reads_txt.cpp

Go to the documentation of this file.

/*
 * 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;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */

#include <nvbio/io/reads/reads_txt.h>
#include <nvbio/basic/types.h>

#include <string.h>
#include <ctype.h>

namespace nvbio {
namespace io {




int ReadDataFile_TXT::nextChunk(ReadDataRAM *output, uint32 max_reads, uint32 max_bps)
{
    const char* name = "";

    uint32 n_reads = 0;
    uint32 n_bps   = 0;

    const uint32 read_mult =
        ((m_flags & FORWARD)            ? 1u : 0u) +
        ((m_flags & REVERSE)            ? 1u : 0u) +
        ((m_flags & FORWARD_COMPLEMENT) ? 1u : 0u) +
        ((m_flags & REVERSE_COMPLEMENT) ? 1u : 0u);

    while (n_reads + read_mult                       <= max_reads &&
           n_bps + read_mult*ReadDataFile::LONG_READ <= max_bps)
    {
        // reset the read
        m_read_bp.erase( m_read_bp.begin(), m_read_bp.end() );

        // read an entire line
        for (uint8 c = get(); c != '\n' && c != 0; c = get())
        {
            // if (isgraph(c))
            if (c >= 0x21 && c <= 0x7E)
                m_read_bp.push_back( c );
        }

        ++m_line;

        if (m_read_q.size() < m_read_bp.size())
        {
            // extend the quality score vector if needed
            const size_t old_size = m_read_q.size();
            m_read_q.resize( m_read_bp.size() );
            for (size_t i = old_size; i < m_read_bp.size(); ++i)
                m_read_q[i] = char(255);
        }

        if (m_read_bp.size())
        {
            if (m_flags & FORWARD)
            {
                output->push_back(uint32( m_read_bp.size() ),
                                  name,
                                  &m_read_bp[0],
                                  &m_read_q[0],
                                  m_quality_encoding,
                                  m_truncate_read_len,
                                  ReadDataRAM::NO_OP );
            }
            if (m_flags & REVERSE)
            {
                output->push_back(uint32( m_read_bp.size() ),
                                  name,
                                  &m_read_bp[0],
                                  &m_read_q[0],
                                  m_quality_encoding,
                                  m_truncate_read_len,
                                  ReadDataRAM::REVERSE_OP );
            }
            if (m_flags & FORWARD_COMPLEMENT)
            {
                output->push_back(uint32( m_read_bp.size() ),
                                  name,
                                  &m_read_bp[0],
                                  &m_read_q[0],
                                  m_quality_encoding,
                                  m_truncate_read_len,
                                  ReadDataRAM::COMPLEMENT_OP );
            }
            if (m_flags & REVERSE_COMPLEMENT)
            {
                output->push_back(uint32( m_read_bp.size() ),
                                  name,
                                  &m_read_bp[0],
                                  &m_read_q[0],
                                  m_quality_encoding,
                                  m_truncate_read_len,
                                  ReadDataRAM::REVERSE_COMPLEMENT_OP );
            }

            n_bps   += read_mult * (uint32)m_read_bp.size();
            n_reads += read_mult;
        }

        // check for end-of-file
        if (m_file_state != FILE_OK)
            break;
    }
    return n_reads;
}

ReadDataFile_TXT_gz::ReadDataFile_TXT_gz(const char *read_file_name,
                                             const QualityEncoding qualities,
                                             const uint32 max_reads,
                                             const uint32 max_read_len,
                                             const ReadEncoding flags,
                                             const uint32 buffer_size)
    : ReadDataFile_TXT(read_file_name, qualities, max_reads, max_read_len, flags, buffer_size)
{
    m_file = gzopen(read_file_name, "r");
    if (!m_file) {
        m_file_state = FILE_OPEN_FAILED;
    } else {
        m_file_state = FILE_OK;
    }

    gzbuffer(m_file, m_buffer_size);
}

ReadDataFile_TXT::FileState ReadDataFile_TXT_gz::fillBuffer(void)
{
    m_buffer_size = gzread(m_file, &m_buffer[0], (uint32)m_buffer.size());
    if (m_buffer_size <= 0)
    {
        // check for EOF separately; zlib will not always return Z_STREAM_END at EOF below
        if (gzeof(m_file))
        {
            return FILE_EOF;
        } else {
            // ask zlib what happened and inform the user
            int err;
            const char *msg;

            msg = gzerror(m_file, &err);
            // we're making the assumption that we never see Z_STREAM_END here
            assert(err != Z_STREAM_END);

            log_error(stderr, "error processing TXT file: zlib error %d (%s)\n", err, msg);
            return FILE_STREAM_ERROR;
        }
    }

    return FILE_OK;
}


} // namespace io
} // namespace nvbio