sequence_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
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL NVIDIA CORPORATION BE LIABLE FOR ANY
 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#pragma once

#include <nvbio/io/sequence/sequence.h>
#include <nvbio/io/sequence/sequence_priv.h>
#include <nvbio/io/output_stream.h>
#include <nvbio/basic/console.h>

#include <zlib/zlib.h>

namespace nvbio {
namespace io {




struct SequenceDataFile_FASTQ_parser : public SequenceDataFile
{
protected:
    SequenceDataFile_FASTQ_parser(
        const char*                         read_file_name,
        const SequenceDataFile::Options&    options,
        const uint32                        buffer_size = 64536u)
      : SequenceDataFile( options ),
        m_file_name(read_file_name),
        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(struct SequenceDataEncoder *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;

    virtual bool gets(char* buffer, int len) = 0;

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

protected:
    // file name we're reading from
    const char *            m_file_name;

    // 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;
};

struct SequenceDataFile_FASTQ_gz : public SequenceDataFile_FASTQ_parser
{
    SequenceDataFile_FASTQ_gz(
        const char*                      read_file_name,
        const SequenceDataFile::Options& options);

    ~SequenceDataFile_FASTQ_gz();

    virtual FileState fillBuffer(void);

    virtual bool gets(char* buffer, int len) { return gzgets( m_file, buffer, len ) != NULL; };

    virtual bool rewind();

private:
    gzFile m_file;
};


struct SequenceDataOutputFile_FASTQ : SequenceDataOutputStream
{
    SequenceDataOutputFile_FASTQ(
        const char* file_name,
        const char* compressor,
        const char* options);

    void next(const SequenceDataHost& sequence_data);

    bool is_ok();

private:
    // file name we're reading from
    const char*   m_file_name;
    OutputStream* m_file;
};


inline char SequenceDataFile_FASTQ_parser::get(void)
{
    if (m_buffer_pos >= m_buffer_size /*|| m_buffer[m_buffer_pos] == '\0'*/)
    {
        // check whether we had already reached the end of file
        if (m_buffer_size < m_buffer.size())
        {
            m_file_state = FILE_EOF;
            return 0;
        }
        else
        {
            // 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