/usr/include/pbbam/ReadAccuracyQuery.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 | // 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 ReadAccuracyQuery.h
/// \brief Defines the ReadAccuracyQuery class.
//
// Author: Derek Barnett
#ifndef READACCURACYQUERY_H
#define READACCURACYQUERY_H
#include "pbbam/Accuracy.h"
#include "pbbam/Compare.h"
#include "pbbam/Config.h"
#include "pbbam/internal/QueryBase.h"
#include <vector>
namespace PacBio {
namespace BAM {
/// \brief The ReadAccuracyQuery class provides iterable access to a DataSet's
/// %BAM records, limiting results to those matching a read accuracy
/// criterion.
///
/// Example:
/// \include code/ReadAccuracyQuery.txt
///
/// \note Currently, all %BAM files must have a corresponding ".pbi" index file.
/// Use BamFile::EnsurePacBioIndexExists before creating the query if one
/// may not be present.
///
class PBBAM_EXPORT ReadAccuracyQuery : public internal::IQuery
{
public:
/// \brief Creates a new ReadAccuracyQuery, limiting record results to only
/// those matching a read accuracy criterion.
///
/// \param[in] accuracy read accuracy value
/// \param[in] compareType compare operator
/// \param[in] dataset input data source(s)
///
/// \sa BamRecord::ReadAccuracy
///
/// \throws std::runtime_error on failure to open/read underlying %BAM or PBI
/// files.
///
ReadAccuracyQuery(const Accuracy accuracy,
const Compare::Type compareType,
const DataSet& dataset);
~ReadAccuracyQuery(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 ReadAccuracyQueryPrivate;
std::unique_ptr<ReadAccuracyQueryPrivate> d_;
};
} // namespace BAM
} // namespace PacBio
#endif // READACCURACYQUERY_H
|