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

GATKSAMRecord.getReadNegativeStrandFlag介绍

暂无

代码示例

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

private void updateTable(final int[] table, final int alleleIndex, final GATKSAMRecord read) {
  if (alleleIndex < 0 || (alleleIndex+1)*2 > table.length) return;
  final int offset = alleleIndex * 2;
  //Unstranded reads are not meaningful for this annotation, they can be found in the AD annotation
  if (!read.isStrandless()) {
    final boolean isFW = !read.getReadNegativeStrandFlag();
    table[offset + (isFW ? 0 : 1)]++;
  }
}

代码示例来源：origin: broadgsa/gatk

final byte[] inconsistency = (byte[]) attr;
if (read.getReadNegativeStrandFlag()) { // Negative direction
  return inconsistency[inconsistency.length - offset - 1] == (byte) 0;

代码示例来源：origin: broadgsa/gatk

public void addAlignment(GATKSAMRecord read) {
  output.println("@" + read.getReadName());
  if (read.getReadNegativeStrandFlag()) {
    output.println(ReadUtils.getBasesReverseComplement(read));
    output.println("+");
    output.println(ReadUtils.convertReadQualToString(invertQuals(read.getBaseQualities())));
  } else {
    output.println(ReadUtils.convertReadBasesToString(read));
    output.println("+");
    output.println(ReadUtils.convertReadQualToString(read));
  }
}

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

private void splitPRALMintoForwardAndReverseReads(final PerReadAlleleLikelihoodMap originalPRALM, final PerReadAlleleLikelihoodMap forwardPRALM, final PerReadAlleleLikelihoodMap reversePRALM) {
    final Map<GATKSAMRecord, Map<Allele, Double>> origReadAlleleLikelihoodMap = originalPRALM.getLikelihoodReadMap();
    for (final GATKSAMRecord read : origReadAlleleLikelihoodMap.keySet()) {
      if (read.isStrandless())
        continue;

      for (final Map.Entry<Allele, Double> alleleLikelihoodMap : origReadAlleleLikelihoodMap.get(read).entrySet()) {
        final Allele allele = alleleLikelihoodMap.getKey();
        final Double likelihood = alleleLikelihoodMap.getValue();
        if (read.getReadNegativeStrandFlag())
          reversePRALM.add(read, allele, likelihood);
        else
          forwardPRALM.add(read, allele, likelihood);
      }
    }
  }
}

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

private static void updateTable(final int[] table, final Allele allele, final GATKSAMRecord read, final Allele ref, final List<Allele> allAlts) {
  final boolean matchesRef = allele.equals(ref, true);
  final boolean matchesAnyAlt = allAlts.contains(allele);
  if ( matchesRef || matchesAnyAlt ) {
    final int offset = matchesRef ? 0 : ARRAY_DIM;
    if ( read.isStrandless() ) {
      // a strandless read counts as observations on both strand, at 50% weight, with a minimum of 1
      // (the 1 is to ensure that a strandless read always counts as an observation on both strands, even
      // if the read is only seen once, because it's a merged read or other)
      table[offset]++;
      table[offset + 1]++;
    } else {
      // a normal read with an actual strand
      final boolean isFW = !read.getReadNegativeStrandFlag();
      table[offset + (isFW ? 0 : 1)]++;
    }
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * is this base inside the adaptor of the read?
 *
 * There are two cases to treat here:
 *
 * 1) Read is in the negative strand => Adaptor boundary is on the left tail
 * 2) Read is in the positive strand => Adaptor boundary is on the right tail
 *
 * Note: We return false to all reads that are UNMAPPED or have an weird big insert size (probably due to mismapping or bigger event)
 *
 * @param read the read to test
 * @param basePos base position in REFERENCE coordinates (not read coordinates)
 * @return whether or not the base is in the adaptor
 */
public static boolean isBaseInsideAdaptor(final GATKSAMRecord read, long basePos) {
  final int adaptorBoundary = read.getAdaptorBoundary();
  if (adaptorBoundary == CANNOT_COMPUTE_ADAPTOR_BOUNDARY || read.getInferredInsertSize() > DEFAULT_ADAPTOR_SIZE)
    return false;
  return read.getReadNegativeStrandFlag() ? basePos <= adaptorBoundary : basePos >= adaptorBoundary;
}

