/usr/include/pbbam/internal/QualityValues.inl is in libpbbam-dev 0.7.4+ds-1build2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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//
// All rights reserved.
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// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) 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 Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS 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,
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// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
//
// File Description
/// \file QualityValues.inl
/// \brief Inline implementations for the QualityValues class.
//
// Author: Derek Barnett
#include "pbbam/QualityValues.h"
#include <algorithm>
namespace PacBio {
namespace BAM {
inline QualityValues::QualityValues(void)
: std::vector<QualityValue>()
{ }
inline QualityValues::QualityValues(const std::string& fastqString)
: std::vector<QualityValue>()
{
resize(fastqString.size());
std::transform(fastqString.cbegin(), fastqString.cend(),
begin(), QualityValue::FromFastq);
}
inline QualityValues::QualityValues(const std::vector<QualityValue>& quals)
: std::vector<QualityValue>(quals)
{ }
inline QualityValues::QualityValues(const std::vector<uint8_t>& quals)
: std::vector<QualityValue>()
{
resize(quals.size());
std::copy(quals.cbegin(), quals.cend(), begin());
}
inline QualityValues::QualityValues(const std::vector<uint8_t>::const_iterator first,
const std::vector<uint8_t>::const_iterator last)
: std::vector<QualityValue>(first, last)
{ }
inline QualityValues::QualityValues(const QualityValues::const_iterator first,
const QualityValues::const_iterator last)
: std::vector<QualityValue>()
{
assign(first, last);
}
inline QualityValues::QualityValues(const QualityValues& other)
: std::vector<QualityValue>(other)
{ }
inline QualityValues::QualityValues(std::vector<QualityValue>&& quals)
: std::vector<QualityValue>(std::move(quals))
{ }
inline QualityValues::QualityValues(QualityValues&& other)
: std::vector<QualityValue>(std::move(other))
{ }
inline QualityValues& QualityValues::operator=(const QualityValues& other)
{ std::vector<QualityValue>::operator=(other); return *this; }
inline QualityValues& QualityValues::operator=(const std::vector<QualityValue>& quals)
{ std::vector<QualityValue>::operator=(quals); return *this; }
inline QualityValues& QualityValues::operator=(QualityValues&& other)
{ std::vector<QualityValue>::operator=(std::move(other)); return *this; }
inline QualityValues& QualityValues::operator=(std::vector<QualityValue>&& quals)
{ std::vector<QualityValue>::operator=(std::move(quals)); return *this; }
inline QualityValues::~QualityValues(void) { }
inline std::vector<QualityValue>::const_iterator QualityValues::cbegin(void) const
{ return std::vector<QualityValue>::cbegin(); }
inline std::vector<QualityValue>::const_iterator QualityValues::cend(void) const
{ return std::vector<QualityValue>::cend(); }
inline std::vector<QualityValue>::const_iterator QualityValues::begin(void) const
{ return std::vector<QualityValue>::begin(); }
inline std::vector<QualityValue>::const_iterator QualityValues::end(void) const
{ return std::vector<QualityValue>::end(); }
inline std::vector<QualityValue>::iterator QualityValues::begin(void)
{ return std::vector<QualityValue>::begin(); }
inline std::vector<QualityValue>::iterator QualityValues::end(void)
{ return std::vector<QualityValue>::end(); }
inline QualityValues QualityValues::FromFastq(const std::string& fastq)
{ return QualityValues(fastq); }
inline std::string QualityValues::Fastq(void) const
{
std::string result;
result.reserve(size());
auto iter = cbegin();
const auto end = cend();
for (; iter != end; ++iter)
result.push_back((*iter).Fastq());
return result;
}
inline bool QualityValues::operator==(const std::string& fastq) const
{ return *this == QualityValues(fastq); }
inline bool QualityValues::operator!=(const std::string& fastq) const
{ return *this != QualityValues(fastq); }
} // namespace BAM
} // namespace PacBio
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