public FastqWriter newWriter(final File out) { final FastqWriter writer = new BasicFastqWriter(out, createMd5); if (useAsyncIo) { return new AsyncFastqWriter(writer, AsyncFastqWriter.DEFAULT_QUEUE_SIZE); } else { return writer; } } }
private void encodeArray(final FastqRecord[] recs) { for (final FastqRecord rec : recs) { writer.write(rec); } }
@Override public String toString() { return "FastqReader[" + (this.fastqFile == null ? "" : this.fastqFile) + " Line:" + getLineNumber() + "]"; } }
private void write(final FastqWriter[] writers, final FastqRecord[] records) { for (int i = 0; i < writers.length; ++i) { writers[i].write(records[i]); } }
/** * Encodes a SAMRecord in the String FASTQ format. * @see #encode(FastqRecord) * @see #asSAMRecord(FastqRecord, SAMFileHeader) */ public static String encode(final SAMRecord record) { return encode(asFastqRecord(record)); }
/** * Constructor * @param file Name of FASTQ being read, or null if not known. * @param reader input reader . Will be closed by the close method * @param skipBlankLines should we skip blank lines ? */ public FastqReader(final File file, final BufferedReader reader,boolean skipBlankLines) { this.fastqFile = file; this.reader = reader; this.skipBlankLines = skipBlankLines; this.nextRecord = readNextRecord(); }
private void decodeArray(final FastqRecord[] recs) { for (int i = 0; i < recs.length; ++i) { recs[i] = reader.next(); } }
/** * Converts a {@link FastqRecord} into a simple unmapped {@link SAMRecord}. */ public static SAMRecord asSAMRecord(final FastqRecord record, final SAMFileHeader header) { return asSAMRecord(record, header, (s, r) -> {}); }
/** * Returns the record as the String FASTQ format. * @see FastqEncoder#encode(FastqRecord) */ public String toFastQString() { return FastqEncoder.encode(this); }
public FastqWriter newWriter(final File out) { final FastqWriter writer = new BasicFastqWriter(out, createMd5); if (useAsyncIo) { return new AsyncFastqWriter(writer, AsyncFastqWriter.DEFAULT_QUEUE_SIZE); } else { return writer; } } }
@Override public String toString() { return "FastqReader["+(this.fastqFile == null?"":this.fastqFile)+ " Line:"+getLineNumber()+"]"; } }
private void write(final FastqWriter[] writers, final FastqRecord[] records) { for (int i = 0; i < writers.length; ++i) { writers[i].write(records[i]); } }
/** * Encodes a SAMRecord in the String FASTQ format. * @see #encode(FastqRecord) * @see #asSAMRecord(FastqRecord, SAMFileHeader) */ public static String encode(final SAMRecord record) { return encode(asFastqRecord(record)); }
/** * Constructor * @param file Name of FASTQ being read, or null if not known. * @param reader input reader . Will be closed by the close method * @param skipBlankLines should we skip blank lines ? */ public FastqReader(final File file, final BufferedReader reader,boolean skipBlankLines) { this.fastqFile = file; this.reader = reader; this.nextRecord = readNextRecord(); this.skipBlankLines = skipBlankLines; }
private void decodeArray(final FastqRecord[] recs) { for (int i = 0; i < recs.length; ++i) { recs[i] = reader.next(); } }
/** * Converts a {@link FastqRecord} into a simple unmapped {@link SAMRecord}. */ public static SAMRecord asSAMRecord(final FastqRecord record, final SAMFileHeader header) { return asSAMRecord(record, header, (s, r) -> {}); }
private void encodeArray(final FastqRecord[] recs) { for (final FastqRecord rec : recs) { writer.write(rec); } }
public FastqWriter newWriter(final File out) { final FastqWriter writer = new BasicFastqWriter(out, createMd5); if (useAsyncIo) { return new AsyncFastqWriter(writer, AsyncFastqWriter.DEFAULT_QUEUE_SIZE); } else { return writer; } } }
@Override public String toString() { return "FastqReader[" + (this.fastqFile == null ? "" : this.fastqFile) + " Line:" + getLineNumber() + "]"; } }
/** * Constructor * @param file Name of FASTQ being read, or null if not known. * @param reader input reader . Will be closed by the close method * @param skipBlankLines should we skip blank lines ? */ public FastqReader(final File file, final BufferedReader reader,boolean skipBlankLines) { this.fastqFile = file; this.reader = reader; this.skipBlankLines = skipBlankLines; this.nextRecord = readNextRecord(); }