Examples with ContigPos com.github.lindenb.jvarkit.util.vcf.ContigPos used on opensource projects

Example 1 with ContigPos

use of com.github.lindenb.jvarkit.util.vcf.ContigPos in project jvarkit by lindenb.

the class DepthOfCoverage method doWork.

@Override
public int doWork(final List<String> args) {
    PrintWriter out = null;
    if (this.auto_mask && this.faidx == null) {
        LOG.error("Cannot auto mask if REF is not defined");
        return -1;
    }
    if (this.maskBed != null && this.includeBed != null) {
        LOG.error("both --mask and --bed both defined");
        return -1;
    }
    ReferenceSequenceFile referenceSequenceFile = null;
    try {
        final Predicate<String> isRejectContigRegex;
        if (!StringUtils.isBlank(this.skipContigExpr)) {
            final Pattern pat = Pattern.compile(this.skipContigExpr);
            isRejectContigRegex = S -> pat.matcher(S).matches();
        } else {
            isRejectContigRegex = S -> false;
        }
        final SamReaderFactory srf = super.createSamReaderFactory();
        if (this.faidx != null) {
            srf.referenceSequence(this.faidx);
            srf.setUseAsyncIo(this.asyncIo);
            referenceSequenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(this.faidx);
        }
        out = super.openPathOrStdoutAsPrintWriter(this.outputFile);
        out.print("#BAM\tSample\tContig\tContig-Length\tMasked-Contig-Length\tCount\tDepth\tMedian\tMin\tMax\tMaxPos");
        for (RangeOfIntegers.Range r : this.summaryCov.getRanges()) {
            if (r.getMinInclusive() == null)
                continue;
            out.print("\t");
            out.print(r.toString());
        }
        out.println();
        for (final Path path : IOUtils.unrollPaths(args)) {
            try (final SamReader sr = srf.open(path)) {
                if (!sr.hasIndex()) {
                    LOG.error("File " + path + " is not indexed.");
                    return -1;
                }
                final SAMFileHeader header = sr.getFileHeader();
                final SAMSequenceDictionary dict = SequenceDictionaryUtils.extractRequired(header);
                final Set<String> rejectContigSet = dict.getSequences().stream().map(SSR -> SSR.getSequenceName()).filter(isRejectContigRegex).collect(Collectors.toCollection(HashSet::new));
                rejectContigSet.addAll(dict.getSequences().stream().filter(SSR -> SSR.getSequenceLength() < this.skipContigLength).map(SSR -> SSR.getSequenceName()).collect(Collectors.toCollection(HashSet::new)));
                if (!header.getSortOrder().equals(SAMFileHeader.SortOrder.coordinate)) {
                    LOG.error("file is not sorted on coordinate :" + header.getSortOrder() + " " + path);
                    return -1;
                }
                final QueryInterval[] intervals;
                if (this.useBamIndexFlag && this.includeBed != null) {
                    if (!sr.hasIndex()) {
                        LOG.error("Bam is not indexed. " + path);
                        return -1;
                    }
                    final ContigNameConverter contigNameConverter = ContigNameConverter.fromOneDictionary(dict);
                    final List<QueryInterval> L = new ArrayList<>();
                    try (BedLineReader br = new BedLineReader(this.includeBed)) {
                        while (br.hasNext()) {
                            final BedLine bed = br.next();
                            final String ctg = contigNameConverter.apply(bed.getContig());
                            if (StringUtils.isBlank(ctg))
                                continue;
                            final int tid = dict.getSequenceIndex(ctg);
                            if (tid < 0)
                                continue;
                            L.add(new QueryInterval(tid, bed.getStart(), bed.getEnd()));
                        }
                    }
                    intervals = QueryInterval.optimizeIntervals(L.toArray(new QueryInterval[L.size()]));
                } else {
                    intervals = null;
                }
                Integer minCov = null;
                Integer maxCov = null;
                ContigPos maxCovPosition = null;
                long count_raw_bases = 0L;
                long count_bases = 0L;
                long sum_coverage = 0L;
                final DiscreteMedian<Integer> discreteMedian_wg = new DiscreteMedian<>();
                final Counter<RangeOfIntegers.Range> countMap_wg = new Counter<>();
                final String sample = header.getReadGroups().stream().map(RG -> RG.getSample()).filter(S -> !StringUtils.isBlank(S)).findFirst().orElse(path.toString());
                int[] coverage = null;
                String prevContig = null;
                BitSet mask = null;
                final ProgressFactory.Watcher<SAMRecord> progress = ProgressFactory.newInstance().dictionary(dict).logger(LOG).build();
                try (CloseableIterator<SAMRecord> iter = intervals == null ? sr.iterator() : sr.queryOverlapping(intervals)) {
                    for (; ; ) {
                        final SAMRecord rec = iter.hasNext() ? progress.apply(iter.next()) : null;
                        if (rec != null) {
                            if (!SAMRecordDefaultFilter.accept(rec, this.mapping_quality))
                                continue;
                            if (rejectContigSet.contains(rec.getContig()))
                                continue;
                        }
                        if (rec == null || !rec.getContig().equals(prevContig)) {
                            if (coverage != null) {
                                // DUMP
                                long count_bases_ctg = 0L;
                                long sum_coverage_ctg = 0L;
                                Integer minV_ctg = null;
                                Integer maxV_ctg = null;
                                ContigPos maxPos_ctg = null;
                                final DiscreteMedian<Integer> discreteMedian_ctg = new DiscreteMedian<>();
