/usr/include/pbbam/PbiFile.h is in libpbbam-dev 0.7.4+ds-1build2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
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//
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// SUCH DAMAGE.
//
// File Description
/// \file PbiFile.h
/// \brief Defines the PbiFile enums, typedefs, and methods.
//
// Author: Derek Barnett
#ifndef PBIFILE_H
#define PBIFILE_H
#include "pbbam/Config.h"
#include "pbbam/PbiBuilder.h"
#include <string>
namespace PacBio {
namespace BAM {
class BamFile;
namespace PbiFile
{
/// \brief This enum describes the PBI file sections
///
enum Section
{
BASIC = 0x0000 ///< BasicData (required)
, MAPPED = 0x0001 ///< MappedData (always optional)
, REFERENCE = 0x0002 ///< ReferenceData (always optional)
, BARCODE = 0x0004 ///< BarcodeData (always optional)
, ALL = BASIC | MAPPED | REFERENCE | BARCODE ///< Synonym for 'all sections'
};
/// \brief Helper typedef for storing multiple Section flags.
///
typedef uint16_t Sections;
/// \brief This enum describes the PBI file version.
enum VersionEnum
{
Version_3_0_0 = 0x030000 ///< v3.0.0
, Version_3_0_1 = 0x030001 ///< v3.0.1
, CurrentVersion = Version_3_0_1 ///< Synonym for the current PBI version.
};
/// \brief Builds PBI index data from the supplied %BAM file and writes a
/// ".pbi" file.
///
/// \param[in] bamFile source %BAM file
///
/// \throws std::runtime_error if index file could not be created
///
PBBAM_EXPORT void CreateFrom(const BamFile& bamFile,
const PbiBuilder::CompressionLevel compressionLevel = PbiBuilder::DefaultCompression,
const size_t numThreads = 4);
} // namespace PbiFile
} // namespace BAM
} // namespace PacBio
#endif // PBIFILE_H
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