Examples with FilterIterator com.github.lindenb.jvarkit.util.iterator.FilterIterator used on opensource projects

Example 1 with FilterIterator

use of com.github.lindenb.jvarkit.util.iterator.FilterIterator in project jvarkit by lindenb.

the class SamTranslocations method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.max_distance <= 0) {
        LOG.error("max_distance <=0 (" + max_distance + ")");
        return -1;
    }
    PrintWriter pw = null;
    ConcatSam.ConcatSamIterator samIter = null;
    ForwardPeekIterator<SAMRecord> forwardPeekIterator = null;
    try {
        samIter = new ConcatSam.Factory().addInterval(this.region_str).open(args);
        final SAMSequenceDictionary dict = samIter.getFileHeader().getSequenceDictionary();
        if (dict.size() < 2) {
            LOG.error("Not enough contigs in sequence dictionary. Expected at least 2.");
            return -1;
        }
        forwardPeekIterator = new ForwardPeekIteratorImpl<>(new FilterIterator<>(samIter, rec -> {
            if (rec.getReadUnmappedFlag())
                return false;
            if (!rec.getReadPairedFlag())
                return false;
            if (rec.getMateUnmappedFlag())
                return false;
            final int tid1 = rec.getReferenceIndex();
            final int tid2 = rec.getMateReferenceIndex();
            if (tid1 == tid2)
                return false;
            if (this.samRecordFilter.filterOut(rec))
                return false;
            return true;
        }));
        pw = openFileOrStdoutAsPrintWriter(this.outputFile);
        pw.print("#chrom1");
        pw.print('\t');
        pw.print("chrom1-start");
        pw.print('\t');
        pw.print("chrom1-end");
        pw.print('\t');
        pw.print("middle1\tstrand_plus_before_mid1_count\tstrand_plus_before_mid1_percent\tstrand_minus_after_mid1_count\tstrand_minus_after_mid1_percent");
        pw.print('\t');
        pw.print("chrom2");
        pw.print('\t');
        pw.print("chrom2-start");
        pw.print('\t');
        pw.print("chrom2-end");
        pw.print('\t');
        pw.print("middle2\tstrand_plus_before_mid2_count\tstrand_plus_before_mid2_percent\tstrand_minus_after_mid2_count\tstrand_minus_after_mid2_percent");
        pw.print('\t');
        pw.print("count-reads");
        pw.print('\t');
        pw.print("count-clipped");
        pw.print('\t');
        pw.print("partition");
        pw.println();
        final Map<String, PartitionState> partition2state = new HashMap<>();
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(dict).logger(LOG);
        while (forwardPeekIterator.hasNext()) {
            final SAMRecord rec = progress.watch(forwardPeekIterator.next());
            final String partition = this.samRecordPartition.getPartion(rec, "N/A");
            PartitionState partitionState = partition2state.get(partition);
            if (partitionState == null) {
                partitionState = new PartitionState(partition);
                partition2state.put(partition, partitionState);
            }
            if (partitionState.last_rec != null) {
                if (partitionState.last_rec == rec) {
                    // reset last
                    partitionState.last_rec = null;
                }
                continue;
            }
            // searching for -->
            if (rec.getReadNegativeStrandFlag())
                continue;
            // find forward records
            final List<SAMRecord> positiveStrandList = new ArrayList<>();
            positiveStrandList.add(rec);
            int x = 0;
            for (; ; ) {
                final SAMRecord rec2 = forwardPeekIterator.peek(x);
                if (rec2 == null) {
                    break;
                }
                if (!rec.getReferenceIndex().equals(rec2.getReferenceIndex())) {
                    break;
                }
                if (rec2.getStart() - rec.getEnd() > this.max_distance) {
                    break;
                }
                if (rec2.getReadNegativeStrandFlag() || Math.abs(rec2.getEnd() - rec.getEnd()) > this.fully_distance || !rec2.getMateReferenceName().equals(rec.getMateReferenceName())) {
                    ++x;
                    continue;
                }
                positiveStrandList.add(rec2);
                partitionState.last_rec = rec2;
                ++x;
            }
            if (positiveStrandList.size() < this.min_count_forward) {
                partitionState.last_rec = null;
