Examples with NullOuputStream com.github.lindenb.jvarkit.io.NullOuputStream used on opensource projects

Example 6 with NullOuputStream

use of com.github.lindenb.jvarkit.io.NullOuputStream in project jvarkit by lindenb.

the class ForkVcf method doWork.

@Override
public int doWork(List<String> args) {
    if (this.outputFile == null || !this.outputFile.getName().contains(REPLACE_GROUPID)) {
        LOG.error("Output file pattern undefined or doesn't contain " + REPLACE_GROUPID + " : " + this.outputFile);
        return -1;
    }
    if (!(this.outputFile.getName().endsWith(".vcf") || this.outputFile.getName().endsWith(".vcf.gz"))) {
        LOG.error("output file must end with '.vcf' or '.vcf.gz'");
        return -1;
    }
    if (this.number_of_files <= 0) {
        LOG.error("Bad value for number of files:" + this.number_of_files);
        return -1;
    }
    BufferedReader r = null;
    VcfIterator in = null;
    PrintWriter manifestWriter = null;
    final List<SplitGroup> groups = new ArrayList<>();
    VCFBuffer vcfBuffer = null;
    try {
        in = openVcfIterator(oneFileOrNull(args));
        manifestWriter = (this.manifestFile == null ? new PrintWriter(new NullOuputStream()) : IOUtils.openFileForPrintWriter(this.manifestFile));
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(in.getHeader());
        if (!this.split_by_chunk) {
            while (groups.size() < this.number_of_files) {
                final SplitGroup sg = new SplitGroup(groups.size() + 1);
                sg.open(in.getHeader());
                manifestWriter.println(sg.getFile().getPath());
                groups.add(sg);
            }
            int idx = 0;
            while (in.hasNext()) {
                final VariantContext ctx = progress.watch(in.next());
                groups.get(idx % this.number_of_files)._writer.add(ctx);
                ++idx;
            }
            in.close();
        } else {
            long count_variants = 0;
            vcfBuffer = new VCFBuffer(this.maxRecordsInRam, this.tmpDir);
            vcfBuffer.writeHeader(in.getHeader());
            while (in.hasNext()) {
                final VariantContext ctx = progress.watch(in.next());
                vcfBuffer.add(ctx);
                ++count_variants;
            }
            in.close();
            final long variant_per_file = Math.max(1L, (long) Math.ceil(count_variants / (double) this.number_of_files));
            LOG.info("done buffering. n=" + count_variants + " now forking " + variant_per_file + " variants for " + this.number_of_files + " files.");
            VcfIterator iter2 = vcfBuffer.iterator();
            long count_ctx = 0L;
            while (iter2.hasNext()) {
                if (groups.isEmpty() || count_ctx >= variant_per_file) {
                    if (!groups.isEmpty())
                        groups.get(groups.size() - 1).close();
                    final SplitGroup last = new SplitGroup(groups.size() + 1);
                    last.open(in.getHeader());
                    manifestWriter.println(last.getFile().getPath());
                    groups.add(last);
                    count_ctx = 0;
                }
                final VariantContext ctx = iter2.next();
                groups.get(groups.size() - 1)._writer.add(ctx);
                count_ctx++;
            }
            iter2.close();
            vcfBuffer.close();
            vcfBuffer.dispose();
            vcfBuffer = null;
            // save remaining empty VCFs
            while (groups.size() < this.number_of_files) {
                LOG.info("creating empty vcf");
                final SplitGroup sg = new SplitGroup(groups.size() + 1);
                sg.open(in.getHeader());
                manifestWriter.println(sg.getFile().getPath());
                sg.close();
                groups.add(sg);
            }
        }
        progress.finish();
        for (final SplitGroup g : groups) {
            g.close();
        }
        manifestWriter.flush();
        manifestWriter.close();
        manifestWriter = null;
        return RETURN_OK;
    } catch (final Exception err) {
        LOG.error(err);
        for (final SplitGroup g : groups) {
            CloserUtil.close(g);
            if (in != null)
                g.getFile().delete();
        }
        return -1;
    } finally {
        if (vcfBuffer != null)
            vcfBuffer.dispose();
        CloserUtil.close(r);
        CloserUtil.close(in);
        IOUtils.flush(manifestWriter);
        CloserUtil.close(manifestWriter);
    }
}

Example 7 with NullOuputStream

use of com.github.lindenb.jvarkit.io.NullOuputStream in project jvarkit by lindenb.