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

} else {
  final boolean isFW = !read.getReadNegativeStrandFlag();
  if (isFW)
    alleleStrandCounts.set(FORWARD, alleleStrandCounts.get(FORWARD)+1);

代码示例来源：origin: broadgsa/gatk

/**
 * Checks if a read contains adaptor sequences. If it does, hard clips them out.
 *
 * Note: To see how a read is checked for adaptor sequence see {@link ReadUtils::getAdaptorBoundary}
 *
 * @return a new read without adaptor sequence
 */
private GATKSAMRecord hardClipAdaptorSequence () {
  final int adaptorBoundary = ReadUtils.getAdaptorBoundary(read);
  if (adaptorBoundary == ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY || !ReadUtils.isInsideRead(read, adaptorBoundary))
    return read;
  return read.getReadNegativeStrandFlag() ? hardClipByReferenceCoordinatesLeftTail(adaptorBoundary) : hardClipByReferenceCoordinatesRightTail(adaptorBoundary);
}
public static GATKSAMRecord hardClipAdaptorSequence (GATKSAMRecord read) {

代码示例来源：origin: broadgsa/gatk

/**
 * Convenence function that takes a read and the start / stop clipping positions based on the forward
 * strand, and returns start/stop values appropriate for the strand of the read.
 *
 * @param read
 * @param start
 * @param stop
 * @return
 */
private Pair<Integer, Integer> strandAwarePositions(GATKSAMRecord read, int start, int stop) {
  if (read.getReadNegativeStrandFlag())
    return new Pair<Integer, Integer>(read.getReadLength() - stop - 1, read.getReadLength() - start - 1);
  else
    return new Pair<Integer, Integer>(start, stop);
}

代码示例来源：origin: broadgsa/gatk

Pattern pattern = read.getReadNegativeStrandFlag() ? stc.revPat : stc.fwdPat;
String bases = read.getReadString();
Matcher match = pattern.matcher(bases);

代码示例来源：origin: broadgsa/gatk

int baseIndex = read.getReadNegativeStrandFlag() ? readLen - i - 1 : i;
byte qual = quals[baseIndex];
clipSum += (qTrimmingThreshold - qual);
int start = read.getReadNegativeStrandFlag() ? 0 : clipPoint;
int stop = read.getReadNegativeStrandFlag() ? clipPoint : readLen - 1;

代码示例来源：origin: broadgsa/gatk

@Test
public void testStrandlessReads() {
  final byte [] bases = {'A', 'A', 'A', 'A', 'A', 'A', 'A', 'A'};
  final byte [] quals = {20 , 20 , 20 , 20 , 20 , 20 , 20 , 20 };
  GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(bases, quals, "6M");
  Assert.assertEquals(read.isStrandless(), false);
  read.setReadNegativeStrandFlag(false);
  Assert.assertEquals(read.isStrandless(), false);
  Assert.assertEquals(read.getReadNegativeStrandFlag(), false);
  read.setReadNegativeStrandFlag(true);
  Assert.assertEquals(read.isStrandless(), false);
  Assert.assertEquals(read.getReadNegativeStrandFlag(), true);
  read.setReadNegativeStrandFlag(true);
  read.setIsStrandless(true);
  Assert.assertEquals(read.isStrandless(), true);
  Assert.assertEquals(read.getReadNegativeStrandFlag(), false, "negative strand flag should return false even through its set for a strandless read");
}

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

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++;
  else
  if (el.getKey().getReadNegativeStrandFlag() == el.getKey().getFirstOfPairFlag())
    ALT_F2R1++;
  else

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

final int index = ( read.getReadNegativeStrandFlag() ? readPos : readPos - 1 );
updateIndel(indel, index, mode, EventType.BASE_DELETION);
break;
final boolean forwardStrandRead = !read.getReadNegativeStrandFlag();
if( forwardStrandRead ) {
  updateIndel(indel, readPos - 1, mode, EventType.BASE_INSERTION);

代码示例来源：origin: broadgsa/gatk

final boolean negativeStrand = clippedRead.getReadNegativeStrandFlag();
byte[] bases = clippedRead.getReadBases();
if (negativeStrand)