                continue;
            }
            // find reverse records
            x = 0;
            final List<SAMRecord> negativeStrandList = new ArrayList<>();
            for (; ; ) {
                final SAMRecord rec2 = forwardPeekIterator.peek(x);
                if (rec2 == null) {
                    break;
                }
                if (!rec.getReferenceIndex().equals(rec2.getReferenceIndex())) {
                    break;
                }
                if (rec2.getStart() - rec.getEnd() > this.max_distance) {
                    break;
                }
                if (!rec2.getReadNegativeStrandFlag() || (rec2.getStart() < rec.getEnd() && (rec.getEnd() - rec2.getStart()) > this.fully_distance) || !rec2.getMateReferenceName().equals(rec.getMateReferenceName())) {
                    ++x;
                    continue;
                }
                negativeStrandList.add(rec2);
                ++x;
            }
            if (negativeStrandList.size() < this.min_count_forward) {
                partitionState.last_rec = null;
                continue;
            }
            final int start1 = (int) Percentile.median().evaluate(positiveStrandList.stream().mapToInt(R -> R.getEnd()));
            final int end1 = (int) Percentile.median().evaluate(negativeStrandList.stream().mapToInt(R -> R.getStart()));
            final int mid1 = (start1 + end1) / 2;
            final int mid2 = (int) Percentile.median().evaluate(negativeStrandList.stream().mapToInt(R -> R.getMateAlignmentStart()));
            pw.print(rec.getReferenceName());
            pw.print('\t');
            pw.print(positiveStrandList.stream().mapToInt(R -> R.getEnd()).max().getAsInt());
            pw.print('\t');
            pw.print(negativeStrandList.stream().mapToInt(R -> R.getStart()).min().getAsInt());
            pw.print('\t');
            pw.print(mid1);
            pw.print('\t');
            pw.print(positiveStrandList.stream().filter(R -> R.getEnd() <= mid1).count());
            pw.print('\t');
            pw.print((int) (100.0 * (positiveStrandList.stream().filter(R -> R.getEnd() <= mid1).count()) / positiveStrandList.size()));
            pw.print('\t');
            pw.print(negativeStrandList.stream().filter(R -> R.getStart() >= mid1).count());
            pw.print('\t');
            pw.print((int) (100.0 * (negativeStrandList.stream().filter(R -> R.getStart() >= mid1).count()) / positiveStrandList.size()));
            pw.print('\t');
            pw.print(rec.getMateReferenceName());
            pw.print('\t');
            pw.print(negativeStrandList.stream().mapToInt(R -> R.getMateAlignmentStart()).min().getAsInt());
            pw.print('\t');
            pw.print(negativeStrandList.stream().mapToInt(R -> R.getMateAlignmentStart()).max().getAsInt());
            pw.print('\t');
            pw.print(mid2);
            pw.print('\t');
            pw.print(negativeStrandList.stream().filter(R -> R.getMateAlignmentStart() <= mid2).count());
            pw.print('\t');
            pw.print((int) (100.0 * (negativeStrandList.stream().filter(R -> R.getMateAlignmentStart() <= mid2).count()) / negativeStrandList.size()));
            pw.print('\t');
            pw.print(negativeStrandList.stream().filter(R -> R.getMateAlignmentStart() >= mid2).count());
            pw.print('\t');
            pw.print((int) (100.0 * (negativeStrandList.stream().filter(R -> R.getMateAlignmentStart() >= mid2).count()) / negativeStrandList.size()));
            pw.print('\t');
            pw.print(positiveStrandList.size() + negativeStrandList.size());
            pw.print('\t');
            pw.print(positiveStrandList.stream().filter(R -> R.getCigar() != null && R.getCigar().isClipped()).count() + negativeStrandList.stream().filter(R -> R.getCigar() != null && R.getCigar().isClipped()).count());
            pw.print('\t');
            pw.print(partition);
            pw.println();
        }
        progress.finish();
        forwardPeekIterator.close();
        forwardPeekIterator = null;
        samIter.close();
        samIter = null;
        pw.flush();
        pw.close();
        pw = null;
        return 0;
    } catch (final Throwable err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(forwardPeekIterator);
        CloserUtil.close(samIter);
        CloserUtil.close(pw);
    }
}

Example 2 with FilterIterator

use of com.github.lindenb.jvarkit.util.iterator.FilterIterator in project jvarkit by lindenb.