                                final Counter<RangeOfIntegers.Range> countMap_ctg = new Counter<>();
                                for (int i = 0; i < coverage.length; i++) {
                                    if (mask.get(i))
                                        continue;
                                    final int covi = coverage[i];
                                    if (covi > this.max_depth)
                                        continue;
                                    if (minV_ctg == null || minV_ctg.intValue() > covi)
                                        minV_ctg = covi;
                                    if (maxV_ctg == null || maxV_ctg.intValue() < covi) {
                                        maxV_ctg = covi;
                                        maxPos_ctg = new ContigPos(prevContig, i + 1);
                                    }
                                    countMap_ctg.incr(this.summaryCov.getRange(covi));
                                    count_bases_ctg++;
                                    sum_coverage_ctg += covi;
                                    discreteMedian_ctg.add(covi);
                                }
                                out.print(path);
                                out.print("\t");
                                out.print(sample);
                                out.print("\t");
                                out.print(prevContig);
                                out.print("\t");
                                out.print(coverage.length);
                                out.print("\t");
                                out.print(count_bases_ctg);
                                out.print("\t");
                                out.print(sum_coverage_ctg);
                                out.print("\t");
                                if (count_bases_ctg > 0) {
                                    out.printf("%.2f", sum_coverage_ctg / (double) count_bases_ctg);
                                } else {
                                    out.print("N/A");
                                }
                                out.print("\t");
                                final OptionalDouble median = discreteMedian_ctg.getMedian();
                                if (median.isPresent()) {
                                    out.print(median.getAsDouble());
                                } else {
                                    out.print("N/A");
                                }
                                out.print("\t");
                                if (minV_ctg != null) {
                                    out.print(minV_ctg);
                                } else {
                                    out.print("N/A");
                                }
                                out.print("\t");
                                if (maxV_ctg != null) {
                                    out.print(maxV_ctg);
                                    out.print("\t");
                                    out.print(maxPos_ctg);
                                } else {
                                    out.print("N/A\tN/A");
                                }
                                for (final RangeOfIntegers.Range r : this.summaryCov.getRanges()) {
                                    if (r.getMinInclusive() == null)
                                        continue;
                                    out.print("\t");
                                    out.print(countMap_ctg.count(r));
                                    if (!countMap_ctg.isEmpty()) {
                                        out.print(" ");
                                        out.printf("(%.2f%%)", (countMap_ctg.count(r) / (countMap_ctg.getTotal() * 1.0)) * 100.0);
                                    }
                                }
                                out.println();
                                if (minCov == null || (minV_ctg != null && minV_ctg.compareTo(minCov) < 0))
                                    minCov = minV_ctg;
                                if (maxCov == null || (maxV_ctg != null && maxV_ctg.compareTo(maxCov) > 0)) {
                                    maxCov = maxV_ctg;
                                    maxCovPosition = maxPos_ctg;
                                }
                                count_bases += count_bases_ctg;
                                sum_coverage += sum_coverage_ctg;
                                count_raw_bases += coverage.length;
                                discreteMedian_wg.add(discreteMedian_ctg);
                                countMap_wg.putAll(countMap_ctg);
                            }
                            coverage = null;
                            mask = null;
                            // /
                            System.gc();
                            if (rec == null)
                                break;
                            final SAMSequenceRecord ssr = Objects.requireNonNull(dict.getSequence(rec.getContig()));
                            coverage = new int[ssr.getSequenceLength()];
                            mask = new BitSet(ssr.getSequenceLength());
                            if (this.auto_mask && referenceSequenceFile != null) {
                                final byte[] refSeq = Objects.requireNonNull(referenceSequenceFile.getSequence(ssr.getSequenceName())).getBases();
                                for (int i = 0; i < refSeq.length; i++) {
                                    if (AcidNucleics.isATGC(refSeq[i]))
                                        continue;
                                    mask.set(i);
                                }
                            }
                            /* read mask */
                            if (this.maskBed != null) {
                                final ContigNameConverter contigNameConverter = ContigNameConverter.fromOneDictionary(dict);
                                try (BedLineReader br = new BedLineReader(this.maskBed)) {
