New upstream version 0.19.0+dfsg (25ba6fde) · Commits · Debian Med / pbbam

CHANGELOG.md

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		## Active

		## [0.19.0] - 2018-09-11

		### Added
		- TranscriptAlignmentSet to XML support

		## [0.17.0] - 2018-03-18

		### Added

CMakeLists.txt

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		########################################################################

		cmake_policy(SET CMP0048 NEW) # lets us set version in project()
		project(PacBioBAM VERSION 0.17.0 LANGUAGES CXX C)
		project(PacBioBAM VERSION 0.19.0 LANGUAGES CXX C)
		cmake_minimum_required(VERSION 3.0)

		# project name & version

include/pbbam/BamWriter.h

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		@@ -87,14 +87,39 @@ public:
		BinCalculation_OFF
		};

		///
		/// \brief The Config struct provides a "parameter object" for BamWriter
		/// settings. This allows for writer configuration without having to
		/// refer to ordering of parameters, default values, etc.
		///
		struct Config
		{
		Config() = default;

		// zlib compression level
		CompressionLevel compressionLevel = DefaultCompression;

		// The number of threads for compression. If set to 0, BamWriter 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.
		size_t numThreads = 4;

		// If ON, ensures that proper BAI bin numbers are provided for all records.
		BamWriter::BinCalculationMode binCalculationMode = BamWriter::BinCalculation_ON;

		// If true, write to <filename>.tmp, and rename to <filename> in dtor.
		// This allows downstream checks to see if BAM file may be truncated
		// due to early termination (e.g. a thrown exception). If false, write
		// directly to <filename>.
		bool useTempFile = true;
		};

		public:
		/// \name Constructors & Related Methods
		/// \{

		/// \brief Opens a %BAM file for writing & writes the header information.
		///
		/// The error status will be set if either operation fails.
		///
		/// \note Set \p filename to "-" for stdout.
		///
		/// \param[in] filename path to output %BAM file
		@@ -111,13 +136,32 @@ public:
		/// records written. This extra step may turned off when bin
		/// numbers are not needed. Though if in doubt, keep the default.
		///
		/// \param[in] useTempFile If true, write to <filename>.tmp, and rename
		/// to <filename>. This provides for downstream
		/// checks to see if BAM file may be truncated
		/// due to early termination (a thrown exception).
		///
		/// \throws std::runtmie_error if there was a problem opening the file for
		/// writing or if an error occurred while writing the header
		///
		BamWriter(const std::string& filename, const BamHeader& header,
		const BamWriter::CompressionLevel compressionLevel = BamWriter::DefaultCompression,
		const size_t numThreads = 4,
		const BinCalculationMode binCalculationMode = BamWriter::BinCalculation_ON);
		const BinCalculationMode binCalculationMode = BamWriter::BinCalculation_ON,
		const bool useTempFile = true);

		///
		/// \brief Opens a %BAM file for writing & writes the header information.
		///
		/// \param[in] filename path to output %BAM file
		/// \param[in] header BamHeader object
		/// \param[in] config container for add'l configuration options
		///
		/// \throws std::runtmie_error if there was a problem opening the file for
		/// writing or if an error occurred while writing the header
		///
		BamWriter(const std::string& filename, const BamHeader& header,
		const BamWriter::Config& config);

		/// Fully flushes all buffered data & closes file.
		~BamWriter() override;

include/pbbam/Compare.h

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		};

		/// \}

		template <typename T>
		static inline bool Check(const T& lhs, const T& rhs, const Compare::Type cmp)
		{
		switch (cmp) {
		case Compare::EQUAL:
		return lhs == rhs;
		case Compare::LESS_THAN:
		return lhs < rhs;
		case Compare::LESS_THAN_EQUAL:
		return lhs <= rhs;
		case Compare::GREATER_THAN:
		return lhs > rhs;
		case Compare::GREATER_THAN_EQUAL:
		return lhs >= rhs;
		case Compare::NOT_EQUAL:
		return lhs != rhs;
		default:
		assert(false);
		throw std::runtime_error{"unsupported compare type requested"};
		}
		}
		};

		} // namespace BAM

include/pbbam/DataSet.h

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		HDF_SUBREAD,
		REFERENCE,
		SUBREAD,
		TRANSCRIPT
		TRANSCRIPT,
		TRANSCRIPT_ALIGNMENT
		};

		/// \brief Converts printable dataset type to type enum.