the class Biostar78285 method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.gc_percent_window < 1) {
        LOG.error("Bad GC% window size:" + this.gc_percent_window);
        return -1;
    }
    final List<File> bamFiles = IOUtil.unrollFiles(args.stream().map(F -> new File(F)).collect(Collectors.toCollection(HashSet::new)), ".bam");
    SAMSequenceDictionary dict = null;
    final List<SamReader> samReaders = new ArrayList<>();
    final List<CloseableIterator<SAMRecord>> samIterators = new ArrayList<>();
    final TreeSet<String> samples = new TreeSet<>();
    final String DEFAULT_PARTITION = "UNDEFINED_PARTITION";
    IndexedFastaSequenceFile indexedFastaSequenceFile = null;
    VariantContextWriter out = null;
    try {
        final SamReaderFactory samReaderFactory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT);
        for (final File bamFile : bamFiles) {
            LOG.info("Opening " + bamFile);
            final SamReader samReader = samReaderFactory.open(bamFile);
            samReaders.add(samReader);
            final SAMFileHeader header = samReader.getFileHeader();
            if (header == null) {
                LOG.error("No header in " + bamFile);
                return -1;
            }
            if (header.getSortOrder() != SortOrder.coordinate) {
                LOG.error("Sam file " + bamFile + " is not sorted on coordinate :" + header.getSortOrder());
                return -1;
            }
            samples.addAll(header.getReadGroups().stream().map(RG -> this.partition.apply(RG, DEFAULT_PARTITION)).collect(Collectors.toSet()));
            final SAMSequenceDictionary currDict = header.getSequenceDictionary();
            if (currDict == null) {
                LOG.error("SamFile doesn't contain a SAMSequenceDictionary : " + bamFile);
                return -1;
            }
            if (dict == null) {
                dict = currDict;
            } else if (!SequenceUtil.areSequenceDictionariesEqual(dict, currDict)) {
                LOG.error(JvarkitException.DictionariesAreNotTheSame.getMessage(dict, currDict));
                return -1;
            }
        }
        if (samReaders.isEmpty()) {
            LOG.error("no bam");
            return -1;
        }
        if (dict == null) {
            LOG.error("no dictionary");
            return -1;
        }
        final QueryInterval[] intervals;
        if (this.captureBed != null) {
            LOG.info("Opening " + this.captureBed);
            ContigNameConverter.setDefaultAliases(dict);
            final List<QueryInterval> L = new ArrayList<>();
            final BedLineCodec codec = new BedLineCodec();
            final LineIterator li = IOUtils.openFileForLineIterator(this.captureBed);
            while (li.hasNext()) {
                final BedLine bed = codec.decode(li.next());
                if (bed == null)
                    continue;
                final QueryInterval q = bed.toQueryInterval(dict);
                L.add(q);
            }
            CloserUtil.close(li);
            intervals = QueryInterval.optimizeIntervals(L.toArray(new QueryInterval[L.size()]));
        } else {
            intervals = null;
        }
        for (final SamReader samReader : samReaders) {
            LOG.info("querying " + samReader.getResourceDescription());
            final CloseableIterator<SAMRecord> iter;
            if (intervals == null) {
                iter = samReader.iterator();
            } else {
                iter = samReader.queryOverlapping(intervals);
            }
            samIterators.add(new FilterIterator<SAMRecord>(iter, R -> !R.getReadUnmappedFlag() && !filter.filterOut(R)));
        }
        if (this.refFile != null) {
            LOG.info("opening " + refFile);
            indexedFastaSequenceFile = new IndexedFastaSequenceFile(this.refFile);
            final SAMSequenceDictionary refdict = indexedFastaSequenceFile.getSequenceDictionary();
            ContigNameConverter.setDefaultAliases(refdict);
            if (refdict == null) {
                throw new JvarkitException.FastaDictionaryMissing(this.refFile);
            }
            if (!SequenceUtil.areSequenceDictionariesEqual(dict, refdict)) {
                LOG.error(JvarkitException.DictionariesAreNotTheSame.getMessage(dict, refdict));
                return -1;
            }
        }
        out = openVariantContextWriter(this.outputFile);
        final Set<VCFHeaderLine> metaData = new HashSet<>();
        VCFStandardHeaderLines.addStandardFormatLines(metaData, true, VCFConstants.DEPTH_KEY, VCFConstants.GENOTYPE_KEY);
        VCFStandardHeaderLines.addStandardInfoLines(metaData, true, VCFConstants.DEPTH_KEY);
        metaData.add(new VCFFormatHeaderLine("DF", 1, VCFHeaderLineType.Integer, "Number of Reads on plus strand"));
