コード例 #1
0
ファイル: HaplotypeScore.java プロジェクト: jwills/gatk
  private Haplotype getHaplotypeFromRead(
      final PileupElement p, final int contextSize, final int locus) {
    final GATKSAMRecord read = p.getRead();
    int readOffsetFromPileup = p.getOffset();

    final byte[] haplotypeBases = new byte[contextSize];
    Arrays.fill(haplotypeBases, (byte) REGEXP_WILDCARD);
    final double[] baseQualities = new double[contextSize];
    Arrays.fill(baseQualities, 0.0);

    byte[] readBases = read.getReadBases();
    readBases =
        AlignmentUtils.readToAlignmentByteArray(
            read.getCigar(), readBases); // Adjust the read bases based on the Cigar string
    byte[] readQuals = read.getBaseQualities();
    readQuals =
        AlignmentUtils.readToAlignmentByteArray(
            read.getCigar(),
            readQuals); // Shift the location of the qual scores based on the Cigar string

    readOffsetFromPileup =
        AlignmentUtils.calcAlignmentByteArrayOffset(
            read.getCigar(), p, read.getAlignmentStart(), locus);
    final int baseOffsetStart = readOffsetFromPileup - (contextSize - 1) / 2;

    for (int i = 0; i < contextSize; i++) {
      final int baseOffset = i + baseOffsetStart;
      if (baseOffset < 0) {
        continue;
      }
      if (baseOffset >= readBases.length) {
        break;
      }
      if (readQuals[baseOffset] == PileupElement.DELETION_BASE) {
        readQuals[baseOffset] = PileupElement.DELETION_QUAL;
      }
      if (!BaseUtils.isRegularBase(readBases[baseOffset])) {
        readBases[baseOffset] = (byte) REGEXP_WILDCARD;
        readQuals[baseOffset] = (byte) 0;
      } // N's shouldn't be treated as distinct bases
      readQuals[baseOffset] = (byte) Math.min((int) readQuals[baseOffset], p.getMappingQual());
      if (((int) readQuals[baseOffset]) < 5) {
        readQuals[baseOffset] = (byte) 0;
      } // quals less than 5 are used as codes and don't have actual probabilistic meaning behind
        // them
      haplotypeBases[i] = readBases[baseOffset];
      baseQualities[i] = (double) readQuals[baseOffset];
    }

    return new Haplotype(haplotypeBases, baseQualities);
  }
コード例 #2
0
ファイル: ReadClipper.java プロジェクト: mlovci/gatk
  /**
   * Hard clip the read to the variable region (from refStart to refStop)
   *
   * @param read the read to be clipped
   * @param refStart the beginning of the variant region (inclusive)
   * @param refStop the end of the variant region (inclusive)
   * @return the read hard clipped to the variant region
   */
  public static GATKSAMRecord hardClipToRegion(
      final GATKSAMRecord read, final int refStart, final int refStop) {
    final int start = read.getAlignmentStart();
    final int stop = read.getAlignmentEnd();

    // check if the read is contained in region
    if (start <= refStop && stop >= refStart) {
      if (start < refStart && stop > refStop)
        return hardClipBothEndsByReferenceCoordinates(read, refStart - 1, refStop + 1);
      else if (start < refStart) return hardClipByReferenceCoordinatesLeftTail(read, refStart - 1);
      else if (stop > refStop) return hardClipByReferenceCoordinatesRightTail(read, refStop + 1);
      return read;
    } else return GATKSAMRecord.emptyRead(read);
  }
コード例 #3
0
ファイル: ReadClipper.java プロジェクト: mlovci/gatk
  /**
   * Hard clips away soft clipped bases that are below the given quality threshold
   *
   * @param read the read
   * @param minQual the mininum base quality score to revert the base (inclusive)
   * @return a new read without low quality soft clipped bases
   */
  public static GATKSAMRecord hardClipLowQualitySoftClips(GATKSAMRecord read, byte minQual) {
    int nLeadingSoftClips = read.getAlignmentStart() - read.getSoftStart();
    if (read.isEmpty() || nLeadingSoftClips > read.getReadLength())
      return GATKSAMRecord.emptyRead(read);

