org.broadinstitute.gatk.utils.sam.GATKSAMRecord.getMappingQuality()方法的使用及代码示例

x33g5p2x  于2022-01-20 转载在 其他  
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本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.getMappingQuality()方法的一些代码示例，展示了GATKSAMRecord.getMappingQuality()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.getMappingQuality()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：getMappingQuality

GATKSAMRecord.getMappingQuality介绍

暂无

代码示例

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

protected boolean isUsableRead(final GATKSAMRecord read) {
    return !( read.getMappingQuality() == 0 ||
        read.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE );
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * Get the mapping quality of the read of this element
 * @return the mapping quality of the underlying SAM record
 */
public int getMappingQual() {
  return read.getMappingQuality();
}

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

/**
 * Can the read be used in comparative tests between ref / alt bases?
 *
 * @param read   the read to consider
 * @return false if MQ is either 0 or unavailable. true otherwise.
 */
private boolean isUsableRead(final GATKSAMRecord read) {
  return( read.getMappingQuality() != 0 || read.getMappingQuality() != QualityUtils.MAPPING_QUALITY_UNAVAILABLE);
}

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

/**
 * Can the read be used in comparative tests between ref / alt bases?
 *
 * @param read   the read to consider
 * @param refLoc the reference location
 * @return true if this read is meaningful for comparison, false otherwise
 */
protected boolean isUsableRead(final GATKSAMRecord read, final int refLoc) {
  return !( read.getMappingQuality() == 0 ||
      read.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE );
}

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

@Override
  protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) {
    return (double)read.getMappingQuality();
  }
}

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

protected boolean isUsableRead(final GATKSAMRecord read) {
  return !( read.getMappingQuality() == 0 ||
      read.getMappingQuality() == QualityUtils.MAPPING_QUALITY_UNAVAILABLE );
}

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

@Override
protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) {
  return (double)read.getMappingQuality();
}

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

private void capMinimumReadQualities(GATKSAMRecord read, byte[] readQuals, byte[] readInsQuals, byte[] readDelQuals) {
  for( int kkk = 0; kkk < readQuals.length; kkk++ ) {
    readQuals[kkk] = (byte) Math.min( 0xff & readQuals[kkk], read.getMappingQuality()); // cap base quality by mapping quality, as in UG
    readQuals[kkk] = ( readQuals[kkk] < PairHMM.BASE_QUALITY_SCORE_THRESHOLD ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] );
    readInsQuals[kkk] = ( readInsQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readInsQuals[kkk] );
    readDelQuals[kkk] = ( readDelQuals[kkk] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : readDelQuals[kkk] );
  }
}

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

@Override
  protected Double getElementForPileupElement(final PileupElement p) {
    return (double)p.getRead().getMappingQuality();
  }
}

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

private Map<String, Object> annotateWithLikelihoods(final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap,
                          final VariantContext vc) {
  if ( stratifiedPerReadAlleleLikelihoodMap == null )
    return null;
  int mq0 = 0;
  for ( PerReadAlleleLikelihoodMap likelihoodMap : stratifiedPerReadAlleleLikelihoodMap.values() ) {
    for (GATKSAMRecord read : likelihoodMap.getLikelihoodReadMap().keySet()) {
       if (read.getMappingQuality() == 0 )
        mq0++;
    }
  }
  Map<String, Object> map = new HashMap<String, Object>();
  map.put(getKeyNames().get(0), String.format("%d", mq0));
  return map;
}

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

@Override
public void calculateRawData(final VariantContext vc, final Map<String, PerReadAlleleLikelihoodMap> pralm, final ReducibleAnnotationData rawAnnotations) {
  Double squareSum = 0.0;
  if ( pralm.size() == 0 )
    return;
  for ( final PerReadAlleleLikelihoodMap perReadLikelihoods : pralm.values() ) {
    for ( final GATKSAMRecord read : perReadLikelihoods.getStoredElements() ) {
      int mq = read.getMappingQuality();
      if ( mq != QualityUtils.MAPPING_QUALITY_UNAVAILABLE ) {
        squareSum += mq * mq;
      }
    }
  }
  rawAnnotations.putAttribute(Allele.NO_CALL,squareSum);
}

代码示例来源：origin: broadgsa/gatk

@Override
public int getNumberOfMappingQualityZeroReads() {
  if ( nMQ0Reads == UNINITIALIZED_CACHED_INT_VALUE ) {
    nMQ0Reads = 0;
    for (PileupElement p : pileupElementTracker.unorderedIterable()) {
      if (p.getRead().getMappingQuality() == 0) {
        nMQ0Reads++;
      }
    }
  }
  return nMQ0Reads;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Get an array of the mapping qualities
 *
 * @return
 */
@Override
public int[] getMappingQuals() {
  final int[] v = new int[getNumberOfElements()];
  int pos = 0;
  for ( final PileupElement pile : pileupElementTracker ) {
    v[pos++] = pile.getRead().getMappingQuality();
  }
  return v;
}

