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; } } }
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(); } }