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

GATKSAMRecord.setReadNegativeStrandFlag介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

@Test(expectedExceptions = IllegalStateException.class)
  public void testStrandlessReadsFailSetStrand() {
    final byte [] bases = {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
    final byte [] quals = {20 , 20 , 20 , 20 , 20 , 20 , 20 , 20 };
    GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, "6M");
    read.setIsStrandless(true);
    read.setReadNegativeStrandFlag(true);
  }
}

代码示例来源：origin: broadgsa/gatk

@Test
public void testStrandlessReads() {
  final byte [] bases = {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
  final byte [] quals = {20 , 20 , 20 , 20 , 20 , 20 , 20 , 20 };
  GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, "6M");
  Assert.assertEquals(read.isStrandless(), false);
  read.setReadNegativeStrandFlag(false);
  Assert.assertEquals(read.isStrandless(), false);
  Assert.assertEquals(read.getReadNegativeStrandFlag(), false);
  read.setReadNegativeStrandFlag(true);
  Assert.assertEquals(read.isStrandless(), false);
  Assert.assertEquals(read.getReadNegativeStrandFlag(), true);
  read.setReadNegativeStrandFlag(true);
  read.setIsStrandless(true);
  Assert.assertEquals(read.isStrandless(), true);
  Assert.assertEquals(read.getReadNegativeStrandFlag(), false, "negative strand flag should return false even through its set for a strandless 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

read.setReadNegativeStrandFlag(true);
  read.setMateNegativeStrandFlag(false);
  read.setMateAlignmentStart(start + nClips);
  tests.add(new Object[]{nClips, goodBases, 0, read});
} else {
  read.setReadNegativeStrandFlag(false);
  read.setMateNegativeStrandFlag(true);
  read.setMateAlignmentStart(start - 1);

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true)
public void testHardClippingBeforeMergeResultingInCompletelyContainedSecondRead() {
  final String adapter    = "NNNN";
  final int minReadSize   = 7;
  final GATKSAMRecord readLeftAdapter = makeOverlappingRead(adapter, 30, Utils.dupString("A", 10), Utils.dupBytes((byte)30, 10), "", 30, 10);
  final GATKSAMRecord readRightAdapter = makeOverlappingRead("", 30, Utils.dupString("A", minReadSize), Utils.dupBytes((byte)30, minReadSize), adapter, 30, 10);
  readLeftAdapter.setCigarString(adapter.length() + "S10M");
  readLeftAdapter.setProperPairFlag(true);
  readLeftAdapter.setFirstOfPairFlag(true);
  readLeftAdapter.setReadNegativeStrandFlag(true);
  readLeftAdapter.setMateAlignmentStart(10);
  readRightAdapter.setCigarString(minReadSize + "M4S");
  readRightAdapter.setProperPairFlag(true);
  readRightAdapter.setFirstOfPairFlag(false);
  readRightAdapter.setReadNegativeStrandFlag(false);
  final int insertSize = minReadSize;
  readLeftAdapter.setInferredInsertSize(insertSize);
  readRightAdapter.setInferredInsertSize(-insertSize);
  final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(readLeftAdapter, readRightAdapter);
  Assert.assertNull(actual);
}

代码示例来源：origin: broadgsa/gatk

myStart = BEFORE;
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read);
myStart = AFTER;
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read);
myStart = AFTER;
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(true);
read.setMateNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
myStart = BEFORE;
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(true);
read.setMateNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
read.setReadNegativeStrandFlag(true);
read.setMateNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);
read.setReadNegativeStrandFlag(false);

代码示例来源：origin: broadgsa/gatk

readLeftAdapter.setReadPairedFlag(true);
readLeftAdapter.setFirstOfPairFlag(true);
readLeftAdapter.setReadNegativeStrandFlag(true);
readLeftAdapter.setMateNegativeStrandFlag(false);
readLeftAdapter.setMateAlignmentStart(readRightAdapter.getAlignmentStart());
readRightAdapter.setReadPairedFlag(true);
readRightAdapter.setFirstOfPairFlag(false);
readRightAdapter.setReadNegativeStrandFlag(false);
readRightAdapter.setMateNegativeStrandFlag(true);
readRightAdapter.setMateAlignmentStart(readLeftAdapter.getAlignmentStart());

代码示例来源：origin: broadgsa/gatk

read.setInferredInsertSize(80);
read.setFirstOfPairFlag(true);
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
  bad.setReadNegativeStrandFlag(true);
  tests.add( new Object[]{ "read and mate both on negative strand", bad, false });
  bad.setReadNegativeStrandFlag(true);
  bad.setMateNegativeStrandFlag(false);
  bad.setMateAlignmentStart(1000);

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

代码示例来源：origin: broadgsa/gatk

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

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;
}