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

GATKSAMRecord.setFlags介绍

暂无

代码示例

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

@Test
public void testSecondaryAlignmentsDoNotInterfere() {
  final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 10, 30, true, false);
  final GATKSAMRecord read1 = properReads.get(0);
  read1.setAlignmentStart(8); // move the read
  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
  Assert.assertEquals(read1.getInferredInsertSize(), 21);
  final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary);
  read2NonPrimary.setFlags(393);   // second in proper pair, on reverse strand
  final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 1000, 1000, 1000);
  manager.addRead(read1, true, false);
  manager.addRead(read2NonPrimary, false, false);
  manager.addRead(read2Primary, false, false);
  Assert.assertEquals(manager.getNReadsInQueue(), 3);
  for ( final SAMRecord read : manager.getReadsInQueueForTesting() ) {
    if ( read.getFirstOfPairFlag() ) {
      Assert.assertEquals(read.getFlags(), 99);
      Assert.assertEquals(read.getInferredInsertSize(), 23);
    } else if ( read.getNotPrimaryAlignmentFlag() ) {
      Assert.assertEquals(read.getFlags(), 393);
      Assert.assertEquals(read.getInferredInsertSize(), -21);
    } else {
      Assert.assertEquals(read.getFlags(), 147);
      Assert.assertEquals(read.getInferredInsertSize(), -23);
    }
  }
}

代码示例来源：origin: broadgsa/gatk

final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 1000, 2000, true, false);
final GATKSAMRecord read1 = properReads.get(0);
read1.setFlags(99);   // first in pair, negative strand
read2.setFlags(161);   // second in pair, mate negative strand
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

emptyRead.setMappingQuality(0);
emptyRead.setFlags(read.getFlags());
emptyRead.setMateReferenceIndex(read.getMateReferenceIndex());
emptyRead.setMateAlignmentStart(read.getMateAlignmentStart());

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

/**
 * Write out a representation of this haplotype as a read
 *
 * @param haplotype a haplotype to write out.  Cannot be null
 * @param paddedRefLoc the reference location.  Cannot be null
 * @param isAmongBestHaplotypes true if among the best haplotypes, false if it was just one possible but not so good
 */
private void writeHaplotype(final Haplotype haplotype,
              final GenomeLoc paddedRefLoc,
              final boolean isAmongBestHaplotypes) {
  final GATKSAMRecord record = new GATKSAMRecord(output.getHeader());
  record.setReadBases(haplotype.getBases());
  record.setAlignmentStart(paddedRefLoc.getStart() + haplotype.getAlignmentStartHapwrtRef());
  record.setBaseQualities(Utils.dupBytes((byte) '!', haplotype.getBases().length));
  record.setCigar(AlignmentUtils.consolidateCigar(haplotype.getCigar()));
  record.setMappingQuality(isAmongBestHaplotypes ? 60 : 0);
  record.setReadName("HC" + uniqueNameCounter++);
  record.setAttribute(AlignmentUtils.HAPLOTYPE_TAG,haplotype.hashCode());
  record.setReadUnmappedFlag(false);
  record.setReferenceIndex(paddedRefLoc.getContigIndex());
  record.setAttribute(SAMTag.RG.toString(), READ_GROUP_ID);
  record.setFlags(16);
  output.add(record);
}