the class VcfLoopOverGenes method doWork.

@SuppressWarnings("resource")
@Override
public int doWork(final List<String> args) {
    PrintWriter pw = null;
    VCFFileReader vcfFileReader = null;
    CloseableIterator<VariantContext> iter = null;
    CloseableIterator<GeneLoc> iter2 = null;
    BufferedReader br = null;
    ArchiveFactory archive = null;
    try {
        final File vcf = new File(oneAndOnlyOneFile(args));
        vcfFileReader = new VCFFileReader(vcf, (this.geneFile != null || !StringUtil.isBlank(this.regionStr)));
        this.dictionary = vcfFileReader.getFileHeader().getSequenceDictionary();
        if (this.dictionary == null) {
            throw new JvarkitException.VcfDictionaryMissing(vcf);
        }
        final VcfTools tools = new VcfTools(vcfFileReader.getFileHeader());
        if (!this.prefix.isEmpty() && !this.prefix.endsWith(".")) {
            this.prefix += ".";
        }
        if (this.geneFile == null) {
            final SortingCollection<GeneLoc> sortingCollection = SortingCollection.newInstance(GeneLoc.class, new GeneLocCodec(), (A, B) -> A.compareTo(B), this.writingSortingCollection.getMaxRecordsInRam(), this.writingSortingCollection.getTmpPaths());
            sortingCollection.setDestructiveIteration(true);
            if (StringUtil.isBlank(this.regionStr)) {
                iter = vcfFileReader.iterator();
            } else {
                final IntervalParser parser = new IntervalParser(this.dictionary);
                parser.setContigNameIsWholeContig(true);
                final Interval interval = parser.parse(this.regionStr);
                if (interval == null) {
                    LOG.error("Cannot parse interval " + this.regionStr);
                    return -1;
                }
                iter = vcfFileReader.query(interval.getContig(), interval.getStart(), interval.getEnd());
            }
            final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(vcfFileReader.getFileHeader()).logger(LOG);
            if (this.splitMethod.equals(SplitMethod.Annotations)) {
                while (iter.hasNext()) {
                    final VariantContext ctx = progress.watch(iter.next());
                    for (final AnnPredictionParser.AnnPrediction pred : tools.getAnnPredictionParser().getPredictions(ctx)) {
                        if (this.snpEffNoIntergenic && pred.isIntergenicRegion()) {
                            continue;
                        }
                        if (!StringUtil.isBlank(pred.getGeneName())) {
                            sortingCollection.add(create(ctx, pred.getGeneName(), SourceType.ANN_GeneName));
                        }
                        if (!StringUtil.isBlank(pred.getGeneId())) {
                            sortingCollection.add(create(ctx, pred.getGeneId(), SourceType.ANN_GeneID));
                        }
                        if (!StringUtil.isBlank(pred.getFeatureId())) {
                            sortingCollection.add(create(ctx, pred.getFeatureId(), SourceType.ANN_FeatureID));
                        }
                    }
                    for (final VepPredictionParser.VepPrediction pred : tools.getVepPredictionParser().getPredictions(ctx)) {
                        if (!StringUtil.isBlank(pred.getGene())) {
                            sortingCollection.add(create(ctx, pred.getGene(), SourceType.VEP_Gene));
                        }
                        if (!StringUtil.isBlank(pred.getFeature())) {
                            sortingCollection.add(create(ctx, pred.getFeature(), SourceType.VEP_Feature));
                        }
                        if (!StringUtil.isBlank(pred.getSymbol())) {
                            sortingCollection.add(create(ctx, pred.getSymbol(), SourceType.VEP_Symbol));
                        }
                        if (!StringUtil.isBlank(pred.getHgncId())) {
                            sortingCollection.add(create(ctx, pred.getHgncId(), SourceType.VEP_HgncId));
                        }
                    }
                }
            } else /**
             * split VCF per sliding window of variants
             */
            if (this.splitMethod.equals(SplitMethod.VariantSlidingWindow)) {
                if (this.variantsWinCount < 1) {
                    LOG.error("Bad value for variantsWinCount");
                    return -1;
                }
                if (this.variantsWinShift < 1 || this.variantsWinShift > this.variantsWinCount) {
                    LOG.error("Bad value for variantsWinShift");
                    return -1;
                }
                final List<VariantContext> buffer = new ArrayList<>(this.variantsWinCount);
                /**
                 * routine to dump buffer into sorting collection
                 */
