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

GATKSAMRecord.getReadPairedFlag介绍

暂无

代码示例

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

@Override
  public int compare(final ReadCost o1, final ReadCost o2) {
    final String s1 = o1.read.getReadName() + (o1.read.getReadPairedFlag() ? (o1.read.getFirstOfPairFlag() ? "/1" : "/2") : "");
    final String s2 = o2.read.getReadName() + (o2.read.getReadPairedFlag() ? (o2.read.getFirstOfPairFlag() ? "/1" : "/2") : "");
    return s1.compareTo(s2);
  }
};

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

/**
 * Account for the read and check it for any statistics necessary. Reads are marked in the temporary
 * attribute "seen" to make sure they're not counted twice.
 * 
 * @param read the read
 */
private void processRead(GATKSAMRecord read) {
  if (read.getTemporaryAttribute("seen") == null) {
    nReads++;
    if (read.getReadPairedFlag() && !read.getProperPairFlag())
      nBadMates++;
    read.setTemporaryAttribute("seen", true);
  }
}

代码示例来源：origin: broadgsa/gatk

@Override
public Integer map(ReferenceContext referenceContext, GATKSAMRecord read, RefMetaDataTracker RefMetaDataTracker) {
  final String rgID = read.getReadGroup().getId();
  final PerReadGroupInfo info = readGroupInfo.get(rgID);
  if ( info.needsMoreData() ) {
    info.readLength.add(read.getReadLength());
    info.nReadsSeen++;
    if ( read.getReadPairedFlag() ) {
      info.nReadsPaired++;
      if ( read.getInferredInsertSize() != 0) {
        info.insertSize.add(Math.abs(read.getInferredInsertSize()));
      }
    }
  }
  return null;
}

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

if ( ! a.isInformative() || ! isUsableRead(el.getKey()))
  continue; // read is non-informative or MQ0
if (a.getAlleleIfInformative().equals(refAllele, true) && el.getKey().getReadPairedFlag()) {
  if (el.getKey().getReadNegativeStrandFlag() == el.getKey().getFirstOfPairFlag())
    REF_F2R1++;
    REF_F1R2++;
else if (a.getAlleleIfInformative().equals(altAllele,true) && el.getKey().getReadPairedFlag()){
  if (el.getKey().getReadNegativeStrandFlag() == el.getKey().getFirstOfPairFlag())
    ALT_F2R1++;

代码示例来源：origin: broadgsa/gatk

this.mapped++;
if (read.getReadPairedFlag()) {
  this.paired_in_sequencing++;
  } else if (read.getReadPairedFlag()) {
    this.read1++;

代码示例来源：origin: broadgsa/gatk

if ( read.getReadPairedFlag() ) {
    if ( read.getAlignmentStart() == key.getAlignmentStart() && key.getReadPairedFlag() && ( key.getDuplicateReadFlag() || read.getDuplicateReadFlag() ) ) {
  for (List<GATKSAMRecord> reads : readSets) {
    GATKSAMRecord key = reads.get(0);
    boolean v = (! key.getReadPairedFlag()) && read.getAlignmentStart() == key.getAlignmentStart() && ( key.getDuplicateReadFlag() || read.getDuplicateReadFlag() ) && read.getReadLength() == key.getReadLength();

代码示例来源：origin: broadgsa/gatk

rawDepth++;
if (base.getRead().getReadPairedFlag() && (base.getRead().getMateUnmappedFlag() || !base.getRead().getProperPairFlag())){
  improperPairsCount++;
  continue;

代码示例来源：origin: broadgsa/gatk

public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
  for ( final PileupElement p : context.getBasePileup() ) {
    final GATKSAMRecord read = p.getRead();
    final int offset = p.getOffset();
    final boolean firstOfPair = ! read.getReadPairedFlag() || read.getFirstOfPairFlag();
    if ( firstOfPair && read.getMappingQuality() >= MIN_MAPPING_QUAL && p.getQual() >= MIN_BASE_QUAL ) {
      final byte readBase = p.getBase();
      final byte refBase = ref.getBase();
      final int cycle = offset;
      if ( BaseUtils.isRegularBase(readBase) && BaseUtils.isRegularBase(refBase) ) {
        final TableKey key = new TableKey(read.getReadGroup().getReadGroupId(), cycle);
        if ( ! table.containsRowID(key) ) {
          table.set(key, "cycle", cycle);
          table.set(key, "readgroup", read.getReadGroup().getReadGroupId());
          table.set(key, "counts", 0);
          table.set(key, "mismatches", 0);
        }
        table.increment(key, "counts");
        if (readBase != refBase)
          table.increment(key, "mismatches");
      }
    }
  }
  return null;
}

代码示例来源：origin: broadgsa/gatk

final int readOrderFactor = read.getReadPairedFlag() && read.getSecondOfPairFlag() ? -1 : 1;
final int increment;
int cycle;
final boolean multiplyByNegative1 = read.getReadPairedFlag() && read.getSecondOfPairFlag();