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

GATKSAMRecord.getReadUnmappedFlag介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

@Override
public boolean filter(ReferenceContext ref, GATKSAMRecord read) {
  return ! (read.getReadFailsVendorQualityCheckFlag() || read.getReadUnmappedFlag());
}

代码示例来源：origin: broadgsa/gatk

private static boolean unclippedReadOverlapsRegion(final GATKSAMRecord sampleRead, final int referenceIndex, final int start, final int end) {
  final int readReference = sampleRead.getReferenceIndex();
  if (readReference != referenceIndex)
    return false;
  final int readStart = sampleRead.getUnclippedStart();
  if (readStart > end)
    return false;
  final int readEnd = sampleRead.getReadUnmappedFlag() ? sampleRead.getUnclippedEnd()
      : Math.max(sampleRead.getUnclippedEnd(), sampleRead.getUnclippedStart());
  return readEnd >= start;
}

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

this.duplicates++;
if (!read.getReadUnmappedFlag()) {
  this.mapped++;
    this.properly_paired++;
  if (!read.getReadUnmappedFlag() && !read.getMateUnmappedFlag()) {
    this.with_itself_and_mate_mapped++;
  if (!read.getReadUnmappedFlag() && read.getMateUnmappedFlag()) {
    this.singletons++;

代码示例来源：origin: broadgsa/gatk

private boolean doNotTryToClean(GATKSAMRecord read) {
  return read.getReadUnmappedFlag() ||
      read.getNotPrimaryAlignmentFlag() ||
      read.getReadFailsVendorQualityCheckFlag() ||
      read.getMappingQuality() == 0 ||
      read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
      ConstrainedMateFixingManager.iSizeTooBigToMove(read, MAX_ISIZE_FOR_MOVEMENT) ||
      ReadUtils.is454Read(read) ||
      ReadUtils.isIonRead(read);
  // TODO -- it would be nice if we could use indels from 454/Ion reads as alternate consenses
}

代码示例来源：origin: broadgsa/gatk

final CigarShift cigarShift = (read.getReadUnmappedFlag()) ? new CigarShift(new Cigar(), 0, 0) : hardClipCigar(read.getCigar(), start, stop);

代码示例来源：origin: broadgsa/gatk

public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
  // we can not deal with screwy records
  if ( read.getReadUnmappedFlag() || read.getCigar().numCigarElements() == 0 ) {
    emit(read);
    return 0;
  }
  // move existing indels (for 1 indel reads only) to leftmost position within identical sequence
  int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read);
  if ( numBlocks == 2 ) {
    Cigar newCigar = AlignmentUtils.leftAlignIndel(IndelRealigner.unclipCigar(read.getCigar()), ref.getBases(), read.getReadBases(), 0, 0, true);
    newCigar = IndelRealigner.reclipCigar(newCigar, read);
    read.setCigar(newCigar);
  }
  emit(read);
  return 1;
}

代码示例来源：origin: broadgsa/gatk

if (read.getReadUnmappedFlag()) {

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

clippedRead = ( clippedRead.getReadUnmappedFlag() ? clippedRead : ReadClipper.hardClipAdaptorSequence( clippedRead ) );
if( !clippedRead.isEmpty() && clippedRead.getCigar().getReadLength() > 0 ) {
  clippedRead = ReadClipper.hardClipToRegion(clippedRead, activeRegion.getExtendedLoc().getStart(), activeRegion.getExtendedLoc().getStop());

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

clippedRead = ( clippedRead.getReadUnmappedFlag() ? clippedRead : ReadClipper.hardClipAdaptorSequence( clippedRead ) );
if( !clippedRead.isEmpty() && clippedRead.getCigar().getReadLength() > 0 ) {
  clippedRead = ReadClipper.hardClipToRegion( clippedRead, activeRegion.getExtendedLoc().getStart(), activeRegion.getExtendedLoc().getStop() );