pileup, "Pileup for non-existent read group should return null");
}

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

@Test(dataProvider = "ReadAlignedToRefData", enabled = true)
public void testReadAlignedToRef(final GATKSAMRecord read, final Haplotype haplotype, final int refStart, final int expectedReadStart, final String expectedReadCigar) throws Exception {
  final HaplotypeBAMWriter writer = new CalledHaplotypeBAMWriter(new MockDestination());
  final GATKSAMRecord originalReadCopy = (GATKSAMRecord)read.clone();
  if ( expectedReadCigar == null ) {
    Assert.assertNull(AlignmentUtils.createReadAlignedToRef(read, haplotype, haplotype, refStart, true));
  } else {
    final Cigar expectedCigar = TextCigarCodec.decode(expectedReadCigar);
    final GATKSAMRecord alignedRead = AlignmentUtils.createReadAlignedToRef(read, haplotype, haplotype, refStart, true);
    Assert.assertEquals(alignedRead.getReadName(), originalReadCopy.getReadName());
    Assert.assertEquals(alignedRead.getAlignmentStart(), expectedReadStart);
    Assert.assertEquals(alignedRead.getReadBases(), originalReadCopy.getReadBases());
    Assert.assertEquals(alignedRead.getBaseQualities(), originalReadCopy.getBaseQualities());
    Assert.assertEquals(alignedRead.getAlignmentStart(), expectedReadStart);
    Assert.assertEquals(alignedRead.getCigar(), expectedCigar);
    Assert.assertNotNull(alignedRead.getAttribute("HC"));
  }
  Assert.assertEquals(read, originalReadCopy, "createReadAlignedToRef seems be modifying the original read!");
}