/usr/include/pbbam/internal/BamHeader.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.
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//
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// 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
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// 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,
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
//
// File Description
/// \file BamHeader.inl
/// \brief Inline implementations for the BamHeader class.
//
// Author: Derek Barnett
#include "pbbam/BamHeader.h"
namespace PacBio {
namespace BAM {
namespace internal {
class BamHeaderPrivate
{
public:
std::string version_;
std::string pacbioBamVersion_;
std::string sortOrder_;
std::map<std::string, std::string> headerLineCustom_;
std::map<std::string, ReadGroupInfo> readGroups_; // id => read group info
std::map<std::string, ProgramInfo> programs_; // id => program info
std::vector<std::string> comments_;
// we need to preserve insertion order, use lookup for access by name
std::vector<SequenceInfo> sequences_;
std::map<std::string, int32_t> sequenceIdLookup_;
};
} // namespace internal
inline BamHeader::BamHeader(void)
: d_(new internal::BamHeaderPrivate)
{ }
inline BamHeader::BamHeader(const BamHeader& other)
: d_(other.d_)
{ }
inline BamHeader::BamHeader(BamHeader&& other)
: d_(std::move(other.d_))
{ }
inline BamHeader& BamHeader::operator=(const BamHeader& other)
{ d_ = other.d_; return *this; }
inline BamHeader& BamHeader::operator=(BamHeader&& other)
{ d_ = std::move(other.d_); return *this; }
inline BamHeader::~BamHeader(void) { }
inline BamHeader BamHeader::operator+(const BamHeader& other) const
{ return DeepCopy() += other; }
inline BamHeader& BamHeader::AddComment(const std::string& comment)
{ d_->comments_.push_back(comment); return *this; }
inline BamHeader& BamHeader::AddProgram(const ProgramInfo& pg)
{ d_->programs_[pg.Id()] = pg; return *this; }
inline BamHeader& BamHeader::AddReadGroup(const ReadGroupInfo& readGroup)
{ d_->readGroups_[readGroup.Id()] = readGroup; return *this; }
inline BamHeader& BamHeader::ClearComments(void)
{ d_->comments_.clear(); return* this; }
inline BamHeader& BamHeader::ClearPrograms(void)
{ d_->programs_.clear(); return *this; }
inline BamHeader& BamHeader::ClearReadGroups(void)
{ d_->readGroups_.clear(); return *this; }
inline std::vector<std::string> BamHeader::Comments(void) const
{ return d_->comments_; }
inline BamHeader& BamHeader::Comments(const std::vector<std::string>& comments)
{ d_->comments_ = comments; return *this; }
inline bool BamHeader::HasProgram(const std::string& id) const
{ return d_->programs_.find(id) != d_->programs_.cend(); }
inline bool BamHeader::HasReadGroup(const std::string& id) const
{ return d_->readGroups_.find(id) != d_->readGroups_.cend(); }
inline bool BamHeader::HasSequence(const std::string& name) const
{ return d_->sequenceIdLookup_.find(name) != d_->sequenceIdLookup_.cend(); }
inline size_t BamHeader::NumSequences(void) const
{ return d_->sequences_.size(); }
inline std::string BamHeader::PacBioBamVersion(void) const
{ return d_->pacbioBamVersion_; }
inline SequenceInfo BamHeader::Sequence(const int32_t id) const
{ return d_->sequences_.at(id); }
inline std::string BamHeader::SequenceLength(const int32_t id) const
{ return Sequence(id).Length(); }
inline std::string BamHeader::SequenceName(const int32_t id) const
{ return Sequence(id).Name(); }
inline std::vector<SequenceInfo> BamHeader::Sequences(void) const
{ return d_->sequences_; }
inline std::string BamHeader::SortOrder(void) const
{ return d_->sortOrder_; }
inline BamHeader& BamHeader::SortOrder(const std::string& order)
{ d_->sortOrder_ = order; return *this; }
inline std::string BamHeader::Version(void) const
{ return d_->version_; }
inline BamHeader& BamHeader::Version(const std::string& version)
{ d_->version_ = version; return *this; }
} // namespace BAM
} // namespace PacBio
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