reads_fastq.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *    * Redistributions of source code must retain the above copyright
 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include <nvbio/io/reads/reads.h>
#include <nvbio/io/reads/reads_priv.h>
#include <nvbio/basic/console.h>

#include <zlib/zlib.h>

namespace nvbio {
namespace io {




// ReadDataFile from a FASTQ file
// contains the code to parse FASTQ files and dump the results into a ReadDataRAM object
// file access is done via derived classes
struct ReadDataFile_FASTQ_parser : public ReadDataFile
{
protected:
    ReadDataFile_FASTQ_parser(const char *read_file_name,
                              const QualityEncoding quality_encoding,
                              const uint32 max_reads,
                              const uint32 max_read_len,
                              const ReadEncoding flags,
                              const uint32 buffer_size = 64536u)
      : ReadDataFile(max_reads, max_read_len, flags),
        m_file_name(read_file_name),
        m_quality_encoding(quality_encoding),
        m_buffer(buffer_size),
        m_buffer_size(buffer_size),
        m_buffer_pos(buffer_size),
        m_line(0),
        m_name( 1024*1024 ),
        m_read_bp( 1024*1024 ),
        m_read_q( 1024*1024 )
    {};

    // get next read chunk from file and parse it (up to max reads)
    // this can cause m_file_state to change
    virtual int nextChunk(ReadDataRAM *output, uint32 max_reads, uint32 max_bps);

    // fill m_buffer with data from the file, return the new file state
    // this should only report EOF when no more bytes could be read
    // derived classes should override this method to return actual file data
    virtual FileState fillBuffer(void) = 0;

private:
    // get next character from file
    uint8 get();

protected:
    // file name we're reading from
    const char *            m_file_name;
    // the quality encoding we're using (for FASTQ, this comes from the command line or defaults to Phred33)
    QualityEncoding         m_quality_encoding;

    // buffers input from the fastq file
    std::vector<char>       m_buffer;
    uint32                  m_buffer_size;
    uint32                  m_buffer_pos;

    // counter for which line we're at
    uint32                  m_line;

    // error reporting from the parser: stores the character that generated an error
    uint8                   m_error_char;

    // temp buffers for data coming in from the FASTQ file: read name, base pairs and qualities
    std::vector<char>  m_name;
    std::vector<uint8> m_read_bp;
    std::vector<uint8> m_read_q;
};

// loader for gzipped files
// this also works for plain uncompressed files, as zlib does that transparently
struct ReadDataFile_FASTQ_gz : public ReadDataFile_FASTQ_parser
{
    ReadDataFile_FASTQ_gz(const char *read_file_name,
                          const QualityEncoding qualities,
                          const uint32 max_reads,
                          const uint32 max_read_len,
                          const ReadEncoding flags);

    virtual FileState fillBuffer(void);

private:
    gzFile m_file;
};


inline uint8 ReadDataFile_FASTQ_parser::get(void)
{
    if (m_buffer_pos >= m_buffer_size)
    {
        // grab more data from the underlying file
        m_file_state = fillBuffer();
        m_buffer_pos = 0;

        // if we failed to read more data, return \0
        if (m_file_state != FILE_OK)
            return 0;
    }

    return m_buffer[m_buffer_pos++];
}

} // namespace io
} // namespace nvbio