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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2026, Knut Reinert, FU Berlin
// 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 Knut Reinert or the FU Berlin 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 KNUT REINERT OR THE FU BERLIN 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.
//
// ==========================================================================
// Author: David Weese <david.weese@fu-berlin.de>
// ==========================================================================
// Class for reading/writing files in BED format.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_BED_IO_BED_FILE_H_
#define SEQAN_INCLUDE_SEQAN_BED_IO_BED_FILE_H_
namespace seqan2 {
// ============================================================================
// Typedefs
// ============================================================================
// ----------------------------------------------------------------------------
// Type BedFileIn
// ----------------------------------------------------------------------------
/*!
* @class BedFileIn
* @signature typedef FormattedFile<Bed, Input> BedFileIn;
* @extends FormattedFileIn
* @headerfile <seqan/bed_io.h>
* @brief Class for reading BED files.
*
* @see BedRecord
*/
typedef FormattedFile<Bed, Input> BedFileIn;
// ----------------------------------------------------------------------------
// Type BedFileOut
// ----------------------------------------------------------------------------
/*!
* @class BedFileOut
* @signature typedef FormattedFile<Bed, Output> BedFileOut;
* @extends FormattedFileOut
* @headerfile <seqan/bed_io.h>
* @brief Class for writing BED files.
*
* @see BedRecord
*/
typedef FormattedFile<Bed, Output> BedFileOut;
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction FormattedFileContext
// ----------------------------------------------------------------------------
template <typename TDirection, typename TSpec, typename TStorageSpec>
struct FormattedFileContext<FormattedFile<Bed, TDirection, TSpec>, TStorageSpec>
{
typedef CharString Type;
};
// ----------------------------------------------------------------------------
// Metafunction FileFormats
// ----------------------------------------------------------------------------
template <typename TDirection, typename TSpec>
struct FileFormat<FormattedFile<Bed, TDirection, TSpec> >
{
typedef Bed Type;
};
// ----------------------------------------------------------------------------
// Function readRecord(); BedRecord
// ----------------------------------------------------------------------------
// convient BedFile variant
template <typename TRecordSpec, typename TSpec>
inline void
readRecord(BedRecord<TRecordSpec> & record, FormattedFile<Bed, Input, TSpec> & file)
{
readRecord(record, context(file), file.iter, file.format);
}
// ----------------------------------------------------------------------------
// Function write(); BedRecord
// ----------------------------------------------------------------------------
template <typename TSpec, typename TRecordSpec>
inline void
writeRecord(FormattedFile<Bed, Output, TSpec> & file, BedRecord<TRecordSpec> & record)
{
writeRecord(file.iter, record, file.format);
}
} // namespace seqan2
#endif // SEQAN_INCLUDE_SEQAN_BED_IO_BED_FILE_H_
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