代码示例来源：origin: broadgsa/gatk

if (read.getReadNegativeStrandFlag())
  readBases = BaseUtils.simpleReverseComplement(read.getReadBases());

代码示例来源：origin: broadgsa/gatk

@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
  // store the original bases and then write Ns over low quality ones
  final byte[] originalBases = read.getReadBases().clone();
  final boolean negativeStrand = read.getReadNegativeStrandFlag();
  byte[] bases = read.getReadBases();
  if (negativeStrand)
    bases = BaseUtils.simpleReverseComplement(bases);
  // don't record reads with N's
  if (!BaseUtils.isAllRegularBases(bases))
    return;
  for (int i = 0; i < bases.length; i++) {
    final Pair<byte[], Integer> res = findTandemRepeatUnits(bases, i);
    // to merge repeat unit and repeat length to get covariate value:
    final String repeatID =  getCovariateValueFromUnitAndLength(res.first,  res.second);
    final int key = keyForRepeat(repeatID);
    final int readOffset = (negativeStrand ? bases.length - i - 1 : i);
    values.addCovariate(key, key, key, readOffset);
  }
  // put the original bases back in
  read.setReadBases(originalBases);
}

代码示例来源：origin: broadgsa/gatk

public ReadBackedPileupImpl getPositiveStrandPileup() {
  if (pileupElementTracker instanceof PerSamplePileupElementTracker) {
    PerSamplePileupElementTracker<PileupElement> tracker = (PerSamplePileupElementTracker<PileupElement>) pileupElementTracker;
    PerSamplePileupElementTracker<PileupElement> filteredTracker = new PerSamplePileupElementTracker<PileupElement>();
    for (final String sample : tracker.getSamples()) {
      PileupElementTracker<PileupElement> perSampleElements = tracker.getElements(sample);
      ReadBackedPileupImpl pileup = createNewPileup(loc, perSampleElements).getPositiveStrandPileup();
      filteredTracker.addElements(sample, pileup.pileupElementTracker);
    }
    return createNewPileup(loc, filteredTracker);
  } else {
    UnifiedPileupElementTracker<PileupElement> tracker = (UnifiedPileupElementTracker<PileupElement>) pileupElementTracker;
    UnifiedPileupElementTracker<PileupElement> filteredTracker = new UnifiedPileupElementTracker<PileupElement>();
    for (PileupElement p : tracker) {
      if (!p.getRead().getReadNegativeStrandFlag()) {
        filteredTracker.add(p);
      }
    }
    return createNewPileup(loc, filteredTracker);
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * Gets the pileup consisting of only reads on the negative strand.
 *
 * @return A read-backed pileup consisting only of reads on the negative strand.
 */
public ReadBackedPileupImpl getNegativeStrandPileup() {
  if (pileupElementTracker instanceof PerSamplePileupElementTracker) {
    PerSamplePileupElementTracker<PileupElement> tracker = (PerSamplePileupElementTracker<PileupElement>) pileupElementTracker;
    PerSamplePileupElementTracker<PileupElement> filteredTracker = new PerSamplePileupElementTracker<PileupElement>();
    for (final String sample : tracker.getSamples()) {
      PileupElementTracker<PileupElement> perSampleElements = tracker.getElements(sample);
      ReadBackedPileupImpl pileup = createNewPileup(loc, perSampleElements).getNegativeStrandPileup();
      filteredTracker.addElements(sample, pileup.pileupElementTracker);
    }
    return createNewPileup(loc, filteredTracker);
  } else {
    UnifiedPileupElementTracker<PileupElement> tracker = (UnifiedPileupElementTracker<PileupElement>) pileupElementTracker;
    UnifiedPileupElementTracker<PileupElement> filteredTracker = new UnifiedPileupElementTracker<PileupElement>();
    for (PileupElement p : tracker) {
      if (p.getRead().getReadNegativeStrandFlag()) {
        filteredTracker.add(p);
      }
    }
    return createNewPileup(loc, filteredTracker);
  }
}

代码示例来源：origin: broadgsa/gatk

final int increment;
int cycle;
if (read.getReadNegativeStrandFlag()) {
  cycle = readLength * readOrderFactor;
  increment = -1 * readOrderFactor;
if (!read.getReadNegativeStrandFlag()) { // Forward direction
  int iii = 0;
  while (iii < readLength) {