output_file.cpp

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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.
 * 
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#include <nvbio/io/output/output_batch.h>
#include <nvbio/io/output/output_sam.h>
#include <nvbio/io/output/output_bam.h>
#include <nvbio/io/output/output_debug.h>

namespace nvbio {
namespace io {

OutputFile::OutputFile(const char *_file_name, AlignmentType _alignment_type, BNT _bnt)
    : file_name(_file_name),
      alignment_type(_alignment_type),
      bnt(_bnt),
      mapq_filter(-1)
{
}

OutputFile::~OutputFile()
{
}

void OutputFile::configure_mapq_evaluator(int mapq_filter)
{
    OutputFile::mapq_filter = mapq_filter;
}

void OutputFile::close(void)
{
}

IOStats& OutputFile::get_aggregate_statistics(void)
{
    return iostats;
}

OutputFile *OutputFile::open(const char *file_name, AlignmentType aln_type, BNT bnt)
{
    // parse out file extension; look for .sam, .bam suffixes
    uint32 len = uint32(strlen(file_name));

    if (strcmp(file_name, "/dev/null") == 0)
    {
        return new OutputFile(file_name, aln_type, bnt);
    }

    if (len >= strlen(".sam"))
    {
        if (strcmp(&file_name[len - strlen(".sam")], ".sam") == 0)
        {
            return new SamOutput(file_name, aln_type, bnt);
        }
    }

    if (len >= strlen(".bam"))
    {
        if (strcmp(&file_name[len - strlen(".bam")], ".bam") == 0)
        {
            return new BamOutput(file_name, aln_type, bnt);
        }
    }

    if (len >= strlen(".dbg"))
    {
        if (strcmp(&file_name[len - strlen(".dbg")], ".dbg") == 0)
        {
            return new DebugOutput(file_name, aln_type, bnt);
        }
    }

    log_warning(stderr, "could not determine file type for %s; guessing SAM\n", file_name);
    return new SamOutput(file_name, aln_type, bnt);
}

} // namespace io
} // namespace nvbio