代码示例来源：origin: broadgsa/gatk

private static String createVerboseOutput(final ReadBackedPileup pileup) {
  final StringBuilder sb = new StringBuilder();
  boolean isFirst = true;
  sb.append(pileup.getNumberOfDeletions());
  sb.append(" ");
  for ( PileupElement p : pileup ) {
    if ( isFirst )
      isFirst = false;
    else
      sb.append(",");
    sb.append(p.getRead().getReadName());
    sb.append(verboseDelimiter);
    sb.append(p.getOffset());
    sb.append(verboseDelimiter);
    sb.append(p.getRead().getReadLength());
    sb.append(verboseDelimiter);
    sb.append(p.getRead().getMappingQuality());
  }
  return sb.toString();
}

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

private Set<GATKSAMRecord> filterNonPassingReads( final ActiveRegion activeRegion ) {
  final Set<GATKSAMRecord> readsToRemove = new LinkedHashSet<>();
  for( final GATKSAMRecord rec : activeRegion.getReads() ) {
    if( rec.getReadLength() < READ_LENGTH_FILTER_THRESHOLD || rec.getMappingQuality() < READ_QUALITY_FILTER_THRESHOLD || (!isBadMateFilterDisabled && BadMateFilter.hasBadMate(rec)) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
      readsToRemove.add(rec);
    }
  }
  activeRegion.removeAll( readsToRemove );
  return readsToRemove;
}

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

public void getRMSDataFromPRALM(Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap, ReducibleAnnotationData<Number> myData) {
  //over all the samples in the Map...
  for ( final PerReadAlleleLikelihoodMap perReadLikelihoods : perReadAlleleLikelihoodMap.values() ) {
    //for each read...
    for ( final Map.Entry<GATKSAMRecord,Map<Allele,Double>> readLikelihoods : perReadLikelihoods.getLikelihoodReadMap().entrySet() ) {
      final int mq = readLikelihoods.getKey().getMappingQuality();
      if ( mq != QualityUtils.MAPPING_QUALITY_UNAVAILABLE ) {
        if (!PerReadAlleleLikelihoodMap.getMostLikelyAllele(readLikelihoods.getValue()).isInformative())
          continue;
        final Allele bestAllele =PerReadAlleleLikelihoodMap.getMostLikelyAllele(readLikelihoods.getValue()).getMostLikelyAllele();
        double currSquareSum = 0;
        if (myData.hasAttribute(bestAllele))
          currSquareSum += (double)myData.getAttribute(bestAllele);
        myData.putAttribute(bestAllele, currSquareSum + mq * mq);
      }
    }
  }
}

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

protected Set<GATKSAMRecord> filterNonPassingReads( final ActiveRegion activeRegion) {
  final Set<GATKSAMRecord> readsToRemove = new LinkedHashSet<>();
  for( final GATKSAMRecord rec : activeRegion.getReads() ) {
    //TODO: Takuto points out that this is questionable.  Let's think hard abut it.
    // KCIBUL: only perform read quality filtering on tumor reads...
    if (isReadFromNormal(rec)) {
      if( rec.getReadLength() < MIN_READ_LENGTH ) {
        readsToRemove.add(rec);
      }
    } else if( rec.getReadLength() < MIN_READ_LENGTH || rec.getMappingQuality() < MQthreshold || BadMateFilter.hasBadMate(rec) ||
        (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
      readsToRemove.add(rec);
    }
  }
  activeRegion.removeAll(readsToRemove);
  return readsToRemove;
}

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

/**
 * Loads the read that is going to be evaluated in following calls to {@link #calculateLocalLikelihoods}.
 *
 * @param read the target read.
 * @throws NullPointerException if {@code read} is null.
 */
@Override
public void loadRead(final GATKSAMRecord read) {
  loadRead(read.getReadBases(),read.getBaseQualities(),read.getBaseInsertionQualities(),read.getBaseDeletionQualities(),read.getMappingQuality());
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG, dataProvider = "MergeFragmentsTest")
public void testMergingTwoReads(final String name, final GATKSAMRecord read1, final GATKSAMRecord read2, final GATKSAMRecord expectedMerged) {
  final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(read1, read2);
  if ( expectedMerged == null ) {
    Assert.assertNull(actual, "Expected reads not to merge, but got non-null result from merging");
  } else {
    Assert.assertTrue(actual.isStrandless(), "Merged reads should be strandless");
    Assert.assertNotNull(actual, "Expected reads to merge, but got null result from merging");
    // I really care about the bases, the quals, the CIGAR, and the read group tag
    Assert.assertEquals(actual.getCigarString(), expectedMerged.getCigarString());
    Assert.assertEquals(actual.getReadBases(), expectedMerged.getReadBases());
    Assert.assertEquals(actual.getReadGroup(), expectedMerged.getReadGroup());
    Assert.assertEquals(actual.getMappingQuality(), expectedMerged.getMappingQuality());
    for ( final EventType type : EventType.values() )
      Assert.assertEquals(actual.getBaseQualities(type), expectedMerged.getBaseQualities(type), "Failed base qualities for event type " + type);
  }
}

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
}

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