                final Runnable dumpBuffer = () -> {
                    if (buffer.isEmpty())
                        return;
                    final String contig = buffer.get(0).getContig();
                    final int chromStart = buffer.stream().mapToInt(CTX -> CTX.getStart()).min().getAsInt();
                    // use last of start too
                    final int chromEnd0 = buffer.stream().mapToInt(CTX -> CTX.getStart()).max().getAsInt();
                    // final int chromEnd1 = buffer.stream().mapToInt(CTX->CTX.getEnd()).max().getAsInt();
                    final String identifier = contig + "_" + String.format(NUM_FORMAT, chromStart) + "_" + String.format(NUM_FORMAT, chromEnd0);
                    for (final VariantContext ctx : buffer) {
                        sortingCollection.add(create(ctx, identifier, SourceType.SlidingVariants));
                    }
                };
                while (iter.hasNext()) {
                    VariantContext ctx = progress.watch(iter.next());
                    /* reduce the memory footprint for this context */
                    ctx = new VariantContextBuilder(ctx).genotypes(Collections.emptyList()).unfiltered().rmAttributes(new ArrayList<>(ctx.getAttributes().keySet())).make();
                    if (!buffer.isEmpty() && !buffer.get(0).getContig().equals(ctx.getContig())) {
                        dumpBuffer.run();
                        buffer.clear();
                    }
                    buffer.add(ctx);
                    if (buffer.size() >= this.variantsWinCount) {
                        dumpBuffer.run();
                        final int fromIndex = Math.min(this.variantsWinShift, buffer.size());
                        buffer.subList(0, fromIndex).clear();
                    }
                }
                dumpBuffer.run();
                buffer.clear();
            } else if (this.splitMethod.equals(SplitMethod.ContigSlidingWindow)) {
                if (this.contigWinLength < 1) {
                    LOG.error("Bad value for contigWinCount");
                    return -1;
                }
                if (this.contigWinShift < 1 || this.contigWinShift > this.contigWinLength) {
                    LOG.error("Bad value for contigWinShift");
                    return -1;
                }
                while (iter.hasNext()) {
                    VariantContext ctx = progress.watch(iter.next());
                    /* reduce the memory footprint for this context */
                    ctx = new VariantContextBuilder(ctx).genotypes(Collections.emptyList()).unfiltered().rmAttributes(new ArrayList<>(ctx.getAttributes().keySet())).make();
                    int start = 0;
                    while (start <= ctx.getStart()) {
                        if (start + this.contigWinLength >= ctx.getStart()) {
                            final int chromStart = start;
                            final int chromEnd0 = start + this.contigWinLength;
                            final String identifier = ctx.getContig() + "_" + String.format(NUM_FORMAT, chromStart) + "_" + String.format(NUM_FORMAT, chromEnd0);
                            sortingCollection.add(create(ctx, identifier, SourceType.SlidingContig));
                        }
                        start += this.contigWinShift;
                    }
                }
            } else {
                throw new IllegalStateException("No such method: " + this.splitMethod);
            }
            sortingCollection.doneAdding();
            progress.finish();
            iter.close();
            iter = null;
            pw = super.openFileOrStdoutAsPrintWriter(this.outputFile);
            iter2 = sortingCollection.iterator();
            final EqualRangeIterator<GeneLoc> eqiter = new EqualRangeIterator<>(iter2, this.compareGeneName);
            int geneIdentifierId = 0;
            while (eqiter.hasNext()) {
                final List<GeneLoc> gene = eqiter.next();
                pw.print(gene.get(0).contig);
                pw.print('\t');
                // -1 for BED
                pw.print(gene.stream().mapToInt(G -> G.start).min().getAsInt() - 1);
                pw.print('\t');
                pw.print(gene.stream().mapToInt(G -> G.end).max().getAsInt());
                pw.print('\t');
                pw.print(this.prefix + String.format("%09d", ++geneIdentifierId));
                pw.print('\t');
                pw.print(gene.get(0).geneName);
                pw.print('\t');
                pw.print(gene.get(0).sourceType);
                pw.print('\t');
                pw.print(gene.size());
                pw.println();
            }
            pw.flush();
            pw.close();
            pw = null;
            eqiter.close();
            iter2.close();
            iter2 = null;
