/usr/include/pbbam/PbiIndex.h 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 | // 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 PbiIndex.h
/// \brief Defines the PbiIndex class.
//
// Author: Derek Barnett
#ifndef PBIINDEX_H
#define PBIINDEX_H
#include "pbbam/Config.h"
#include "pbbam/PbiFile.h"
#include "pbbam/PbiLookupData.h"
#include <memory>
#include <string>
namespace PacBio {
namespace BAM {
namespace internal { class PbiIndexPrivate; }
/// \brief The PbiIndex class provides an representation of PBI index data that
/// is rearranged for quick lookups.
///
/// The PbiIndex class itself provides access to a few high-level attributes
/// (e.g. version, number of records, etc.). The actual lookup data is stored
/// in its member components:
/// BasicLookupData,
/// MappedLookupData,
/// ReferenceLookupData, &
/// BarcodeLookupData .
///
class PBBAM_EXPORT PbiIndex
{
public:
/// \name Constructors & Related Methods
/// \{
/// \brief Creates a PbiIndex lookup structure from a PBI file.
///
/// \param[in] pbiFilename filename
///
/// \throws std::runtime_error if failed to load data from file
///
PbiIndex(const std::string& pbiFilename);
PbiIndex(const PbiIndex& other);
PbiIndex(PbiIndex&& other);
PbiIndex& operator=(const PbiIndex& other);
PbiIndex& operator=(PbiIndex&& other);
~PbiIndex(void);
/// \}
public:
/// \name PBI General Attributes
/// \{
/// \returns true if index has BarcodeData section
bool HasBarcodeData(void) const;
/// \returns true if index has MappedData section
bool HasMappedData(void) const;
/// \returns true if index has ReferenceData section
bool HasReferenceData(void) const;
/// \returns true if index has \b section
/// \param[in] section PbiFile::Section identifier
///
bool HasSection(const PbiFile::Section section) const;
/// \returns index filename ("*.pbi")
///
/// \note Returns an empty string if the underlying data was generated, not
/// loaded from file.
///
std::string Filename(void) const;
/// \returns enum flags representing the file sections present
PbiFile::Sections FileSections(void) const;
/// \returns the number of records in the PBI (& associated %BAM)
uint32_t NumReads(void) const;
/// \returns the PBI file's version
PbiFile::VersionEnum Version(void) const;
/// \}
public:
/// \name Lookup Data Components
/// \{
/// \returns const reference to BarcodeData lookup structure
///
/// May be empty, check result of HasBarcodeData.
///
const BarcodeLookupData& BarcodeData(void) const;
/// \returns const reference to BasicData lookup structure
const BasicLookupData& BasicData(void) const;
/// \returns const reference to MappedData lookup structure
///
/// May be empty, check result of HasMappedData.
///
const MappedLookupData& MappedData(void) const;
/// \returns const reference to reference data lookup structure
///
/// May be empty, check result of HasReferenceData.
///
const ReferenceLookupData& ReferenceData(void) const;
/// }
private:
PbiIndex(void);
std::unique_ptr<internal::PbiIndexPrivate> d_;
};
} // namespace BAM
} // namespace PacBio
#include "internal/PbiIndex.inl"
#endif // PBIINDEX_H
|