/usr/include/pbbam/PbiIndexedBamReader.h is in libpbbam-dev 0.7.4+ds-1.
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//
// 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
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// 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 PbiIndexedBamReader.h
/// \brief Defines the PbiIndexedBamReader class.
//
// Author: Derek Barnett
#ifndef PBIINDEXEDBAMREADER_H
#define PBIINDEXEDBAMREADER_H
#include "pbbam/BamFile.h"
#include "pbbam/BamReader.h"
#include "pbbam/PbiBasicTypes.h"
#include "pbbam/PbiFilter.h"
#include "pbbam/PbiIndex.h"
#include <string>
namespace PacBio {
namespace BAM {
namespace internal { struct PbiIndexedBamReaderPrivate; }
/// \brief The PbiIndexedBamReader class provides read-only iteration over %BAM
/// records, limited to some filtering criteria.
///
/// The PacBio BAM index (*.pbi) is used to allow random-access operations.
///
class PBBAM_EXPORT PbiIndexedBamReader : public BamReader
{
public:
/// \name Constructors & Related Methods
/// \{
/// \brief Constructs %BAM reader, with an initial filter.
///
/// All reads that satisfy the filter will be available.
///
/// \param[in] filter PbiFilter or compatible object
/// \param[in] bamFilename input %BAM filename
///
/// \throws std::runtime_error if either file (*.bam or *.pbi) cannot be
/// read
///
PbiIndexedBamReader(const PbiFilter& filter, const std::string& bamFilename);
/// \brief Constructs %BAM reader, with an initial filter.
///
/// All reads that satisfy the filter will be available.
///
/// \param[in] filter PbiFilter or compatible object
/// \param[in] bamFile input BamFile object
///
/// \throws std::runtime_error if either file (*.bam or *.pbi) cannot be
/// read
///
PbiIndexedBamReader(const PbiFilter& filter, const BamFile& bamFile);
/// \brief Constructs %BAM reader, with an initial filter.
///
/// All reads that satisfy the filter will be available.
///
/// \param[in] filter PbiFilter or compatible object
/// \param[in] bamFile input BamFile object
///
/// \throws std::runtime_error if either file (*.bam or *.pbi) cannot be
/// read
///
PbiIndexedBamReader(const PbiFilter& filter, BamFile&& bamFile);
/// \brief Constructs %BAM reader, with no initial filter.
///
/// Useful for delaying either specifying the filtering criteria or
/// performing the PBI lookups.
///
/// \param[in] bamFilename input %BAM filename
///
/// \throws std::runtime_error if either file (*.bam or *.pbi) cannot be
/// read
///
PbiIndexedBamReader(const std::string& bamFilename);
/// \brief Constructs %BAM reader, with no initial filter.
///
/// Useful for delaying either specifying the filtering criteria or
/// performing the PBI lookups.
///
/// \param[in] bamFile input BamFile object
///
/// \throws std::runtime_error if either file (*.bam or *.pbi) cannot be
/// read
///
PbiIndexedBamReader(const BamFile& bamFile);
/// \brief Constructs %BAM reader, with no initial filter.
///
/// Useful for delaying either specifying the filtering criteria or
/// performing the PBI lookups.
///
/// \param[in] bamFile input BamFile object
///
/// \throws std::runtime_error if either file (*.bam or *.pbi) cannot be
/// read
///
PbiIndexedBamReader(BamFile&& bamFile);
~PbiIndexedBamReader(void);
/// \}
public:
/// \name Filtering & Index Data
/// \{
/// \returns the current filter active on this reader
const PbiFilter& Filter(void) const;
// /// \returns the reader's underlying index data
// const PbiIndex& Index(void) const;
public:
/// \brief Sets a new filter on the reader.
///
/// \param[in] filter
/// \returns reference to this reader
///
PbiIndexedBamReader& Filter(const PbiFilter& filter);
/// \}
protected:
int ReadRawData(BGZF* bgzf, bam1_t* b);
private:
std::unique_ptr<internal::PbiIndexedBamReaderPrivate> d_;
};
} // namespace internal
} // namespace BAM
#endif // PBIINDEXEDBAMREADER_H
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