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

GATKSAMRecord.setReadPairedFlag介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

private GATKSAMRecord makeRead(final int fragmentSize, final int mateStart) {
  final byte[] bases = {'A', 'C', 'G', 'T', 'A', 'C', 'G', 'T'};
  final byte[] quals = {30, 30, 30, 30, 30, 30, 30, 30};
  final String cigar = "8M";
  GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, cigar);
  read.setProperPairFlag(true);
  read.setReadPairedFlag(true);
  read.setMateAlignmentStart(mateStart);
  read.setInferredInsertSize(fragmentSize);
  return read;
}

代码示例来源：origin: broadgsa/gatk

public final static List<GATKSAMRecord> createPair(SAMFileHeader header, String name, int readLen, int leftStart, int rightStart, boolean leftIsFirst, boolean leftIsNegative) {
  GATKSAMRecord left = ArtificialSAMUtils.createArtificialRead(header, name, 0, leftStart, readLen);
  GATKSAMRecord right = ArtificialSAMUtils.createArtificialRead(header, name, 0, rightStart, readLen);
  left.setReadPairedFlag(true);
  right.setReadPairedFlag(true);
  left.setProperPairFlag(true);
  right.setProperPairFlag(true);
  left.setFirstOfPairFlag(leftIsFirst);
  right.setFirstOfPairFlag(!leftIsFirst);
  left.setReadNegativeStrandFlag(leftIsNegative);
  left.setMateNegativeStrandFlag(!leftIsNegative);
  right.setReadNegativeStrandFlag(!leftIsNegative);
  right.setMateNegativeStrandFlag(leftIsNegative);
  left.setMateAlignmentStart(right.getAlignmentStart());
  right.setMateAlignmentStart(left.getAlignmentStart());
  left.setMateReferenceIndex(0);
  right.setMateReferenceIndex(0);
  int isize = rightStart + readLen - leftStart;
  left.setInferredInsertSize(isize);
  right.setInferredInsertSize(-isize);
  return Arrays.asList(left, right);
}

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

GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "read1" , 0, start, readLength);
read.setProperPairFlag(true);
read.setReadPairedFlag(true);
read.setReadUnmappedFlag(false);
read.setMateUnmappedFlag(false);

代码示例来源：origin: broadgsa/gatk

readLeftAdapter.setCigarString(adapter.length() + "S" + common.length() + "M");
readLeftAdapter.setProperPairFlag(true);
readLeftAdapter.setReadPairedFlag(true);
readLeftAdapter.setFirstOfPairFlag(true);
readLeftAdapter.setReadNegativeStrandFlag(true);
readRightAdapter.setCigarString(common.length() + "M4S");
readRightAdapter.setProperPairFlag(true);
readRightAdapter.setReadPairedFlag(true);
readRightAdapter.setFirstOfPairFlag(false);
readRightAdapter.setReadNegativeStrandFlag(false);

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.setReadPairedFlag(true);
read.setProperPairFlag(true);
read.setReadUnmappedFlag(false);
  bad1.setReadPairedFlag(false);
  tests.add( new Object[]{ "not paired", bad1, false });

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

read.setReadPairedFlag(false);
read.setAlignmentStart(readStart);
read.setMappingQuality(artificialMappingQuality);

代码示例来源：origin: broadgsa/gatk

read.setReadPairedFlag(true);
read.setProperPairFlag(false);
Assert.assertEquals(get.getAdaptor(read), ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
  read = makeRead(fragmentSize, mateStart);
  read.setAlignmentStart(BEFORE);
  read.setReadPairedFlag(true);
  read.setProperPairFlag(true);
  read.setReadNegativeStrandFlag(negFlag);
  read.setReadPairedFlag(true);
  read.setProperPairFlag(true);
  read.setReadNegativeStrandFlag(negFlag);

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;
}