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

GATKSAMRecord.setMateNegativeStrandFlag介绍

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代码示例

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.setMateNegativeStrandFlag(false);
  read.setMateAlignmentStart(start + nClips);
  read.setInferredInsertSize(readLength);
} else {
  read.setReadNegativeStrandFlag(false);
  read.setMateNegativeStrandFlag(true);
  read.setMateAlignmentStart(start - 1);
  read.setInferredInsertSize(goodBases);

代码示例来源：origin: broadgsa/gatk

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

代码示例来源：origin: broadgsa/gatk

readLeftAdapter.setFirstOfPairFlag(true);
readLeftAdapter.setReadNegativeStrandFlag(true);
readLeftAdapter.setMateNegativeStrandFlag(false);
readLeftAdapter.setMateAlignmentStart(readRightAdapter.getAlignmentStart());
readRightAdapter.setCigarString(common.length() + "M4S");
readRightAdapter.setFirstOfPairFlag(false);
readRightAdapter.setReadNegativeStrandFlag(false);
readRightAdapter.setMateNegativeStrandFlag(true);
readRightAdapter.setMateAlignmentStart(readLeftAdapter.getAlignmentStart());

代码示例来源：origin: broadgsa/gatk

read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, myStart + fragmentSize);
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(false);
read.setMateNegativeStrandFlag(true);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, myStart + fragmentSize);
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(true);
read.setMateNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, mateStart - 1);
read.setAlignmentStart(myStart);
read.setReadNegativeStrandFlag(true);
read.setMateNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, mateStart - 1);
read.setInferredInsertSize(0);
read.setReadNegativeStrandFlag(true);
read.setMateNegativeStrandFlag(false);
boundary = get.getAdaptor(read);
Assert.assertEquals(boundary, ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY);

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;
}