    byte[] quals = read.getBaseQualities(EventType.BASE_SUBSTITUTION);
    int left = -1;

    if (nLeadingSoftClips > 0) {
      for (int i = nLeadingSoftClips - 1; i >= 0; i--) {
        if (quals[i] >= minQual) left = i;
        else break;
      }
    }

    int right = -1;
    int nTailingSoftClips = read.getSoftEnd() - read.getAlignmentEnd();
    if (nTailingSoftClips > 0) {
      for (int i = read.getReadLength() - nTailingSoftClips; i < read.getReadLength(); i++) {
        if (quals[i] >= minQual) right = i;
        else break;
      }
    }

    GATKSAMRecord clippedRead = read;
    if (right >= 0
        && right + 1
            < clippedRead
                .getReadLength()) // only clip if there are softclipped bases (right >= 0) and the
                                  // first high quality soft clip is not the last base (right+1 <
                                  // readlength)
    clippedRead =
          hardClipByReadCoordinates(
              clippedRead,
              right + 1,
              clippedRead.getReadLength()
                  - 1); // first we hard clip the low quality soft clips on the right tail
    if (left >= 0
        && left - 1
            > 0) // only clip if there are softclipped bases (left >= 0) and the first high quality
                 // soft clip is not the last base (left-1 > 0)
    clippedRead =
          hardClipByReadCoordinates(
              clippedRead,
              0,
              left - 1); // then we hard clip the low quality soft clips on the left tail

    return clippedRead;
  }
コード例 #4
0
  private ArrayList<Allele> computeConsensusAlleles(
      ReferenceContext ref,
      Map<String, AlignmentContext> contexts,
      AlignmentContextUtils.ReadOrientation contextType) {
    Allele refAllele = null, altAllele = null;
    GenomeLoc loc = ref.getLocus();
    ArrayList<Allele> aList = new ArrayList<Allele>();

    HashMap<String, Integer> consensusIndelStrings = new HashMap<String, Integer>();

    int insCount = 0, delCount = 0;
    // quick check of total number of indels in pileup
    for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
      AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);

      final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
      insCount += indelPileup.getNumberOfInsertions();
      delCount += indelPileup.getNumberOfDeletions();
    }

    if (insCount < minIndelCountForGenotyping && delCount < minIndelCountForGenotyping)
      return aList;

    for (Map.Entry<String, AlignmentContext> sample : contexts.entrySet()) {
      // todo -- warning, can be duplicating expensive partition here
      AlignmentContext context = AlignmentContextUtils.stratify(sample.getValue(), contextType);

      final ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();

      for (ExtendedEventPileupElement p : indelPileup.toExtendedIterable()) {
        // SAMRecord read = p.getRead();
        GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
        if (read == null) continue;
        if (ReadUtils.is454Read(read)) {
          continue;
        }

        /*                if (DEBUG && p.isIndel()) {
                         System.out.format("Read: %s, cigar: %s, aln start: %d, aln end: %d, p.len:%d, Type:%s, EventBases:%s\n",
                                 read.getReadName(),read.getCigar().toString(),read.getAlignmentStart(),read.getAlignmentEnd(),
                                 p.getEventLength(),p.getType().toString(), p.getEventBases());
                     }
        */

        String indelString = p.getEventBases();
        if (p.isInsertion()) {
          boolean foundKey = false;
          if (read.getAlignmentEnd() == loc.getStart()) {
            // first corner condition: a read has an insertion at the end, and we're right at the
            // insertion.
            // In this case, the read could have any of the inserted bases and we need to build a
            // consensus
            for (String s : consensusIndelStrings.keySet()) {
              int cnt = consensusIndelStrings.get(s);
              if (s.startsWith(indelString)) {
                // case 1: current insertion is prefix of indel in hash map
                consensusIndelStrings.put(s, cnt + 1);
                foundKey = true;
                break;
              } else if (indelString.startsWith(s)) {
                // case 2: indel stored in hash table is prefix of current insertion
                // In this case, new bases are new key.
                consensusIndelStrings.remove(s);
                consensusIndelStrings.put(indelString, cnt + 1);
                foundKey = true;
                break;
              }
            }
            if (!foundKey)
              // none of the above: event bases not supported by previous table, so add new key
              consensusIndelStrings.put(indelString, 1);