            sortingCollection.cleanup();
        } else {
            if (this.nJobs < 1) {
                this.nJobs = Math.max(1, Runtime.getRuntime().availableProcessors());
                LOG.info("setting njobs to " + this.nJobs);
            }
            final ExecutorService executorService;
            final List<Future<Integer>> futureResults;
            if (this.nJobs > 1) {
                executorService = new ThreadPoolExecutor(this.nJobs, this.nJobs, 0L, TimeUnit.MILLISECONDS, new LinkedBlockingQueue<Runnable>());
                futureResults = new ArrayList<>();
            } else {
                executorService = null;
                futureResults = Collections.emptyList();
            }
            if (this.outputFile == null) {
                LOG.error("When scanning a VCF with " + this.geneFile + ". Output file must be defined");
            }
            if (!this.exec.isEmpty()) {
                if (this.outputFile.getName().endsWith(".zip")) {
                    LOG.error("Cannot execute " + this.exec + " when saving to a zip.");
                    return -1;
                }
            }
            archive = ArchiveFactory.open(this.outputFile);
            PrintWriter manifest = this.deleteAfterCommand && !this.exec.isEmpty() ? // all files will be deleted, no manifest needed
            new PrintWriter(new NullOuputStream()) : archive.openWriter(this.prefix + "manifest.txt");
            br = IOUtils.openFileForBufferedReading(this.geneFile);
            final BedLineCodec bedCodec = new BedLineCodec();
            for (; ; ) {
                if (!futureResults.isEmpty()) {
                    int i = 0;
                    while (i < futureResults.size()) {
                        final Future<Integer> r = futureResults.get(i);
                        if (r.isCancelled()) {
                            LOG.error("Task was canceled. Break.");
                            return -1;
                        } else if (r.isDone()) {
                            futureResults.remove(i);
                            int rez = r.get();
                            if (rez != 0) {
                                LOG.error("Task Failed (" + rez + "). Break");
                            }
                        } else {
                            i++;
                        }
                    }
                }
                final String line = br.readLine();
                if (line == null)
                    break;
                if (line.startsWith("#") || line.isEmpty())
                    continue;
                final BedLine bedLine = bedCodec.decode(line);
                if (bedLine == null)
                    continue;
                // ID
                final String geneIdentifier = bedLine.get(3);
                // name
                final String geneName = bedLine.get(4);
                final SourceType sourceType = SourceType.valueOf(bedLine.get(5));
                final String filename = geneIdentifier;
                final String outputVcfName = (filename.startsWith(this.prefix) ? "" : this.prefix) + filename + ".vcf" + (this.compress ? ".gz" : "");
                LOG.info(bedLine.getContig() + ":" + bedLine.getStart() + "-" + bedLine.getEnd() + " length :" + (bedLine.getEnd() - bedLine.getStart()));
                if (bedLine.getEnd() - bedLine.getStart() > 1E6) {
                    LOG.warn("That's a large region ! " + bedLine);
                }
                OutputStream vcfOutputStream = null;
                VariantContextWriter vw = null;
                int countVariants = 0;
                final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(vcfFileReader.getFileHeader()).logger(LOG).prefix(geneName + " " + bedLine.getContig() + ":" + bedLine.getStart() + "-" + bedLine.getEnd());
                iter = vcfFileReader.query(bedLine.getContig(), bedLine.getStart(), bedLine.getEnd());
                while (iter.hasNext()) {
                    VariantContext ctx = progress.watch(iter.next());
                    switch(sourceType) {
                        case SlidingVariants:
                            {
                                // nothing
                                break;
                            }
                        case SlidingContig:
                            {
                                // nothing
                                break;
                            }
                        case ANN_GeneName:
                        case ANN_FeatureID:
                        case ANN_GeneID:
                            {
                                final List<String> preds = new ArrayList<>();
                                for (final AnnPredictionParser.AnnPrediction pred : tools.getAnnPredictionParser().getPredictions(ctx)) {
