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

GATKSAMRecord.getReferenceName介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

/**
 * Gets #getGenomePosition but as a 1 bp GenomeLoc
 * @param genomeLocParser the parser to use to create the genome loc
 * @return a non-null genome location with start position of getGenomePosition
 */
@Requires("genomeLocParser != null")
@Ensures("result != null")
public GenomeLoc getLocation(final GenomeLocParser genomeLocParser) {
  // TODO -- may return wonky results if on an edge (could be 0 or could be beyond genome location)
  return genomeLocParser.createGenomeLoc(read.getReferenceName(), getGenomePosition());
}

代码示例来源：origin: broadgsa/gatk

public void add(GATKSAMRecord read) {
  final int readStart = read.getSoftStart();
  final int readStop = read.getSoftEnd();
  if ( loc == null )
    loc = parser.createGenomeLoc(read.getReferenceName(), readStart, Math.max(readStop, readStart)); // in case it's all an insertion
  else if ( readStop > loc.getStop() )
    loc = parser.createGenomeLoc(loc.getContig(), loc.getStart(), readStop);
  reads.add(read);
}

代码示例来源：origin: broadgsa/gatk

public void setCigar(Cigar cigar, boolean fixClippedCigar) {
  if ( cigar == null ) {
    newCigar = null;
    return;
  }
  if ( fixClippedCigar && getReadBases().length < read.getReadLength() )
    cigar = reclipCigar(cigar);
  // no change?
  if ( read.getCigar().equals(cigar) ) {
    newCigar = null;
    return;
  }
  // no indel?
  String str = cigar.toString();
  if ( !str.contains("D") && !str.contains("I") ) {
    logger.debug("Modifying a read with no associated indel; although this is possible, it is highly unlikely.  Perhaps this region should be double-checked: " + read.getReadName() + " near " + read.getReferenceName() + ":" + read.getAlignmentStart());
    //    newCigar = null;
    //    return;
  }
  newCigar = cigar;
}

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

public void setRead(final GATKSAMRecord read) {
    if ( !read.isEmpty() ) {
      this.read = read;
      if ( ! read.getReadUnmappedFlag() )
        loc = genomeLocParser.createGenomeLoc(read.getReferenceName(), read.getSoftStart(), read.getSoftEnd());
    }
  }
}

代码示例来源：origin: broadgsa/gatk

sb.append(reads.get(0).getRead().getReferenceName()).append(":").append(leftmostIndex + i);
if ( stillMismatches )
  sb.append(" SAME_SNP\n");

代码示例来源：origin: broadgsa/gatk

@Test( )
public void testCreationFromSAMRecord() {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5);
  final GenomeLoc loc = genomeLocParser.createGenomeLoc(read);
  Assert.assertEquals(loc.getContig(), read.getReferenceName());
  Assert.assertEquals(loc.getContigIndex(), (int)read.getReferenceIndex());
  Assert.assertEquals(loc.getStart(), read.getAlignmentStart());
  Assert.assertEquals(loc.getStop(), read.getAlignmentEnd());
}

代码示例来源：origin: broadgsa/gatk

/**
 * Tests the GenomeLoc variable in the ReadBin after adding arbitrary reads
 *
 * @param cigarString    the read's cigar string
 * @param alignmentStart the read's alignment start
 */
@Test(enabled = true, dataProvider = "reads")
public void testAddingReads(String cigarString, int alignmentStart) {
  final GATKSAMRecord read = createReadAndAddToBin(cigarString, alignmentStart);
  final GenomeLoc readLoc = parser.createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getSoftStart(), Math.max(read.getSoftStart(), read.getSoftEnd()));
  Assert.assertEquals(readBin.getLocation(), readLoc);
  readBin.clear();
}

代码示例来源：origin: broadgsa/gatk

@Test( )
public void testCreationFromSAMRecordUnmappedButOnGenome() {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5);
  read.setReadUnmappedFlag(true);
  read.setCigarString("*");
  final GenomeLoc loc = genomeLocParser.createGenomeLoc(read);
  Assert.assertEquals(loc.getContig(), read.getReferenceName());
  Assert.assertEquals(loc.getContigIndex(), (int)read.getReferenceIndex());
  Assert.assertEquals(loc.getStart(), read.getAlignmentStart());
  Assert.assertEquals(loc.getStop(), read.getAlignmentStart());
}

代码示例来源：origin: broadgsa/gatk

str.append(reads.get(0).getReferenceName());
int position = bestConsensus.positionOnReference + bestConsensus.cigar.getCigarElement(0).getLength();
str.append("\t").append(leftmostIndex + position - 1);

代码示例来源：origin: broadgsa/gatk

private void AssertWellOrderedPileup(final ReadBackedPileup pileup) {
  if ( ! pileup.isEmpty() ) {
    int leftMostPos = -1;
    for ( final PileupElement pe : pileup ) {
      Assert.assertTrue(pileup.getLocation().getContig().equals(pe.getRead().getReferenceName()), "ReadBackedPileup contains an element " + pe + " that's on a different contig than the pileup itself");
      Assert.assertTrue(pe.getRead().getAlignmentStart() >= leftMostPos,
          "ReadBackedPileup contains an element " + pe + " whose read's alignment start " + pe.getRead().getAlignmentStart()
              + " occurs before the leftmost position we've seen previously " + leftMostPos);
    }
  }
}

代码示例来源：origin: broadgsa/gatk

int uStop = read.getUnclippedEnd();
if ( !read.getReferenceName().equals(interval.getContig()) )
  return ReadAndIntervalOverlap.NO_OVERLAP_CONTIG;

代码示例来源：origin: broadgsa/gatk

returnRead.setBaseQualities( quals );
returnRead.setReadGroup( firstRead.getReadGroup() );
returnRead.setReferenceName( firstRead.getReferenceName() );
returnRead.setReadName( firstRead.getReadName() );
final CigarElement c = new CigarElement(bases.length, CigarOperator.M);

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

final String contig = read.getReferenceName();
final int splitStart = startRefIndex + CigarUtils.countRefBasesBasedOnCigar(read,cigarFirstIndex,cigarEndIndex);  //we use cigarEndIndex instead of cigarSecondIndex so we won't take into account the D's at the end.
final int splitEnd = splitStart + read.getCigar().getCigarElement(cigarEndIndex).getLength() - 1;