                                    while (br.hasNext()) {
                                        final BedLine bed = br.next();
                                        if (bed == null)
                                            continue;
                                        String ctg = contigNameConverter.apply(bed.getContig());
                                        if (StringUtils.isBlank(ctg))
                                            continue;
                                        if (!rec.getContig().equals(ctg))
                                            continue;
                                        for (int p1 = bed.getStart(); p1 <= bed.getEnd() && p1 <= coverage.length; ++p1) {
                                            mask.set(p1 - 1);
                                        }
                                    }
                                }
                            } else if (this.includeBed != null) {
                                final List<Locatable> list = new ArrayList<>();
                                final ContigNameConverter contigNameConverter = ContigNameConverter.fromOneDictionary(dict);
                                try (BedLineReader br = new BedLineReader(this.includeBed)) {
                                    while (br.hasNext()) {
                                        final BedLine bed = br.next();
                                        if (bed == null)
                                            continue;
                                        final String ctg = contigNameConverter.apply(bed.getContig());
                                        if (StringUtils.isBlank(ctg))
                                            continue;
                                        if (!rec.getContig().equals(ctg))
                                            continue;
                                        list.add(new SimpleInterval(ctg, bed.getStart(), bed.getEnd()));
                                    }
                                }
                                // sort on starts
                                Collections.sort(list, (A, B) -> Integer.compare(A.getStart(), B.getStart()));
                                int p1 = 1;
                                while (p1 <= coverage.length) {
                                    while (!list.isEmpty() && list.get(0).getEnd() < p1) {
                                        list.remove(0);
                                    }
                                    if (!list.isEmpty() && list.get(0).getStart() <= p1 && p1 <= list.get(0).getEnd()) {
                                        ++p1;
                                        continue;
                                    }
                                    mask.set(p1 - 1);
                                    p1++;
                                }
                            }
                            prevContig = rec.getContig();
                        }
                        int max_end1 = coverage.length;
                        if (!this.disable_paired_overlap_flag && rec.getReadPairedFlag() && !rec.getMateUnmappedFlag() && rec.getReferenceIndex().equals(rec.getMateReferenceIndex()) && rec.getAlignmentStart() < rec.getMateAlignmentStart() && rec.getAlignmentEnd() > rec.getMateAlignmentStart()) {
                            max_end1 = rec.getMateAlignmentStart() - 1;
                        }
                        for (final AlignmentBlock block : rec.getAlignmentBlocks()) {
                            final int pos1 = block.getReferenceStart();
                            final int len = block.getLength();
                            for (int i = 0; i < len; i++) {
                                if (pos1 + i - 1 >= 0 && pos1 + i <= max_end1) {
                                    coverage[pos1 + i - 1]++;
                                }
                            }
                        }
                    }
                /* end rec */
                }
                /* end iter */
                progress.close();
                out.print(path);
                out.print("\t");
                out.print(sample);
                out.print("\t");
                out.print(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME);
                out.print("\t");
                out.print(count_raw_bases);
                out.print("\t");
                out.print(count_bases);
                out.print("\t");
                out.print(sum_coverage);
                out.print("\t");
                if (count_bases > 0) {
                    out.printf("%.2f", sum_coverage / (double) count_bases);
                } else {
                    out.print("N/A");
                }
                out.print("\t");
                final OptionalDouble median = discreteMedian_wg.getMedian();
                if (median.isPresent()) {
                    out.print(median.getAsDouble());
                } else {
                    out.print("N/A");
                }
                out.print("\t");
                if (minCov != null) {
                    out.print(minCov);
                } else {
                    out.print("N/A");
                }
                out.print("\t");
                if (maxCov != null) {
                    out.print(maxCov + "\t" + maxCovPosition);
                } else {
                    out.print("N/A\tN/A");
                }
                for (final RangeOfIntegers.Range r : this.summaryCov.getRanges()) {
                    if (r.getMinInclusive() == null)
                        continue;
                    out.print("\t");
                    out.print(countMap_wg.count(r));
                    if (!countMap_wg.isEmpty()) {
                        out.print(" ");
                        out.printf("(%.2f%%)", (countMap_wg.count(r) / (countMap_wg.getTotal() * 1.0)) * 100.0);
                    }
                }
                out.println();
            }
        }
        out.flush();
        out.close();
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(referenceSequenceFile);
    }
}