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

GATKSAMRecord.setMateAlignmentStart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

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

代码示例来源：origin: broadgsa/gatk

@Test
public void testSecondaryAlignmentsDoNotCauseAccidentalRemovalOfMate() {
  final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 530, 1594, true, false);
  final GATKSAMRecord read1 = properReads.get(0);
  read1.setFlags(99);   // first in proper pair, mate negative strand
  final GATKSAMRecord read2Primary = properReads.get(1);
  read2Primary.setFlags(147);   // second in pair, mate unmapped, not primary alignment
  read2Primary.setAlignmentStart(1596); // move the read
  final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary);
  read2NonPrimary.setReadName("foo");
  read2NonPrimary.setFlags(393);   // second in proper pair, on reverse strand
  read2NonPrimary.setAlignmentStart(451);
  read2NonPrimary.setMateAlignmentStart(451);
  final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 10000, 200, 10000);
  manager.addRead(read2NonPrimary, false, false);
  manager.addRead(read1, false, false);
  for ( int i = 0; i < ConstrainedMateFixingManager.EMIT_FREQUENCY; i++ )
    manager.addRead(ArtificialSAMUtils.createArtificialRead(header, "foo" + i, 0, 1500, 10), false, false);
  Assert.assertTrue(manager.forMateMatching.containsKey("foo"));
}

代码示例来源：origin: broadgsa/gatk

read2Supp.setFlags(2209);   // second in pair, mate negative strand, supplementary
read2Supp.setAlignmentStart(100);
read2Supp.setMateAlignmentStart(1000);

代码示例来源：origin: broadgsa/gatk

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

代码示例来源：origin: broadgsa/gatk

read.setAlignmentStart(100);
read.setCigarString("50M");
read.setMateAlignmentStart(130);
read.setInferredInsertSize(80);
read.setFirstOfPairFlag(true);
  bad.setReadNegativeStrandFlag(true);
  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

@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

emptyRead.setMateAlignmentStart(read.getMateAlignmentStart());
emptyRead.setInferredInsertSize(read.getInferredInsertSize());

代码示例来源：origin: broadgsa/gatk

read.setAlignmentStart(myStart);
read.setInferredInsertSize(20);
read.setMateAlignmentStart(980);
read.setReadNegativeStrandFlag(false);
boundary = get.getAdaptor(read);

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;
}