private void collectQualityData(final SAMRecord record, final ReferenceSequence reference) {
        // If the read isnt an aligned PF read then look at the read for no-calls
        if (record.getReadUnmappedFlag()
            || record.getReadFailsVendorQualityCheckFlag()
            || !doRefMetrics) {
          final byte[] readBases = record.getReadBases();
          for (int i = 0; i < readBases.length; i++) {
            if (SequenceUtil.isNoCall(readBases[i])) {
              badCycleHistogram.increment(
                  CoordMath.getCycle(record.getReadNegativeStrandFlag(), readBases.length, i));
            }
          }
        } else if (!record.getReadFailsVendorQualityCheckFlag()) {
          final boolean highQualityMapping = isHighQualityMapping(record);
          if (highQualityMapping) metrics.PF_HQ_ALIGNED_READS++;

          final byte[] readBases = record.getReadBases();
          final byte[] refBases = reference.getBases();
          final byte[] qualities = record.getBaseQualities();
          final int refLength = refBases.length;
          long mismatchCount = 0;
          long hqMismatchCount = 0;

          for (final AlignmentBlock alignmentBlock : record.getAlignmentBlocks()) {
            final int readIndex = alignmentBlock.getReadStart() - 1;
            final int refIndex = alignmentBlock.getReferenceStart() - 1;
            final int length = alignmentBlock.getLength();

            for (int i = 0; i < length && refIndex + i < refLength; ++i) {
              final int readBaseIndex = readIndex + i;
              boolean mismatch =
                  !SequenceUtil.basesEqual(readBases[readBaseIndex], refBases[refIndex + i]);
              boolean bisulfiteBase = false;
              if (mismatch && isBisulfiteSequenced) {
                if ((record.getReadNegativeStrandFlag()
                        && (refBases[refIndex + i] == 'G' || refBases[refIndex + i] == 'g')
                        && (readBases[readBaseIndex] == 'A' || readBases[readBaseIndex] == 'a'))
                    || ((!record.getReadNegativeStrandFlag())
                            && (refBases[refIndex + i] == 'C' || refBases[refIndex + i] == 'c')
                            && (readBases[readBaseIndex] == 'T')
                        || readBases[readBaseIndex] == 't')) {

                  bisulfiteBase = true;
                  mismatch = false;
                }
              }

              if (mismatch) mismatchCount++;

              metrics.PF_ALIGNED_BASES++;
              if (!bisulfiteBase) nonBisulfiteAlignedBases++;

              if (highQualityMapping) {
                metrics.PF_HQ_ALIGNED_BASES++;
                if (!bisulfiteBase) hqNonBisulfiteAlignedBases++;
                if (qualities[readBaseIndex] >= BASE_QUALITY_THRESHOLD)
                  metrics.PF_HQ_ALIGNED_Q20_BASES++;
                if (mismatch) hqMismatchCount++;
              }

              if (mismatch || SequenceUtil.isNoCall(readBases[readBaseIndex])) {
                badCycleHistogram.increment(
                    CoordMath.getCycle(record.getReadNegativeStrandFlag(), readBases.length, i));
              }
            }
          }

          mismatchHistogram.increment(mismatchCount);
          hqMismatchHistogram.increment(hqMismatchCount);

          // Add any insertions and/or deletions to the global count
          for (final CigarElement elem : record.getCigar().getCigarElements()) {
            final CigarOperator op = elem.getOperator();
            if (op == CigarOperator.INSERTION || op == CigarOperator.DELETION) ++this.indels;
          }
        }
      }
Exemple #2
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  public void find_coverage(SAMResource sres) {
    int start_base = sres.region.range.start;
    int end_base = sres.region.range.end;

    int coverage_len = (end_base - start_base) + 1;
    int i, end, ref_i, read_i, len;

    int[] coverage = new int[coverage_len];
    Arrays.fill(coverage, 0);

    WorkingFile wf = null;
    if (outfile != null) {
      try {
        wf = new WorkingFile(outfile);
        ps = wf.getPrintStream();
      } catch (Exception e) {
        System.err.println("I/O error: " + e); // debug
        e.printStackTrace();
        System.exit(1);
      }
    }

    try {
      //
      //  gather coverage info:
      //
      CloseableIterator<SAMRecord> iterator = sres.get_iterator();
      int read_count = 0;
      int ref_min = -1;
      int ref_max = -1;

      while (iterator.hasNext()) {
        SAMRecord sr = iterator.next();
        read_count++;

        //	System.err.println(sr.getReadName() + ": " + sr.getAlignmentStart() + "-" +
        // sr.getAlignmentEnd());  // debug

        if (sr.getReadUnmappedFlag()) continue;
        if (sr.getDuplicateReadFlag()) {
          if (verbose_mode)
            System.err.println(
                sr.getReadName()
                    + "."
                    + (sr.getReadNegativeStrandFlag() ? "R" : "F")
                    + " ignoring, duplicate");
          continue;
        }

        byte[] read = sr.getReadBases();
        byte[] quals = sr.getBaseQualities();

        for (AlignmentBlock ab : sr.getAlignmentBlocks()) {
          len = ab.getLength();
          read_i = ab.getReadStart() - 1;
          ref_i = ab.getReferenceStart() - start_base;

          if (ref_min == -1 || ref_i < ref_min) ref_min = ref_i;

          for (i = read_i, end = read_i + len; i < end; i++, ref_i++) {
            if (ref_i >= 0 && ref_i < coverage_len) {
              if (quals[i] >= MIN_QUALITY) {
                if (verbose_mode)
                  System.err.println(
                      sr.getReadName()
                          + "."
                          + (sr.getReadNegativeStrandFlag() ? "R" : "F")
                          + " hit at "
                          + (ref_i + start_base)
                          + " as="
                          + sr.getAlignmentStart()
                          + " ae="
                          + sr.getAlignmentEnd());
                coverage[ref_i]++;
              } else if (verbose_mode) {
                System.err.println(
                    sr.getReadName()
                        + "."
                        + (sr.getReadNegativeStrandFlag() ? "R" : "F")
                        + " qual_reject at "
                        + (ref_i + start_base)
                        + " as="
                        + sr.getAlignmentStart()
                        + " ae="
                        + sr.getAlignmentEnd());
              }
            }
          }
          if (ref_max == -1 || ref_i > ref_max) ref_max = ref_i;
        }
      }
      sres.close();
      System.err.println(
          "records:"
              + read_count
              + " ref_min:"
              + (ref_min + start_base)
              + " ref_max:"
              + (ref_max + start_base)); // debug

      //
      //  report coverage info:
      //
      for (i = 0; i < coverage.length; i++) {
        if (name != null) ps.print(name + ",");
        ps.println((i + start_base) + "," + coverage[i]); // debug
      }
      if (wf != null) wf.finish();

    } catch (Exception e) {
      System.err.println("ERROR: " + e); // debug
      e.printStackTrace();
    }
  }