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

GATKSAMRecord.setReadGroup介绍

暂无

代码示例

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

public static final GATKSAMRecord addReadGroup(GATKSAMRecord rec, String readGroupName) {
  GATKSAMReadGroupRecord rgRec = new GATKSAMReadGroupRecord(readGroupName);
  rgRec.setSample("sample");
  rec.setReadGroup(rgRec);
  return rec;
}

代码示例来源：origin: broadgsa/gatk

final String readName = String.format("%s.%d.%d.%s", baseName, locus, readI, rg.getId());
final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, readName, 0, alignmentStart + locus, readLength);
read.setReadGroup(rg);
reads.add(read);

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

public GATKSAMRecord makeRead(final int start, final int length) {
    final byte[] quals = Utils.dupBytes((byte)30, length);
    final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read " + readCounter++, 0, start + getStart(), ref.substring(start, start + length).getBytes(), quals, length + "M");
    read.setReadGroup(rg);
    return read;
  }
}

代码示例来源：origin: broadgsa/gatk

private GATKSAMRecord makeRead() {
    final SAMReadGroupRecord rg = header.getReadGroups().get(0);
    final String readName = String.format("%s.%d.%s", "read", readI, rg.getId());
    final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, readName, 0, 1, readLength);
    read.setReadGroup(new GATKSAMReadGroupRecord(rg));
    if ( payloadInBytes > 0 )
      // add a payload byte array to push memory use per read even higher
      read.setAttribute("PL", new byte[payloadInBytes]);
    return read;
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * Create an artificial read based on the parameters.  The cigar string will be *M, where * is the length of the read
 *
 * @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
 * @return the artificial read
 */
public static GATKSAMRecord createArtificialRead(SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual) {
  if (bases.length != qual.length) {
    throw new ReviewedGATKException("Passed in read string is different length then the quality array");
  }
  GATKSAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length);
  rec.setReadBases(bases);
  rec.setBaseQualities(qual);
  rec.setReadGroup(new GATKSAMReadGroupRecord("x"));
  if (refIndex == -1) {
    rec.setReadUnmappedFlag(true);
  }
  return rec;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Clears all attributes except ReadGroup of the read.
 */
public GATKSAMRecord simplify () {
  GATKSAMReadGroupRecord rg = getReadGroup(); // save the read group information
  byte[] insQuals = (this.getAttribute(BQSR_BASE_INSERTION_QUALITIES) == null) ? null : getBaseInsertionQualities();
  byte[] delQuals = (this.getAttribute(BQSR_BASE_DELETION_QUALITIES)  == null) ? null : getBaseDeletionQualities();
  this.clearAttributes(); // clear all attributes from the read
  this.setReadGroup(rg); // restore read group
  if (insQuals != null)
    this.setBaseQualities(insQuals, EventType.BASE_INSERTION); // restore base insertion if we had any
  if (delQuals != null)
    this.setBaseQualities(delQuals, EventType.BASE_DELETION); // restore base deletion if we had any
  return this;
}

代码示例来源：origin: broadgsa/gatk

private GATKSAMRecord makeOverlappingRead(final String leftFlank, final int leftQual, final String overlapBases,
                     final byte[] overlapQuals, final String rightFlank, final int rightQual,
                     final int alignmentStart) {
  final String bases = leftFlank + overlapBases + rightFlank;
  final int readLength = bases.length();
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, alignmentStart, readLength);
  final byte[] leftQuals = Utils.dupBytes((byte) leftQual, leftFlank.length());
  final byte[] rightQuals = Utils.dupBytes((byte) rightQual, rightFlank.length());
  final byte[] quals = Utils.concat(leftQuals, overlapQuals, rightQuals);
  read.setCigarString(readLength + "M");
  read.setReadBases(bases.getBytes());
  for ( final EventType type : EventType.values() )
    read.setBaseQualities(quals, type);
  read.setReadGroup(rgForMerged);
  read.setMappingQuality(60);
  return read;
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true)
  public void testMaxCyclePasses() {
    int readLength = RAC.MAXIMUM_CYCLE_VALUE;
    GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
    read.setReadPairedFlag(true);
    read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
    read.getReadGroup().setPlatform("illumina");

    ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
    covariate.recordValues(read, readCovariates);
  }
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true, expectedExceptions={UserException.class})
public void testMoreThanMaxCycleFails() {
  int readLength = RAC.MAXIMUM_CYCLE_VALUE + 1;
  GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
  read.setReadPairedFlag(true);
  read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
  read.getReadGroup().setPlatform("illumina");
  ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
  covariate.recordValues(read, readCovariates);
}

代码示例来源：origin: broadgsa/gatk

private static void runTest(final GATKSAMReadGroupRecord rg, final String expected, final ReadGroupCovariate covariate) {
  GATKSAMRecord read = ReadUtils.createRandomRead(10);
  read.setReadGroup(rg);
  ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
  covariate.recordValues(read, readCovariates);
  verifyCovariateArray(readCovariates.getMismatchesKeySet(), expected, covariate);
}

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

allI.setReadGroup(new GATKSAMReadGroupRecord(bamBuilder.getHeader().getReadGroups().get(0)));

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

read.setReferenceName(loc.getContig());
read.setReadNegativeStrandFlag(false);
read.setReadGroup(sampleRG(sample));

代码示例来源：origin: broadgsa/gatk

final GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(rgs);
rg.setPlatform("illumina");
read.setReadGroup(rg);
read.setReadNegativeStrandFlag(rnd.nextBoolean());
final byte[] mQuals = read.getBaseQualities(EventType.BASE_SUBSTITUTION);

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

correctedRead.setReadBases(inputRead.getReadBases());
correctedRead.setReadString(inputRead.getReadString());
correctedRead.setReadGroup(inputRead.getReadGroup());
return correctedRead;

代码示例来源：origin: broadgsa/gatk

if (samRG != null) {
  GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
  emptyRead.setReadGroup(rg);

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true)
public void testSimpleCycles() {
  short readLength = 10;
  GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
  read.setReadPairedFlag(true);
  read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
  read.getReadGroup().setPlatform("illumina");
  ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
  covariate.recordValues(read, readCovariates);
  verifyCovariateArray(readCovariates.getMismatchesKeySet(), 1, (short) 1);
  read.setReadNegativeStrandFlag(true);
  covariate.recordValues(read, readCovariates);
  verifyCovariateArray(readCovariates.getMismatchesKeySet(), readLength, -1);
  read.setSecondOfPairFlag(true);
  covariate.recordValues(read, readCovariates);
  verifyCovariateArray(readCovariates.getMismatchesKeySet(), -readLength, 1);
  read.setReadNegativeStrandFlag(false);
  covariate.recordValues(read, readCovariates);
  verifyCovariateArray(readCovariates.getMismatchesKeySet(), -1, -1);
}

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;
}

代码示例来源：origin: broadgsa/gatk

setReadGroup(rg);