                                    final String predictionIdentifier;
                                    switch(sourceType) {
                                        case ANN_GeneName:
                                            predictionIdentifier = pred.getGeneName();
                                            break;
                                        case ANN_FeatureID:
                                            predictionIdentifier = pred.getFeatureId();
                                            break;
                                        case ANN_GeneID:
                                            predictionIdentifier = pred.getGeneId();
                                            break;
                                        default:
                                            throw new IllegalStateException(bedLine.toString());
                                    }
                                    if (StringUtil.isBlank(predictionIdentifier))
                                        continue;
                                    if (!geneName.equals(predictionIdentifier))
                                        continue;
                                    preds.add(pred.getOriginalAttributeAsString());
                                }
                                if (preds.isEmpty()) {
                                    ctx = null;
                                } else {
                                    ctx = new VariantContextBuilder(ctx).rmAttribute(tools.getAnnPredictionParser().getTag()).attribute(tools.getAnnPredictionParser().getTag(), preds).make();
                                }
                                break;
                            }
                        case VEP_Gene:
                        case VEP_Feature:
                        case VEP_Symbol:
                        case VEP_HgncId:
                            {
                                final List<String> preds = new ArrayList<>();
                                for (final VepPredictionParser.VepPrediction pred : tools.getVepPredictions(ctx)) {
                                    final String predictionIdentifier;
                                    switch(sourceType) {
                                        case VEP_Gene:
                                            predictionIdentifier = pred.getGene();
                                            break;
                                        case VEP_Feature:
                                            predictionIdentifier = pred.getFeature();
                                            break;
                                        case VEP_Symbol:
                                            predictionIdentifier = pred.getSymbol();
                                            break;
                                        case VEP_HgncId:
                                            predictionIdentifier = pred.getHgncId();
                                            break;
                                        default:
                                            throw new IllegalStateException(bedLine.toString());
                                    }
                                    if (StringUtil.isBlank(predictionIdentifier))
                                        continue;
                                    if (!geneName.equals(predictionIdentifier))
                                        continue;
                                    preds.add(pred.getOriginalAttributeAsString());
                                }
                                if (preds.isEmpty()) {
                                    ctx = null;
                                } else {
                                    ctx = new VariantContextBuilder(ctx).rmAttribute(tools.getVepPredictionParser().getTag()).attribute(tools.getVepPredictionParser().getTag(), preds).make();
                                }
                                break;
                            }
                        default:
                            throw new IllegalStateException(bedLine.toString());
                    }
                    if (ctx == null)
                        continue;
                    if (vcfOutputStream == null) {
                        LOG.info(filename);
                        manifest.println(outputVcfName);
                        final VCFHeader header = new VCFHeader(vcfFileReader.getFileHeader());
                        header.addMetaDataLine(new VCFHeaderLine(VCF_HEADER_SPLITKEY, filename));
                        vcfOutputStream = archive.openOuputStream(outputVcfName);
                        vw = VCFUtils.createVariantContextWriterToOutputStream(vcfOutputStream);
                        vw.writeHeader(header);
                    }
