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// ==========================================================================
// SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, 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>
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================
// Definitions for piggybacking qualities in free bits of bytes.
// ==========================================================================
#ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
#define SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
// TODO(holtgrew): Should the documentation be here?
namespace seqan {
// ============================================================================
// Forwards
// ============================================================================
// ============================================================================
// Tags, Classes, Enums
// ============================================================================
// ============================================================================
// Metafunctions
// ============================================================================
// ----------------------------------------------------------------------------
// Metafunction QualityValueSize
// ----------------------------------------------------------------------------
// TODO(holtgrew): Do we want a default specialization? Should it return 0?
template <typename TValue>
struct QualityValueSize
{
enum { VALUE = ValueSize<TValue>::VALUE };
};
template <typename TValue>
struct QualityValueSize<TValue const> : QualityValueSize<TValue>
{};
// ----------------------------------------------------------------------------
// Metafunction HasQualities
// ----------------------------------------------------------------------------
template <typename TValue>
struct HasQualities
{
typedef False Type;
static const bool VALUE = false;
};
// ============================================================================
// Functions
// ============================================================================
// ----------------------------------------------------------------------------
// Function assignQualityValue()
// ----------------------------------------------------------------------------
// Documentation is in alphabet_concept.h.
// ----------------------------------------------------------------------------
// Function getQualityValue()
// ----------------------------------------------------------------------------
// Documentation is in alphabet_concept.h.
// ----------------------------------------------------------------------------
// Function convertQuality()
// ----------------------------------------------------------------------------
// TODO(holtgrew): This could use some thought, what about other scales?
/*!
* @fn convertQuality
* @headerfile <seqan/basic.h>
*
* @brief Convert an integer quality value into its ASCII representation for FASTQ (Phred scale).
*
* @signature void convertQuality(c, q);
*
* @param[in] q Value of the quality to convert. The quality value is an integral value between 0 and 62
* (inclusive), <tt>int</tt>.
* @param[out] c Character to store the quality in, <tt>char</tt>.
*
* @see AlphabetWithQualitiesConcept#getQualityValue
* @see AlphabetWithQualitiesConcept#assignQualityValue
*/
inline
void convertQuality(char & c, int q)
{
c = '!' + char(q);
}
} // namespace seqan
#endif // #ifndef SEQAN_INCLUDE_SEQAN_BASIC_ALPHABET_QUALITIES_H_
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