Examples with FastqRecordPair com.github.lindenb.jvarkit.fastq.FastqRecordPair used on opensource projects

Example 1 with FastqRecordPair

use of com.github.lindenb.jvarkit.fastq.FastqRecordPair in project jvarkit by lindenb.

the class FastqSplitInterleaved method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.fileA.equals(this.fileB)) {
        LOG.error("R1 file==R2.file.");
        return -1;
    }
    CloseableIterator<FastqRecordPair> iter1 = null;
    FastqPairedWriter pairedWriter = null;
    try {
        final String input = oneFileOrNull(args);
        final FastqPairedReaderFactory fqprf = new FastqPairedReaderFactory().setValidateReadNames(this.validate_read_names);
        if (input == null) {
            iter1 = fqprf.open(stdin());
        } else {
            iter1 = fqprf.open(Paths.get(input));
        }
        final FastqPairedWriterFactory fqwf = new FastqPairedWriterFactory().setCreateMd5(this.write_md5).setAsyncIo(this.with_asynio);
        pairedWriter = fqwf.open(fileA, fileB);
        while (iter1.hasNext()) {
            pairedWriter.write(iter1.next());
        }
        iter1.close();
        pairedWriter.close();
        return 0;
    } catch (final Throwable err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(iter1);
        CloserUtil.close(pairedWriter);
    }
}

Example 2 with FastqRecordPair

use of com.github.lindenb.jvarkit.fastq.FastqRecordPair in project jvarkit by lindenb.

the class FastqJavascript method runPairedEnd.

@Override
protected int runPairedEnd(CloseableIterator<FastqRecordPair> iter, FastqPairedWriter fws) throws IOException {
    try {
        long count = 0L;
        final Bindings bindings = this.script.getEngine().createBindings();
        while (iter.hasNext()) {
            final Pair p = new Pair(iter.next());
            bindings.put("pair", p);
            if (super.evalJavaScriptBoolean(this.script, bindings)) {
                fws.write(p.rec1.toFastqRecord(), p.rec2.toFastqRecord());
            }
            ++count;
            if (this.LIMIT > 0L && count >= this.LIMIT)
                break;
        }
        return 0;
    } catch (final ScriptException err) {
        getLogger().error(err);
        return -1;
    }
}

Example 3 with FastqRecordPair

use of com.github.lindenb.jvarkit.fastq.FastqRecordPair in project jvarkit by lindenb.

the class FastqSplit method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.per_file_number < 1 && this.split_number < 1) {
        LOG.error("Option -n or -s are undefined");
        return -1;
    }
    if (this.per_file_number > 0 && this.split_number > 0) {
        LOG.error("Both Options -n and -s are defined");
        return -1;
    }
    if (!this.basename.contains(TAG)) {
        LOG.error("basename doesn't contain " + TAG + ": " + basename);
        return -1;
    }
    PrintWriter manifest = null;
    try {
        if (this.manifestPath == null) {
            manifest = new PrintWriter(new NullOuputStream());
        } else {
            manifest = super.openPathOrStdoutAsPrintWriter(this.manifestPath);
        }
        if (args.size() == 2 || (this.input_is_interleaved && (args.isEmpty() || args.size() == 1))) {
            final List<FastqPairedWriter> fastqWriters = new ArrayList<>();
            FastqPairedWriter previous = null;
            int count_files = 0;
            long n = 0L;
            try (final CloseableIterator<FastqRecordPair> iter = new FastqPairedReaderFactory().setValidateReadNames(this.validate_read_names).open(args)) {
                while (iter.hasNext()) {
                    final FastqRecordPair pair = iter.next();
                    final FastqPairedWriter w;
                    /* split by number of reads per file */
                    if (this.per_file_number > 0) {
                        if (previous == null || n % this.per_file_number == 0) {
                            if (previous != null)
                                previous.close();
                            previous = openPairedWriter(count_files, manifest);
                            count_files++;
                            n = 0L;
                        }
                        w = previous;
                    } else /* split by file */
                    {
                        final int idx = (int) (n % this.split_number);
                        if (idx >= fastqWriters.size()) {
                            w = openPairedWriter(idx, manifest);
                            fastqWriters.add(w);
                        } else {
                            w = fastqWriters.get(idx);
                        }
                    }
                    w.write(pair);
                    n++;
                }
            }
            if (previous != null)
                previous.close();
            for (final FastqPairedWriter w : fastqWriters) w.close();
        } else if (args.isEmpty() || args.size() == 1) {
            if (this.output_is_interleaved) {
                LOG.error("Cannot set output is interleaved if input is not paired.");
                return -1;
            }
            final List<FastqWriter> fastqWriters = new ArrayList<>();
            FastqWriter previous = null;
            long n = 0L;
            int count_files = 0;
            final FastqReader iter;
            if (args.size() == 1) {
                iter = new FastqReader(new File(args.get(0)));
            } else {
                iter = new FastqReader(IOUtils.openStreamForBufferedReader(stdin()));
            }
            while (iter.hasNext()) {
                final FastqRecord rec = iter.next();
                final FastqWriter w;
                /* split by number of reads per file */
                if (this.per_file_number > 0) {
                    if (previous == null || n % this.per_file_number == 0) {
                        if (previous != null)
                            previous.close();
                        previous = this.openSingleWriter(count_files, manifest);
                        count_files++;
                        n = 0L;
                    }
                    w = previous;
                } else /* split by file */
                {
                    final int idx = (int) (n % this.split_number);
                    if (idx >= fastqWriters.size()) {
                        w = this.openSingleWriter(idx, manifest);
                        fastqWriters.add(w);
                    } else {
                        w = fastqWriters.get(idx);
                    }
                }
                w.write(rec);
                n++;
            }
            iter.close();
            for (final FastqWriter w : fastqWriters) w.close();
        } else {
            LOG.error("Illegal number of arguments.");
            return -1;
        }
        manifest.flush();
        manifest.close();
        return 0;
    } catch (final Throwable err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(manifest);
    }
}

Example 4 with FastqRecordPair

use of com.github.lindenb.jvarkit.fastq.FastqRecordPair in project jvarkit by lindenb.

the class ConvertPhred64toFastq33 method runPairedEnd.

@Override
protected int runPairedEnd(CloseableIterator<FastqRecordPair> iter, FastqPairedWriter fws) throws IOException {
    while (iter.hasNext()) {
        final FastqRecordPair pair = iter.next();
        fws.write(convert(pair.get(0)), convert(pair.get(1)));
    }
    return 0;
}