                    countVariants++;
                    vw.add(ctx);
                    if (countVariants % 1000 == 0) {
                        LOG.info("Loading : " + geneIdentifier + " N=" + countVariants);
                    }
                }
                progress.finish();
                LOG.info(geneIdentifier + " N=" + countVariants);
                if (vcfOutputStream != null) {
                    vw.close();
                    vcfOutputStream.flush();
                    vcfOutputStream.close();
                    vw = null;
                    if (!this.exec.isEmpty()) {
                        final Callable<Integer> callable = () -> {
                            final File vcfOutFile = new File(this.outputFile, outputVcfName);
                            IOUtil.assertFileIsReadable(vcfOutFile);
                            final String vcfPath = vcfOutFile.getPath();
                            final StringTokenizer st = new StringTokenizer(this.exec);
                            final List<String> command = new ArrayList<>(1 + st.countTokens());
                            while (st.hasMoreTokens()) {
                                String token = st.nextToken().replaceAll("__PREFIX__", this.prefix).replaceAll("__CONTIG__", bedLine.getContig()).replaceAll("__CHROM__", bedLine.getContig()).replaceAll("__ID__", geneIdentifier).replaceAll("__NAME__", geneName).replaceAll("__START__", String.valueOf(bedLine.getStart())).replaceAll("__END__", String.valueOf(bedLine.getEnd())).replaceAll("__SOURCE__", sourceType.name()).replaceAll("__VCF__", vcfPath);
                                command.add(token);
                            }
                            LOG.info(command.stream().map(S -> "'" + S + "'").collect(Collectors.joining(" ")));
                            final ProcessBuilder pb = new ProcessBuilder(command);
                            pb.redirectErrorStream(true);
                            final Process p = pb.start();
                            final Thread stdoutThread = new Thread(() -> {
                                try {
                                    InputStream in = p.getInputStream();
                                    IOUtils.copyTo(in, stdout());
                                } catch (Exception err) {
                                    LOG.error(err);
                                }
                            });
                            stdoutThread.start();
                            int exitValue = p.waitFor();
                            if (exitValue != 0) {
                                LOG.error("Command failed (" + exitValue + "):" + String.join(" ", command));
                                return -1;
                            } else {
                                if (deleteAfterCommand) {
                                    if (!vcfOutFile.delete()) {
                                        LOG.warn("Cannot delete " + vcfOutFile);
                                    }
                                }
                                return 0;
                            }
                        };
                        if (executorService != null) {
                            final Future<Integer> rez = executorService.submit(callable);
                            futureResults.add(rez);
                        } else {
                            final int ret = callable.call();
                            if (ret != 0) {
                                LOG.error("Error with process (" + ret + ")");
                                return ret;
                            }
                        }
                    }
                } else {
                    manifest.println("#" + filename);
                    LOG.warn("No Variant Found for " + line);
                }
                iter.close();
            }
            ;
            if (executorService != null) {
                LOG.info("shutdown");
                executorService.shutdown();
                executorService.awaitTermination(365, TimeUnit.DAYS);
            }
            br.close();
            br = null;
            manifest.close();
            archive.close();
            archive = null;
            LOG.info("Done");
        }
        vcfFileReader.close();
        vcfFileReader = null;
        return 0;
    } catch (Exception e) {
        LOG.error(e);
        return -1;
    } finally {
        {
            CloserUtil.close(iter2);
            CloserUtil.close(iter);
            CloserUtil.close(pw);
            CloserUtil.close(vcfFileReader);
            CloserUtil.close(br);
            CloserUtil.close(archive);
        }
    }
}

Example 8 with NullOuputStream

use of com.github.lindenb.jvarkit.io.NullOuputStream in project jvarkit by lindenb.

