Examples with SecondaryAlignmentFilter htsjdk.samtools.filter.SecondaryAlignmentFilter used on opensource projects

Example 1 with SecondaryAlignmentFilter

use of htsjdk.samtools.filter.SecondaryAlignmentFilter in project gatk by broadinstitute.

the class CountingPairedFilter method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(INPUT);
    IOUtil.assertFileIsWritable(OUTPUT);
    IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
    // Setup all the inputs
    final ProgressLogger progress = new ProgressLogger(logger, 10000000, "Processed", "loci");
    final ReferenceSequenceFileWalker refWalker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
    final SamReader in = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).validationStringency(VALIDATION_STRINGENCY).open(INPUT);
    // Load up the reference sequence and double check sequence dictionaries
    if (!in.getFileHeader().getSequenceDictionary().isEmpty()) {
        SequenceUtil.assertSequenceDictionariesEqual(in.getFileHeader().getSequenceDictionary(), refWalker.getSequenceDictionary());
    }
    final SamLocusIterator iterator = new SamLocusIterator(in);
    final List<SamRecordFilter> filters = new ArrayList<>();
    final CountingFilter dupeFilter = new CountingDuplicateFilter();
    final CountingFilter mapqFilter = new CountingMapQFilter(MINIMUM_MAPPING_QUALITY);
    final CountingPairedFilter pairFilter = new CountingPairedFilter();
    filters.add(mapqFilter);
    filters.add(dupeFilter);
    filters.add(pairFilter);
    // Not a counting filter because we never want to count reads twice
    filters.add(new SecondaryAlignmentFilter());
    iterator.setSamFilters(filters);
    iterator.setEmitUncoveredLoci(true);
    // Handled separately because we want to count bases
    iterator.setMappingQualityScoreCutoff(0);
    // Handled separately because we want to count bases
    iterator.setQualityScoreCutoff(0);
    iterator.setIncludeNonPfReads(false);
    final int max = COVERAGE_CAP;
    final long[] HistogramArray = new long[max + 1];
    final long[] baseQHistogramArray = new long[Byte.MAX_VALUE];
    final boolean usingStopAfter = STOP_AFTER > 0;
    final long stopAfter = STOP_AFTER - 1;
    long counter = 0;
    long basesExcludedByBaseq = 0;
    long basesExcludedByOverlap = 0;
    long basesExcludedByCapping = 0;
    // Loop through all the loci
    while (iterator.hasNext()) {
        final SamLocusIterator.LocusInfo info = iterator.next();
        // Check that the reference is not N
        final ReferenceSequence ref = refWalker.get(info.getSequenceIndex());
        final byte base = ref.getBases()[info.getPosition() - 1];
        if (base == 'N')
            continue;
        // Figure out the coverage while not counting overlapping reads twice, and excluding various things
        final Set<String> readNames = new HashSet<>(info.getRecordAndOffsets().size());
        int pileupSize = 0;
        for (final SamLocusIterator.RecordAndOffset recs : info.getRecordAndOffsets()) {
            if (recs.getBaseQuality() < MINIMUM_BASE_QUALITY) {
                ++basesExcludedByBaseq;
                continue;
            }
            if (!readNames.add(recs.getRecord().getReadName())) {
                ++basesExcludedByOverlap;
                continue;
            }
            pileupSize++;
            if (pileupSize <= max) {
                baseQHistogramArray[recs.getRecord().getBaseQualities()[recs.getOffset()]]++;
            }
        }
        final int depth = Math.min(readNames.size(), max);
        if (depth < readNames.size())
            basesExcludedByCapping += readNames.size() - max;
        HistogramArray[depth]++;
        // Record progress and perhaps stop
        progress.record(info.getSequenceName(), info.getPosition());
        if (usingStopAfter && ++counter > stopAfter)
            break;
    }
    // Construct and write the outputs
    final Histogram<Integer> histo = new Histogram<>("coverage", "count");
    for (int i = 0; i < HistogramArray.length; ++i) {
        histo.increment(i, HistogramArray[i]);
    }
    // Construct and write the outputs
    final Histogram<Integer> baseQHisto = new Histogram<>("value", "baseq_count");
    for (int i = 0; i < baseQHistogramArray.length; ++i) {
        baseQHisto.increment(i, baseQHistogramArray[i]);
    }
    final WgsMetrics metrics = generateWgsMetrics();
    metrics.GENOME_TERRITORY = (long) histo.getSumOfValues();
    metrics.MEAN_COVERAGE = histo.getMean();
    metrics.SD_COVERAGE = histo.getStandardDeviation();
    metrics.MEDIAN_COVERAGE = histo.getMedian();
    metrics.MAD_COVERAGE = histo.getMedianAbsoluteDeviation();
    final long basesExcludedByDupes = dupeFilter.getFilteredBases();
    final long basesExcludedByMapq = mapqFilter.getFilteredBases();
    final long basesExcludedByPairing = pairFilter.getFilteredBases();
    final double total = histo.getSum();
    final double totalWithExcludes = total + basesExcludedByDupes + basesExcludedByMapq + basesExcludedByPairing + basesExcludedByBaseq + basesExcludedByOverlap + basesExcludedByCapping;
    metrics.PCT_EXC_DUPE = basesExcludedByDupes / totalWithExcludes;
    metrics.PCT_EXC_MAPQ = basesExcludedByMapq / totalWithExcludes;
    metrics.PCT_EXC_UNPAIRED = basesExcludedByPairing / totalWithExcludes;
    metrics.PCT_EXC_BASEQ = basesExcludedByBaseq / totalWithExcludes;
    metrics.PCT_EXC_OVERLAP = basesExcludedByOverlap / totalWithExcludes;
    metrics.PCT_EXC_CAPPED = basesExcludedByCapping / totalWithExcludes;
    metrics.PCT_EXC_TOTAL = (totalWithExcludes - total) / totalWithExcludes;
    metrics.PCT_5X = MathUtils.sum(HistogramArray, 5, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_10X = MathUtils.sum(HistogramArray, 10, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_15X = MathUtils.sum(HistogramArray, 15, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_20X = MathUtils.sum(HistogramArray, 20, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_25X = MathUtils.sum(HistogramArray, 25, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_30X = MathUtils.sum(HistogramArray, 30, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_40X = MathUtils.sum(HistogramArray, 40, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_50X = MathUtils.sum(HistogramArray, 50, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_60X = MathUtils.sum(HistogramArray, 60, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_70X = MathUtils.sum(HistogramArray, 70, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_80X = MathUtils.sum(HistogramArray, 80, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_90X = MathUtils.sum(HistogramArray, 90, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    metrics.PCT_100X = MathUtils.sum(HistogramArray, 100, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
    final MetricsFile<WgsMetrics, Integer> out = getMetricsFile();
    out.addMetric(metrics);
    out.addHistogram(histo);
    if (INCLUDE_BQ_HISTOGRAM) {
        out.addHistogram(baseQHisto);
    }
    out.write(OUTPUT);
    return null;
}