libpbbam-dev 0.7.4+ds-1 / usr / include / pbbam / PbiIndex.h

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// File Description
/// \file PbiIndex.h
/// \brief Defines the PbiIndex class.
//
// Author: Derek Barnett

#ifndef PBIINDEX_H
#define PBIINDEX_H

#include "pbbam/Config.h"
#include "pbbam/PbiFile.h"
#include "pbbam/PbiLookupData.h"
#include <memory>
#include <string>

namespace PacBio {
namespace BAM {

namespace internal { class PbiIndexPrivate; }

/// \brief The PbiIndex class provides an representation of PBI index data that
///        is rearranged for quick lookups.
///
/// The PbiIndex class itself provides access to a few high-level attributes
/// (e.g. version, number of records, etc.). The actual lookup data is stored
/// in its member components:
///     BasicLookupData,
///     MappedLookupData,
///     ReferenceLookupData, &
///     BarcodeLookupData .
///
class PBBAM_EXPORT PbiIndex
{
public:
    /// \name Constructors & Related Methods
    /// \{

    /// \brief Creates a PbiIndex lookup structure from a PBI file.
    ///
    /// \param[in] pbiFilename  filename
    ///
    /// \throws std::runtime_error if failed to load data from file
    ///
    PbiIndex(const std::string& pbiFilename);

    PbiIndex(const PbiIndex& other);
    PbiIndex(PbiIndex&& other);
    PbiIndex& operator=(const PbiIndex& other);
    PbiIndex& operator=(PbiIndex&& other);
    ~PbiIndex(void);

    /// \}

public:
    /// \name PBI General Attributes
    /// \{

    /// \returns true if index has BarcodeData section
    bool HasBarcodeData(void) const;

    /// \returns true if index has MappedData section
    bool HasMappedData(void) const;

    /// \returns true if index has ReferenceData section
    bool HasReferenceData(void) const;

    /// \returns true if index has \b section
    /// \param[in] section PbiFile::Section identifier
    ///
    bool HasSection(const PbiFile::Section section) const;

    /// \returns index filename ("*.pbi")
    ///
    /// \note Returns an empty string if the underlying data was generated, not
    ///       loaded from file.
    ///
    std::string Filename(void) const;

    /// \returns enum flags representing the file sections present
    PbiFile::Sections FileSections(void) const;

    /// \returns the number of records in the PBI (& associated %BAM)
    uint32_t NumReads(void) const;

    /// \returns the PBI file's version
    PbiFile::VersionEnum Version(void) const;

    /// \}

public:
    /// \name Lookup Data Components
    /// \{

    /// \returns const reference to BarcodeData lookup structure
    ///
    /// May be empty, check result of HasBarcodeData.
    ///
    const BarcodeLookupData& BarcodeData(void) const;

    /// \returns const reference to BasicData lookup structure
    const BasicLookupData& BasicData(void) const;

    /// \returns const reference to MappedData lookup structure
    ///
    /// May be empty, check result of HasMappedData.
    ///
    const MappedLookupData& MappedData(void) const;

    /// \returns const reference to reference data lookup structure
    ///
    /// May be empty, check result of HasReferenceData.
    ///
    const ReferenceLookupData& ReferenceData(void) const;

    /// }

private:
    PbiIndex(void);
    std::unique_ptr<internal::PbiIndexPrivate> d_;
};

} // namespace BAM
} // namespace PacBio

#include "internal/PbiIndex.inl"

#endif // PBIINDEX_H