          } else if (read.getAlignmentStart() == loc.getStart() + 1) {
            // opposite corner condition: read will start at current locus with an insertion
            for (String s : consensusIndelStrings.keySet()) {
              int cnt = consensusIndelStrings.get(s);
              if (s.endsWith(indelString)) {
                // case 1: current insertion is suffix of indel in hash map
                consensusIndelStrings.put(s, cnt + 1);
                foundKey = true;
                break;
              } else if (indelString.endsWith(s)) {
                // case 2: indel stored in hash table is suffix of current insertion
                // In this case, new bases are new key.

                consensusIndelStrings.remove(s);
                consensusIndelStrings.put(indelString, cnt + 1);
                foundKey = true;
                break;
              }
            }
            if (!foundKey)
              // none of the above: event bases not supported by previous table, so add new key
              consensusIndelStrings.put(indelString, 1);

          } else {
            // normal case: insertion somewhere in the middle of a read: add count to hash map
            int cnt =
                consensusIndelStrings.containsKey(indelString)
                    ? consensusIndelStrings.get(indelString)
                    : 0;
            consensusIndelStrings.put(indelString, cnt + 1);
          }

        } else if (p.isDeletion()) {
          indelString = String.format("D%d", p.getEventLength());
          int cnt =
              consensusIndelStrings.containsKey(indelString)
                  ? consensusIndelStrings.get(indelString)
                  : 0;
          consensusIndelStrings.put(indelString, cnt + 1);
        }
      }

      /*            if (DEBUG) {
          int icount = indelPileup.getNumberOfInsertions();
          int dcount = indelPileup.getNumberOfDeletions();
          if (icount + dcount > 0)
          {
              List<Pair<String,Integer>> eventStrings = indelPileup.getEventStringsWithCounts(ref.getBases());
              System.out.format("#ins: %d, #del:%d\n", insCount, delCount);

              for (int i=0 ; i < eventStrings.size() ; i++ ) {
                  System.out.format("%s:%d,",eventStrings.get(i).first,eventStrings.get(i).second);
                  //                int k=0;
              }
              System.out.println();
          }
      }             */
    }

    int maxAlleleCnt = 0;
    String bestAltAllele = "";
    for (String s : consensusIndelStrings.keySet()) {
      int curCnt = consensusIndelStrings.get(s);
      if (curCnt > maxAlleleCnt) {
        maxAlleleCnt = curCnt;
        bestAltAllele = s;
      }
      //            if (DEBUG)
      //                System.out.format("Key:%s, number: %d\n",s,consensusIndelStrings.get(s)  );
    } // gdebug-

    if (maxAlleleCnt < minIndelCountForGenotyping) return aList;

    if (bestAltAllele.startsWith("D")) {
      // get deletion length
      int dLen = Integer.valueOf(bestAltAllele.substring(1));
      // get ref bases of accurate deletion
      int startIdxInReference = (int) (1 + loc.getStart() - ref.getWindow().getStart());

      // System.out.println(new String(ref.getBases()));
      byte[] refBases =
          Arrays.copyOfRange(ref.getBases(), startIdxInReference, startIdxInReference + dLen);

      if (Allele.acceptableAlleleBases(refBases)) {
        refAllele = Allele.create(refBases, true);
        altAllele = Allele.create(Allele.NULL_ALLELE_STRING, false);
      }
    } else {
      // insertion case
      if (Allele.acceptableAlleleBases(bestAltAllele)) {
        refAllele = Allele.create(Allele.NULL_ALLELE_STRING, true);
        altAllele = Allele.create(bestAltAllele, false);
      }
    }
    if (refAllele != null && altAllele != null) {
      aList.add(0, refAllele);
      aList.add(1, altAllele);
    }
    return aList;
  }
コード例 #5
0
  @Override
  public T traverse(
      final ActiveRegionWalker<M, T> walker, final LocusShardDataProvider dataProvider, T sum) {
    logger.debug(String.format("TraverseActiveRegion.traverse: Shard is %s", dataProvider));

