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

Example 1 with NoCloseInputStream

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

the class VcfToBed method doWork.

@Override
public int doWork(final List<String> args) {
    if (!StringUtil.isBlank(this.maxLengthStr)) {
        this.maxLength = new DistanceParser.StringConverter().convert(this.maxLengthStr);
    }
    if (!StringUtil.isBlank(this.minLengthStr)) {
        this.minLength = new DistanceParser.StringConverter().convert(this.minLengthStr);
    }
    PrintWriter pw = null;
    try {
        if (this.faidx != null) {
            this.samSequenceDictionary = SequenceDictionaryUtils.extractRequired(this.faidx);
        }
        pw = super.openPathOrStdoutAsPrintWriter(this.outputFile);
        if (printHeader) {
            switch(this.outputFormat) {
                case bed:
                    {
                        pw.println("track name=vcf2bed type=bed description=\"__DESCRIPTION__\"");
                        break;
                    }
                case interval:
                    {
                        if (this.samSequenceDictionary != null) {
                            final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
                            codec.encode(pw, new SAMFileHeader(this.samSequenceDictionary));
                        }
                        break;
                    }
                default:
                    {
                        throw new IllegalStateException("" + this.outputFormat);
                    }
            }
        }
        if (args.size() == 1 && args.get(0).endsWith(".list")) {
            final PrintWriter finalpw = pw;
            Files.lines(Paths.get(args.get(0))).filter(L -> !StringUtil.isBlank(L)).forEach(L -> {
                scan(L, finalpw);
            });
        } else if (args.size() == 1 && args.get(0).endsWith(".zip")) {
            try (InputStream in = new BufferedInputStream(Files.newInputStream(Paths.get(args.get(0))))) {
                ZipInputStream zin = new ZipInputStream(in);
                for (; ; ) {
                    final ZipEntry entry = zin.getNextEntry();
                    if (entry == null)
                        break;
                    if (entry.isDirectory()) {
                        // zin.closeEntry();
                        continue;
                    }
                    if (!FileExtensions.VCF_LIST.stream().anyMatch(X -> entry.getName().endsWith(X))) {
                        // zin.closeEntry();
                        continue;
                    }
                    /* prevent zip from being closed */
                    final InputStream do_not_close_in = new NoCloseInputStream(zin);
                    try (VCFIterator iter = new VCFIteratorBuilder().open(do_not_close_in)) {
                        scan(args.get(0) + "!" + entry.getName(), iter, pw);
                    }
                // zin.closeEntry();
                }
                zin.close();
            }
        } else if (args.size() == 1 && (args.get(0).endsWith(".tar") || args.get(0).endsWith(".tar.gz"))) {
            try (InputStream in = new BufferedInputStream(Files.newInputStream(Paths.get(args.get(0))))) {
                InputStream in2 = args.get(0).endsWith(".tar") ? in : new GZIPInputStream(in);
                final TarArchiveInputStream tarin = new TarArchiveInputStream(in2);
                for (; ; ) {
                    final TarArchiveEntry entry = tarin.getNextTarEntry();
                    if (entry == null)
                        break;
                    if (!tarin.canReadEntryData(entry))
                        continue;
                    if (entry.isDirectory()) {
                        continue;
                    }
                    if (!FileExtensions.VCF_LIST.stream().anyMatch(X -> entry.getName().endsWith(X))) {
                        continue;
                    }
                    /* prevent tar from being closed */
                    final InputStream do_not_close_in = new NoCloseInputStream(tarin);
                    try (VCFIterator iter = new VCFIteratorBuilder().open(do_not_close_in)) {
                        scan(args.get(0) + "!" + entry.getName(), iter, pw);
                    }
                }
                tarin.close();
                in2.close();
            }
        } else if (args.isEmpty()) {
            LOG.info("reading vcf from stdin");
            scan(null, pw);
        } else {
            final PrintWriter finalpw = pw;
            args.stream().forEach(L -> {
                scan(L, finalpw);
            });
        }
        if (!this.contigsNotFound.isEmpty()) {
            LOG.warn("The following contigs: " + String.join(",", this.contigsNotFound) + " were not found in the dictionaries.");
        }
        pw.flush();
        pw.close();
        pw = null;
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(pw);
    }
}