/usr/include/pbbam/EntireFileQuery.h 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.
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 | // 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 EntireFileQuery.h
/// \brief Defines the EntireFileQuery class.
//
// Author: Derek Barnett
#ifndef ENTIREFILEQUERY_H
#define ENTIREFILEQUERY_H
#include "pbbam/internal/QueryBase.h"
#include <memory>
namespace PacBio {
namespace BAM {
/// \brief The EntireFileQuery class provides iterable access to a DataSet's
/// %BAM records, reading through the entire contents of each file.
///
/// Input files will be accessed in the order listed in the DataSet.
///
/// \include code/EntireFileQuery.txt
///
/// Iteration is not limited to only 'const' records. The files themselves will
/// not be affected, but individual records may be modified if needed.
///
/// \include code/EntireFileQuery_NonConst.txt
///
/// \note DataSets can be implicitly constructed from %BAM filenames as well.
/// Thus a single %BAM file can be read through using the following:
///
/// \include code/EntireFileQuery_BamFilename.txt
///
class PBBAM_EXPORT EntireFileQuery : public internal::IQuery
{
public:
/// \brief Creates a new EntireFileQuery, reading through the entire
/// contents of a dataset.
///
/// \param[in] dataset input data source(s)
/// \throws std::runtime_error on failure to open/read underlying %BAM
/// files.
///
EntireFileQuery(const PacBio::BAM::DataSet& dataset);
~EntireFileQuery(void);
public:
/// \brief Main iteration point for record access.
///
/// Most client code should not need to use this method directly. Use
/// iterators instead.
///
bool GetNext(BamRecord& r);
private:
struct EntireFileQueryPrivate;
std::unique_ptr<EntireFileQueryPrivate> d_;
};
} // namespace BAM
} // namspace PacBio
#endif // ENTIREFILEQUERY_H
|