    final LocusView locusView = getLocusView(walker, dataProvider);
    final GenomeLocSortedSet initialIntervals = engine.getIntervals();

    final LocusReferenceView referenceView = new LocusReferenceView(walker, dataProvider);
    final int activeRegionExtension =
        walker.getClass().getAnnotation(ActiveRegionExtension.class).extension();
    final int maxRegionSize =
        walker.getClass().getAnnotation(ActiveRegionExtension.class).maxRegion();

    if (locusView
        .hasNext()) { // trivial optimization to avoid unnecessary processing when there's nothing
                      // here at all
      int minStart = Integer.MAX_VALUE;
      ActivityProfile profile =
          new ActivityProfile(engine.getGenomeLocParser(), walker.hasPresetActiveRegions());

      ReferenceOrderedView referenceOrderedDataView =
          getReferenceOrderedView(walker, dataProvider, locusView);

      // We keep processing while the next reference location is within the interval
      GenomeLoc prevLoc = null;
      while (locusView.hasNext()) {
        final AlignmentContext locus = locusView.next();
        GenomeLoc location = locus.getLocation();

        if (prevLoc != null) {
          // fill in the active / inactive labels from the stop of the previous location to the
          // start of this location
          // TODO refactor to separate function
          for (int iii = prevLoc.getStop() + 1; iii < location.getStart(); iii++) {
            final GenomeLoc fakeLoc =
                engine.getGenomeLocParser().createGenomeLoc(prevLoc.getContig(), iii, iii);
            if (initialIntervals == null || initialIntervals.overlaps(fakeLoc)) {
              profile.add(
                  fakeLoc,
                  new ActivityProfileResult(
                      walker.hasPresetActiveRegions()
                              && walker.presetActiveRegions.overlaps(fakeLoc)
                          ? 1.0
                          : 0.0));
            }
          }
        }

        dataProvider.getShard().getReadMetrics().incrementNumIterations();

        // create reference context. Note that if we have a pileup of "extended events", the context
        // will
        // hold the (longest) stretch of deleted reference bases (if deletions are present in the
        // pileup).
        final ReferenceContext refContext = referenceView.getReferenceContext(location);

        // Iterate forward to get all reference ordered data covering this location
        final RefMetaDataTracker tracker =
            referenceOrderedDataView.getReferenceOrderedDataAtLocus(
                locus.getLocation(), refContext);

        // Call the walkers isActive function for this locus and add them to the list to be
        // integrated later
        if (initialIntervals == null || initialIntervals.overlaps(location)) {
          profile.add(location, walkerActiveProb(walker, tracker, refContext, locus, location));
        }

        // Grab all the previously unseen reads from this pileup and add them to the massive read
        // list
        for (final PileupElement p : locus.getBasePileup()) {
          final GATKSAMRecord read = p.getRead();
          if (!myReads.contains(read)) {
            myReads.add(read);
          }

          // If this is the last pileup for this shard calculate the minimum alignment start so that
          // we know
          // which active regions in the work queue are now safe to process
          minStart = Math.min(minStart, read.getAlignmentStart());
        }

        prevLoc = location;

        printProgress(locus.getLocation());
      }

      updateCumulativeMetrics(dataProvider.getShard());

      // Take the individual isActive calls and integrate them into contiguous active regions and
      // add these blocks of work to the work queue
      // band-pass filter the list of isActive probabilities and turn into active regions
      final ActivityProfile bandPassFiltered = profile.bandPassFilter();
      final List<ActiveRegion> activeRegions =
          bandPassFiltered.createActiveRegions(activeRegionExtension, maxRegionSize);

