@Override
protected int doWork() {
IOUtil.assertFileIsReadable(INPUT);
IOUtil.assertFileIsWritable(OUTPUT);
IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
// Setup all the inputs
final ProgressLogger progress = new ProgressLogger(log, 10000000, "Processed", "loci");
final ReferenceSequenceFileWalker refWalker =
new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE);
final SamReader in =
SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
final SamLocusIterator iterator = getLocusIterator(in);
final List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
final CountingFilter dupeFilter = new CountingDuplicateFilter();
final CountingFilter mapqFilter = new CountingMapQFilter(MINIMUM_MAPPING_QUALITY);
final CountingPairedFilter pairFilter = new CountingPairedFilter();
filters.add(mapqFilter);
filters.add(dupeFilter);
if (!COUNT_UNPAIRED) {
filters.add(pairFilter);
}
filters.add(
new SecondaryAlignmentFilter()); // Not a counting filter because we never want to count
// reads twice
iterator.setSamFilters(filters);
iterator.setEmitUncoveredLoci(true);
iterator.setMappingQualityScoreCutoff(0); // Handled separately because we want to count bases
iterator.setQualityScoreCutoff(0); // Handled separately because we want to count bases
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 HashSet<String> readNames = new HashSet<String>(info.getRecordAndPositions().size());
int pileupSize = 0;
for (final SamLocusIterator.RecordAndOffset recs : info.getRecordAndPositions()) {
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<Integer>("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<Integer>("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 = getBasesExcludedBy(dupeFilter);
final long basesExcludedByMapq = getBasesExcludedBy(mapqFilter);
final long basesExcludedByPairing = getBasesExcludedBy(pairFilter);
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_1X =
MathUtil.sum(HistogramArray, 1, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_5X =
MathUtil.sum(HistogramArray, 5, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_10X =
MathUtil.sum(HistogramArray, 10, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_15X =
MathUtil.sum(HistogramArray, 15, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_20X =
MathUtil.sum(HistogramArray, 20, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_25X =
MathUtil.sum(HistogramArray, 25, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_30X =
MathUtil.sum(HistogramArray, 30, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_40X =
MathUtil.sum(HistogramArray, 40, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_50X =
MathUtil.sum(HistogramArray, 50, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_60X =
MathUtil.sum(HistogramArray, 60, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_70X =
MathUtil.sum(HistogramArray, 70, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_80X =
MathUtil.sum(HistogramArray, 80, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_90X =
MathUtil.sum(HistogramArray, 90, HistogramArray.length) / (double) metrics.GENOME_TERRITORY;
metrics.PCT_100X =
MathUtil.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 0;
}