the class BamQueryReadNames method doWork.

@Override
public int doWork(final List<String> args) {
    PrintWriter notFoundStream = new PrintWriter(new NullOuputStream());
    SamReader sfr = null;
    SAMFileWriter bamw = null;
    try {
        if (!(2 == args.size() || 1 == args.size())) {
            LOG.error("illegal.number.of.arguments");
            return -1;
        }
        if (this.notFoundFile == null) {
            notFoundStream.close();
            notFoundStream = openFileOrStdoutAsPrintWriter(notFoundFile);
        }
        File bamFile = new File(args.get(0));
        sfr = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT).open(bamFile);
        File nameIdxFile = new File(bamFile.getParentFile(), bamFile.getName() + NAME_IDX_EXTENSION);
        this.indexDef = new NameIndexDef();
        this.raf = new RandomAccessFile(nameIdxFile, "r");
        indexDef.countReads = raf.readLong();
        indexDef.maxNameLengt = raf.readInt();
        LineIterator r = null;
        if (args.size() == 2) {
            r = IOUtils.openURIForLineIterator(args.get(1));
        } else {
            r = IOUtils.openStdinForLineIterator();
        }
        SAMFileHeader header = sfr.getFileHeader().clone();
        bamw = writingBamArgs.openSAMFileWriter(this.outputFile, header, true);
        long iter_start = 0L;
        while (r.hasNext()) {
            String line = r.next();
            String searchRead = null;
            int side = -1;
            if (line.isEmpty() || line.startsWith("#"))
                continue;
            /* forward or reverse is specified ? */
            if (line.endsWith("/1")) {
                side = 1;
                searchRead = line.substring(0, line.length() - 2);
            } else if (line.endsWith("/2")) {
                side = 2;
                searchRead = line.substring(0, line.length() - 2);
            } else {
                side = -1;
                searchRead = line;
            }
            long index = lower_bound(iter_start, this.indexDef.countReads, searchRead);
            if (index >= this.indexDef.countReads) {
                notFoundStream.println(line);
                continue;
            }
            if (query_reads_is_sorted) {
                iter_start = index;
            }
            Set<SAMRecord> found = new LinkedHashSet<SAMRecord>();
            while (index < this.indexDef.countReads) {
                NameAndPos nap = getNameAndPosAt(index);
                if (nap.name.compareTo(searchRead) < 0) {
                    ++index;
                    continue;
                } else if (nap.name.compareTo(searchRead) > 0) {
                    break;
                }
                SAMRecordIterator iter;
                if (nap.tid < 0) {
                    iter = sfr.queryUnmapped();
                } else {
                    iter = sfr.query(header.getSequence(nap.tid).getSequenceName(), nap.pos, 0, true);
                }
                while (iter.hasNext()) {
                    SAMRecord rec = iter.next();
                    if (nap.tid >= 0) {
                        if (nap.tid != rec.getReferenceIndex())
                            throw new IllegalStateException();
                        if (rec.getAlignmentStart() < nap.pos) {
                            continue;
                        }
                        if (rec.getAlignmentStart() > nap.pos) {
                            break;
                        }
                    }
                    if (rec.getReadName().equals(searchRead)) {
                        if (side == 1 && !(rec.getReadPairedFlag() && rec.getFirstOfPairFlag())) {
                            continue;
                        } else if (side == 2 && !(rec.getReadPairedFlag() && rec.getSecondOfPairFlag())) {
                            continue;
                        }
                        found.add(rec);
                    }
                }
                iter.close();
                ++index;
            }
            if (found.isEmpty()) {
                notFoundStream.println(line);
            } else {
                for (SAMRecord rec : found) {
                    bamw.addAlignment(rec);
                }
            }
        }
        CloserUtil.close(r);
        notFoundStream.flush();
        notFoundStream.close();
        notFoundStream = null;
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(notFoundStream);
        CloserUtil.close(raf);
        CloserUtil.close(sfr);
        CloserUtil.close(bamw);
    }
}