/usr/include/pbbam/internal/QualityValues.inl is in libpbbam-dev 0.7.4+ds-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 | // Copyright (c) 2014-2015, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// 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,
// 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.
//
// 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
|