/usr/include/pbbam/BaiIndexedBamReader.h is in libpbbam-dev 0.7.4+ds-1.
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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.
//
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// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
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// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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// SUCH DAMAGE.
//
// File Description
/// \file BaiIndexedBamReader.h
/// \brief Defines the BaiIndexedBamReader class.
//
// Author: Derek Barnett
#ifndef BAIINDEXEDBAMREADER_H
#define BAIINDEXEDBAMREADER_H
#include "pbbam/BamReader.h"
#include "pbbam/BamFile.h"
#include "pbbam/GenomicInterval.h"
namespace PacBio {
namespace BAM {
namespace internal { struct BaiIndexedBamReaderPrivate; }
/// \brief The BaiIndexedBamReader class provides read-only iteration over %BAM
/// records, bounded by a particular genomic interval.
///
/// The SAM/BAM standard index (*.bai) is used to allow random-access operations.
///
class PBBAM_EXPORT BaiIndexedBamReader : public BamReader
{
public:
/// \name Constructors & Related Methods
/// \{
/// \brief Constructs %BAM reader, bounded by a genomic interval.
///
/// All reads that overlap the interval will be available.
///
/// \param[in] interval iteration will be bounded by this GenomicInterval.
/// \param[in] filename input %BAM filename
///
/// \throws std::runtime_error if either file (*.bam or *.bai) fails to open
/// for reading, or if the interval is invalid
///
BaiIndexedBamReader(const GenomicInterval& interval,
const std::string& filename);
/// \brief Constructs BAM reader, bounded by a genomic interval.
///
/// All reads that overlap the interval will be available.
///
/// \param[in] interval iteration will be bounded by this GenomicInterval.
/// \param[in] bamFile input BamFile object
///
/// \throws std::runtime_error if either file (*.bam or *.bai) fails to open
/// for reading, or if the interval is invalid
///
BaiIndexedBamReader(const GenomicInterval& interval, const BamFile& bamFile);
/// \brief Constructs %BAM reader, bounded by a genomic interval.
///
/// All reads that overlap the interval will be available.
///
/// \param[in] interval iteration will be bounded by this GenomicInterval.
/// \param[in] bamFile input BamFile object
///
/// \throws std::runtime_error if either file (*.bam or *.bai) fails to open
/// for reading, or if the interval is invalid
///
BaiIndexedBamReader(const GenomicInterval& interval, BamFile&& bamFile);
/// \}
public:
/// \name Random-Access
/// \{
/// \returns the current GenomicInterval in use by this reader
const GenomicInterval& Interval(void) const;
/// \brief Sets a new genomic interval on the reader.
///
/// \param[in] interval
/// \returns reference to this reader
///
BaiIndexedBamReader& Interval(const GenomicInterval& interval);
/// \}
protected:
int ReadRawData(BGZF* bgzf, bam1_t* b);
private:
std::unique_ptr<internal::BaiIndexedBamReaderPrivate> d_;
};
} // namespace BAM
} // namespace PacBio
#endif // BAIINDEXEDBAMREADER_H
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