        metaData.add(new VCFFormatHeaderLine("DR", 1, VCFHeaderLineType.Integer, "Number of Reads on minus strand"));
        metaData.add(new VCFInfoHeaderLine("AVG_DP", 1, VCFHeaderLineType.Float, "Mean depth"));
        metaData.add(new VCFInfoHeaderLine("MEDIAN_DP", 1, VCFHeaderLineType.Float, "Median depth"));
        metaData.add(new VCFInfoHeaderLine("MIN_DP", 1, VCFHeaderLineType.Integer, "Min depth"));
        metaData.add(new VCFInfoHeaderLine("MAX_DP", 1, VCFHeaderLineType.Integer, "Max depth"));
        metaData.add(new VCFHeaderLine(Biostar78285.class.getSimpleName() + ".SamFilter", this.filter.toString()));
        for (final Integer treshold : this.minDepthTresholds) {
            metaData.add(new VCFFilterHeaderLine("DP_LT_" + treshold, "All  genotypes have DP< " + treshold));
            metaData.add(new VCFInfoHeaderLine("NUM_DP_LT_" + treshold, 1, VCFHeaderLineType.Integer, "Number of genotypes having DP< " + treshold));
            metaData.add(new VCFInfoHeaderLine("FRACT_DP_LT_" + treshold, 1, VCFHeaderLineType.Float, "Fraction of genotypes having DP< " + treshold));
        }
        if (indexedFastaSequenceFile != null) {
            metaData.add(new VCFInfoHeaderLine("GC_PERCENT", 1, VCFHeaderLineType.Integer, "GC% window_size:" + this.gc_percent_window));
        }
        final List<Allele> refAlleles = Collections.singletonList(Allele.create("N", true));
        final List<Allele> NO_CALLS = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
        final VCFHeader vcfHeader = new VCFHeader(metaData, samples);
        vcfHeader.setSequenceDictionary(dict);
        out.writeHeader(vcfHeader);
        final SAMRecordCoordinateComparator samRecordCoordinateComparator = new SAMRecordCoordinateComparator();
        final PeekableIterator<SAMRecord> peekIter = new PeekableIterator<>(new MergingIterator<>((R1, R2) -> samRecordCoordinateComparator.fileOrderCompare(R1, R2), samIterators));
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(dict);
        for (final SAMSequenceRecord ssr : dict.getSequences()) {
            final IntervalTree<Boolean> capturePos;
            if (intervals != null) {
                if (!Arrays.stream(intervals).anyMatch(I -> I.referenceIndex == ssr.getSequenceIndex())) {
                    continue;
                }
                capturePos = new IntervalTree<>();
                Arrays.stream(intervals).filter(I -> I.referenceIndex == ssr.getSequenceIndex()).forEach(I -> capturePos.put(I.start, I.end, true));
                ;
            } else {
                capturePos = null;
            }
            final GenomicSequence genomicSequence;
            if (indexedFastaSequenceFile != null && indexedFastaSequenceFile.getSequenceDictionary().getSequence(ssr.getSequenceName()) != null) {
                genomicSequence = new GenomicSequence(indexedFastaSequenceFile, ssr.getSequenceName());
            } else {
                genomicSequence = null;
            }
            final List<SAMRecord> buffer = new ArrayList<>();
            for (int ssr_pos = 1; ssr_pos <= ssr.getSequenceLength(); ++ssr_pos) {
                if (capturePos != null && !capturePos.overlappers(ssr_pos, ssr_pos).hasNext())
                    continue;
                progress.watch(ssr.getSequenceName(), ssr_pos);
                while (peekIter.hasNext()) {
                    final SAMRecord rec = peekIter.peek();
                    if (rec.getReadUnmappedFlag()) {
                        // consumme
                        peekIter.next();
                        continue;
                    }
                    if (this.filter.filterOut(rec)) {
                        // consumme
                        peekIter.next();
                        continue;
                    }
                    if (rec.getReferenceIndex() < ssr.getSequenceIndex()) {
                        throw new IllegalStateException("should not happen");
                    }
                    if (rec.getReferenceIndex() > ssr.getSequenceIndex()) {
                        break;
                    }
                    if (rec.getAlignmentEnd() < ssr_pos) {
                        throw new IllegalStateException("should not happen");
                    }
                    if (rec.getAlignmentStart() > ssr_pos) {
                        break;
                    }
                    buffer.add(peekIter.next());
                }
                int x = 0;
                while (x < buffer.size()) {
                    final SAMRecord R = buffer.get(x);
                    if (R.getReferenceIndex() != ssr.getSequenceIndex() || R.getAlignmentEnd() < ssr_pos) {
                        buffer.remove(x);
                    } else {
