/usr/include/pbbam/PbiBuilder.h is in libpbbam-dev 0.7.4+ds-1.
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//
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// 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.
//
// 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
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// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
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// 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 PbiBuilder.h
/// \brief Defines the PbiBuilder class.
//
// Author: Derek Barnett
#ifndef PBIBUILDER_H
#define PBIBUILDER_H
#include "pbbam/Config.h"
#include <memory>
#include <string>
namespace PacBio {
namespace BAM {
class BamRecord;
class PbiRawData;
namespace internal { class PbiBuilderPrivate; }
/// \brief The PbiBuilder class construct PBI index data from %BAM record data.
///
/// Records are added one-by-one. This allows for either whole-file indexing of
/// existing %BAM files or for indexing "on-the-fly" alongside a %BAM file as it
/// is generated.
///
/// For simple PBI creation from existing %BAM files, see PbiFile::CreateFrom.
/// This is the recommended approach, unless finer control or additional
/// processing is needed.
///
class PBBAM_EXPORT PbiBuilder
{
public:
/// \brief This enum allows you to control the compression level of the
/// output PBI file.
///
/// Values are equivalent to zlib compression levels. See its documentation
/// for more details: http://www.zlib.net/manual.html
///
enum CompressionLevel
{
CompressionLevel_0 = 0
, CompressionLevel_1 = 1
, CompressionLevel_2 = 2
, CompressionLevel_3 = 3
, CompressionLevel_4 = 4
, CompressionLevel_5 = 5
, CompressionLevel_6 = 6
, CompressionLevel_7 = 7
, CompressionLevel_8 = 8
, CompressionLevel_9 = 9
, DefaultCompression = -1
, NoCompression = CompressionLevel_0
, FastCompression = CompressionLevel_1
, BestCompression = CompressionLevel_9
};
public:
/// \name Constructors & Related Methods
/// \{
/// \brief Initializes builder to write data to \p pbiFilename.
///
/// \param[in] pbiFilename output filename
/// \param[in] compressionLevel zlib compression level
/// \param[in] numThreads number of threads for compression. If set to
/// 0, PbiBuilder will attempt to determine a
/// reasonable estimate. If set to 1, this will
/// force single-threaded execution. No checks
/// are made against an upper limit.
///
/// \throws std::runtime_error if PBI file cannot be opened for writing
///
PbiBuilder(const std::string& pbiFilename,
const PbiBuilder::CompressionLevel compressionLevel = PbiBuilder::DefaultCompression,
const size_t numThreads = 4);
/// \brief Initializes builder to write data to \p pbiFilename.
///
/// Reference data-tracking structures will be initialized to expect
/// \p numReferenceSequences. (This is useful so that we can mark any
/// references that lack observed data appropriately).
///
/// \param[in] pbiFilename output filename
/// \param[in] numReferenceSequences number of possible reference
/// sequences, e.g. BamHeader::NumSequences
/// \param[in] compressionLevel zlib compression level
/// \param[in] numThreads number of threads for compression. If set to
/// 0, PbiBuilder will attempt to determine a
/// reasonable estimate. If set to 1, this will
/// force single-threaded execution. No checks
/// are made against an upper limit.
///
/// \throws std::runtime_error if PBI file cannot be opened for writing
///
PbiBuilder(const std::string& pbiFilename,
const size_t numReferenceSequences,
const PbiBuilder::CompressionLevel compressionLevel = PbiBuilder::DefaultCompression,
const size_t numThreads = 4);
/// \brief Initializes builder to write data to \p pbiFilename.
///
/// Reference data-tracking structures will be initialized to expect
/// \p numReferenceSequences, but only if \p isCoordinateSorted is true.
///
/// \param[in] pbiFilename output filename
/// \param[in] numReferenceSequences number of possible reference
/// sequences, e.g. BamHeader::NumSequences
/// \param[in] isCoordinateSorted if false, disables reference
/// sequence tracking
/// (BamHeader::SortOrder != "coordinate")
/// \param[in] compressionLevel zlib compression level
/// \param[in] numThreads number of threads for compression. If set to
/// 0, PbiBuilder will attempt to determine a
/// reasonable estimate. If set to 1, this will
/// force single-threaded execution. No checks
/// are made against an upper limit.
///
/// \throws std::runtime_error if PBI file cannot be opened for writing
///
PbiBuilder(const std::string& pbiFilename,
const size_t numReferenceSequences,
const bool isCoordinateSorted,
const PbiBuilder::CompressionLevel compressionLevel = PbiBuilder::DefaultCompression,
const size_t numThreads = 4);
/// \brief Destroys builder, writing its data out to PBI file.
///
/// On destruction, data summaries are calculated, raw data is written to
/// file, and file handle closed.
///
~PbiBuilder(void);
/// \}
public:
/// \name Index Building
/// \{
/// \brief Adds \p record's data to underlying raw data structure.
///
/// \note \p vOffset is a BGZF \b virtual offset into the %BAM file. To get
/// this value, you should use one of the following: \n
/// - while reading existing %BAM: BamReader::VirtualTell \n
/// - while writing new %BAM: BamWriter::Write(const BamRecord& record, int64_t* vOffset) \n
///
///
/// To build a PBI index while generating a %BAM file:
/// \include code/PbiBuilder_WithWriter.txt
///
/// To build a PBI index from an existing %BAM file:
/// \include code/PbiBuilder_WithReader.txt
///
/// \param[in] record input BamRecord to pull index data from
/// \param[in] vOffset \b virtual offset into %BAM file where record begins
///
void AddRecord(const BamRecord& record, const int64_t vOffset);
/// \returns const reference to current raw index data. Mostly only used for
/// testing; shouldn't be needed by most client code.
///
const PbiRawData& Index(void) const;
/// \}
private:
std::unique_ptr<internal::PbiBuilderPrivate> d_;
};
} // namespace BAM
} // namespace PacBio
#endif // PBIBUILDER_H
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