Examples with FastqReader com.github.lindenb.jvarkit.util.picard.FastqReader used on opensource projects

Example 6 with FastqReader

use of com.github.lindenb.jvarkit.util.picard.FastqReader in project jvarkit by lindenb.

the class PadEmptyFastq method doWork.

@Override
public int doWork(final List<String> args) {
    FastqWriter fqw = null;
    try {
        if (this.outFile == null) {
            LOG.info("writing to stdout");
            fqw = new BasicFastqWriter(stdout());
        } else {
            LOG.info("writing to " + this.outFile);
            fqw = new FastqWriterFactory().newWriter(this.outFile);
        }
        if (args.isEmpty()) {
            LOG.info("Reading from stdin");
            FastqReader fqr = new FourLinesFastqReader(stdin());
            copyTo(fqr, fqw);
            fqr.close();
        } else {
            for (final String filename : args) {
                LOG.info("Reading from " + filename);
                FastqReader fqr = new FourLinesFastqReader(new File(filename));
                copyTo(fqr, fqw);
                fqr.close();
            }
        }
        return 0;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(fqw);
    }
}

Example 7 with FastqReader

use of com.github.lindenb.jvarkit.util.picard.FastqReader in project jvarkit by lindenb.

the class FastqRevComp method doWork.

@Override
public int doWork(List<String> args) {
    if (only_R1 && only_R2) {
        LOG.error("Both options -1 && -2 used.");
        return -1;
    }
    PrintStream out = null;
    try {
        out = super.openFileOrStdoutAsPrintStream(outputFile);
        if (args.isEmpty()) {
            LOG.info("Reading from stdin");
            FastqReader fqR = new FourLinesFastqReader(stdin());
            run(fqR, out);
            fqR.close();
        } else
            for (final String fn : args) {
                File f = new File(fn);
                LOG.info("Reading from " + f);
                FastqReader fqR = new FourLinesFastqReader(f);
                run(fqR, out);
                fqR.close();
            }
        out.flush();
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(out);
    }
    return 0;
}

Example 8 with FastqReader

use of com.github.lindenb.jvarkit.util.picard.FastqReader in project jvarkit by lindenb.

the class FastqGrep method doWork.

@Override
public int doWork(List<String> args) {
    BufferedReader in = null;
    FastqWriter out = null;
    try {
        if (this.readNameFile != null) {
            in = IOUtils.openFileForBufferedReading(this.readNameFile);
            String line;
            while ((line = in.readLine()) != null) {
                line = line.trim();
                if (line.isEmpty())
                    continue;
                this.readNames.put(getReadName(line), 0);
            }
            in.close();
        }
        for (final String r : this.readNamesInput) {
            this.readNames.put(getReadName(r), 0);
        }
        if (readNames.isEmpty()) {
            LOG.warn("no read name found.");
        }
        if (this.outputFile != null) {
            LOG.info("Writing to " + this.outputFile);
            out = new BasicFastqWriter(this.outputFile);
        } else {
            LOG.info("Writing to stdout");
            out = new BasicFastqWriter(stdout());
        }
        if (args.isEmpty()) {
            LOG.info("Reading from stdin");
            FastqReader fqR = new FourLinesFastqReader(System.in);
            run(fqR, out);
            fqR.close();
        } else
            for (String fname : args) {
                File f = new File(fname);
                LOG.info("Reading from " + f);
                FastqReader fqR = new FourLinesFastqReader(f);
                run(fqR, out);
                fqR.close();
            }
        CloserUtil.close(out);
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(in);
    }
}

Example 9 with FastqReader

use of com.github.lindenb.jvarkit.util.picard.FastqReader in project jvarkit by lindenb.

the class FastqToFasta method doWork.

@Override
public int doWork(final List<String> args) {
    PrintStream out = null;
    try {
        out = super.openFileOrStdoutAsPrintStream(outputFile);
        if (args.isEmpty()) {
            LOG.info("Reading from stdin");
            FastqReader fqR = new FourLinesFastqReader(stdin());
            run(fqR, out);
            fqR.close();
        } else
            for (String fname : args) {
                File f = new File(fname);
                LOG.info("Reading from " + f);
                FastqReader fqR = new FourLinesFastqReader(f);
                run(fqR, out);
                fqR.close();
            }
        out.flush();
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(out);
    }
    return 0;
}

Example 10 with FastqReader

use of com.github.lindenb.jvarkit.util.picard.FastqReader in project jvarkit by lindenb.

the class FindCorruptedFiles method testFastq.

private void testFastq(File f) {
    long n = 0;
    LOG.fine("Test Fastq for " + f);
    FastqReader r = null;
    try {
        r = new FourLinesFastqReader(f);
        r.setValidationStringency(this.validationStringency);
        while (r.hasNext() && (NUM < 0 || n < NUM)) {
            r.next();
            ++n;
        }
        if (n == 0) {
            emptyFile(f);
        }
    } catch (Exception err) {
        LOG.fine("Cannot read " + f);
        stdout().println(f);
    } finally {
        CloserUtil.close(r);
    }
}