                        x++;
                    }
                }
                final Map<String, PosInfo> count = samples.stream().map(S -> new PosInfo(S)).collect(Collectors.toMap(P -> P.sample, Function.identity()));
                for (final SAMRecord rec : buffer) {
                    if (rec.getReferenceIndex() != ssr.getSequenceIndex())
                        throw new IllegalStateException("should not happen");
                    if (rec.getAlignmentEnd() < ssr_pos)
                        continue;
                    if (rec.getAlignmentStart() > ssr_pos)
                        continue;
                    final Cigar cigar = rec.getCigar();
                    if (cigar == null)
                        continue;
                    int refpos = rec.getAlignmentStart();
                    final String sample = this.partition.getPartion(rec, DEFAULT_PARTITION);
                    for (final CigarElement ce : cigar.getCigarElements()) {
                        if (refpos > ssr_pos)
                            break;
                        final CigarOperator op = ce.getOperator();
                        if (op.consumesReferenceBases()) {
                            if (op.consumesReadBases()) {
                                if (refpos <= ssr_pos && ssr_pos <= refpos + ce.getLength()) {
                                    final PosInfo posInfo = count.get(sample);
                                    if (posInfo != null) {
                                        posInfo.dp++;
                                        if (rec.getReadNegativeStrandFlag()) {
                                            posInfo.negative_strand++;
                                        }
                                    }
                                    break;
                                }
                            }
                            refpos += ce.getLength();
                        }
                    }
                }
                final VariantContextBuilder vcb = new VariantContextBuilder();
                final Set<String> filters = new HashSet<>();
                vcb.chr(ssr.getSequenceName());
                vcb.start(ssr_pos);
                vcb.stop(ssr_pos);
                if (genomicSequence == null) {
                    vcb.alleles(refAlleles);
                } else {
                    vcb.alleles(Collections.singletonList(Allele.create((byte) genomicSequence.charAt(ssr_pos - 1), true)));
                    final GenomicSequence.GCPercent gcp = genomicSequence.getGCPercent(Math.max((ssr_pos - 1) - this.gc_percent_window, 0), Math.min(ssr_pos + this.gc_percent_window, ssr.getSequenceLength()));
                    if (!gcp.isEmpty()) {
                        vcb.attribute("GC_PERCENT", gcp.getGCPercentAsInteger());
                    }
                }
                vcb.attribute(VCFConstants.DEPTH_KEY, (int) count.values().stream().mapToInt(S -> S.dp).sum());
                vcb.genotypes(count.values().stream().map(C -> new GenotypeBuilder(C.sample, NO_CALLS).DP((int) C.dp).attribute("DR", C.negative_strand).attribute("DF", C.dp - C.negative_strand).make()).collect(Collectors.toList()));
                for (final Integer treshold : this.minDepthTresholds) {
                    final int count_lt = (int) count.values().stream().filter(S -> S.dp < treshold).count();
                    if (count_lt == samples.size()) {
                        filters.add("DP_LT_" + treshold);
                    }
                    vcb.attribute("NUM_DP_LT_" + treshold, count_lt);
                    if (!samples.isEmpty()) {
                        vcb.attribute("FRACT_DP_LT_" + treshold, count_lt / (float) samples.size());
                    }
                }
                if (!samples.isEmpty()) {
                    final int[] array = count.values().stream().mapToInt(S -> S.dp).toArray();
                    vcb.attribute("AVG_DP", Percentile.average().evaluate(array));
                    vcb.attribute("MEDIAN_DP", Percentile.median().evaluate(array));
                    vcb.attribute("MIN_DP", (int) Percentile.min().evaluate(array));
                    vcb.attribute("MAX_DP", (int) Percentile.max().evaluate(array));
                }
                if (filters.isEmpty()) {
                    vcb.passFilters();
                } else {
                    vcb.filters(filters);
                }
                out.add(vcb.make());
            }
        }
        progress.finish();
        peekIter.close();
        out.close();
        out = null;
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(out);
        CloserUtil.close(samIterators);
        CloserUtil.close(samReaders);
        CloserUtil.close(indexedFastaSequenceFile);
    }
}