/usr/include/pbbam/GenomicIntervalQuery.h is in libpbbam-dev 0.7.4+ds-1.
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// File Description
/// \file GenomicIntervalQuery.h
/// \brief Defines the GenomicIntervalQuery class.
//
// Author: Derek Barnett
#ifndef GENOMICINTERVALQUERY_H
#define GENOMICINTERVALQUERY_H
#include "pbbam/GenomicInterval.h"
#include "pbbam/internal/QueryBase.h"
#include <memory>
namespace PacBio {
namespace BAM {
/// \brief The GenomicIntervalQuery class provides iterable access to a
/// DataSet's %BAM records, limiting results to those overlapping a
/// GenomicInterval.
///
/// Example:
/// \include code/GenomicIntervalQuery.txt
///
/// \note Currently, all %BAM files must have a corresponding ".bai" index file.
/// Use BamFile::EnsureStandardIndexExists before creating the query if
/// one may not be present.
///
class PBBAM_EXPORT GenomicIntervalQuery : public internal::IQuery
{
public:
/// \brief Constructs a new GenomiIntervalQuery, limiting record results to
/// only those overalpping a GenomicInterval.
///
/// \param[in] interval genomic interval of interest
/// \param[in] dataset input data source(s)
///
/// \throws std::runtime_error on failure to open/read underlying %BAM or
/// BAI files.
///
GenomicIntervalQuery(const GenomicInterval& interval,
const PacBio::BAM::DataSet& dataset);
~GenomicIntervalQuery(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);
public:
/// \brief Sets a new genomic interval.
///
/// This allows the same dataset/query to be re-used over multiple regions of
/// interest:
///
/// \include code/GenomicIntervalQuery_Reuse.txt
///
/// \param[in] interval new genomic interval
/// \returns reference to this query
///
GenomicIntervalQuery& Interval(const GenomicInterval& interval);
/// \returns Current genomic interval active on this query.
const GenomicInterval& Interval(void) const;
private:
struct GenomicIntervalQueryPrivate;
std::unique_ptr<GenomicIntervalQueryPrivate> d_;
};
} // namespace BAM
} // namspace PacBio
#endif // GENOMICINTERVALQUERY_H
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