      // add active regions to queue of regions to process
      // first check if can merge active regions over shard boundaries
      if (!activeRegions.isEmpty()) {
        if (!workQueue.isEmpty()) {
          final ActiveRegion last = workQueue.getLast();
          final ActiveRegion first = activeRegions.get(0);
          if (last.isActive == first.isActive
              && last.getLocation().contiguousP(first.getLocation())
              && last.getLocation().size() + first.getLocation().size() <= maxRegionSize) {
            workQueue.removeLast();
            activeRegions.remove(first);
            workQueue.add(
                new ActiveRegion(
                    last.getLocation().union(first.getLocation()),
                    first.isActive,
                    this.engine.getGenomeLocParser(),
                    activeRegionExtension));
          }
        }
        workQueue.addAll(activeRegions);
      }

      logger.debug(
          "Integrated "
              + profile.size()
              + " isActive calls into "
              + activeRegions.size()
              + " regions.");

      // now go and process all of the active regions
      sum = processActiveRegions(walker, sum, minStart, dataProvider.getLocus().getContig());
    }

    return sum;
  }
コード例 #6
0
ファイル: HaplotypeScore.java プロジェクト: jwills/gatk
  private double scoreReadAgainstHaplotype(
      final PileupElement p, final int contextSize, final Haplotype haplotype, final int locus) {
    double expected = 0.0;
    double mismatches = 0.0;

    // What's the expected mismatch rate under the model that this read is actually sampled from
    // this haplotype?  Let's assume the consensus base c is a random choice one of A, C, G, or T,
    // and that
    // the observed base is actually from a c with an error rate e.  Since e is the rate at which
    // we'd
    // see a miscalled c, the expected mismatch rate is really e.  So the expected number of
    // mismatches
    // is just sum_i e_i for i from 1..n for n sites
    //
    // Now, what's the probabilistic sum of mismatches?  Suppose that the base b is equal to c.
    // Well, it could
    // actually be a miscall in a matching direction, which would happen at a e / 3 rate.  If b !=
    // c, then
    // the chance that it is actually a mismatch is 1 - e, since any of the other 3 options would be
    // a mismatch.
    // so the probability-weighted mismatch rate is sum_i ( matched ? e_i / 3 : 1 - e_i ) for i = 1
    // ... n
    final byte[] haplotypeBases = haplotype.getBases();
    final GATKSAMRecord read = p.getRead();
    byte[] readBases = read.getReadBases();

    readBases =
        AlignmentUtils.readToAlignmentByteArray(
            p.getRead().getCigar(), readBases); // Adjust the read bases based on the Cigar string
    byte[] readQuals = read.getBaseQualities();
    readQuals =
        AlignmentUtils.readToAlignmentByteArray(
            p.getRead().getCigar(),
            readQuals); // Shift the location of the qual scores based on the Cigar string
    int readOffsetFromPileup = p.getOffset();
    readOffsetFromPileup =
        AlignmentUtils.calcAlignmentByteArrayOffset(
            p.getRead().getCigar(), p, read.getAlignmentStart(), locus);
    final int baseOffsetStart = readOffsetFromPileup - (contextSize - 1) / 2;

    for (int i = 0; i < contextSize; i++) {
      final int baseOffset = i + baseOffsetStart;
      if (baseOffset < 0) {
        continue;
      }
      if (baseOffset >= readBases.length) {
        break;
      }

      final byte haplotypeBase = haplotypeBases[i];
      final byte readBase = readBases[baseOffset];

      final boolean matched =
          (readBase == haplotypeBase || haplotypeBase == (byte) REGEXP_WILDCARD);
      byte qual = readQuals[baseOffset];
      if (qual == PileupElement.DELETION_BASE) {
        qual = PileupElement.DELETION_QUAL;
      } // calcAlignmentByteArrayOffset fills the readQuals array with DELETION_BASE at deletions
      qual = (byte) Math.min((int) qual, p.getMappingQual());
      if (((int) qual)
          >= 5) { // quals less than 5 are used as codes and don't have actual probabilistic meaning
                  // behind them
        final double e = QualityUtils.qualToErrorProb(qual);
        expected += e;
        mismatches += matched ? e : 1.0 - e / 3.0;
      }

      // a more sophisticated calculation would include the reference quality, but it's nice to
      // actually penalize
      // the mismatching of poorly determined regions of the consensus
    }

    return mismatches - expected;
  }