Fastx.hpp File Reference

#include <algorithm>
#include <concepts>
#include <cstdint>
#include <filesystem>
#include <format>
#include <fstream>
#include <istream>
#include <memory>
#include <span>
#include <stdexcept>
#include <string>
#include <string_view>
#include <utility>
#include <vector>
#include <cusbf/error.hpp>
#include <cusbf/gzstreambuf.hpp>

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Classes
struct	cusbf::RecordRange
	Ordered non-overlapping byte range for one record inside a dense sequence batch. More...
struct	cusbf::RecordBatchView
	Dense host-resident sequence batch plus explicit record boundaries. More...
class	cusbf::DenseRecordBatchBuilder
	Accumulates parsed FASTX records into a dense RecordBatchView. More...
struct	cusbf::RecordQueryView
	Per-record query payload emitted by query_record_batch(). More...
struct	cusbf::FastxInsertReport
	Summary statistics returned by Filter insert operations on FASTX and record-batch input. More...
struct	cusbf::FastxQueryReport
	Summary statistics returned by Filter query operations on FASTX and record-batch input. More...
struct	cusbf::FastxRecordView
	Per-record query payload emitted by FASTX streaming query APIs. More...
struct	cusbf::FastxDetailedQueryRecord
	Detailed per-record query results returned by Filter FASTX detail APIs. More...
struct	cusbf::FastxDetailedQueryReport
	Aggregate and per-record results returned by Filter FASTX detail APIs. More...
struct	cusbf::detail::FastxRecord
	A single sequence record extracted from a FASTA/FASTQ stream. More...
class	cusbf::detail::FastxReader
	Streaming FASTA/FASTQ parser. More...

Namespaces
namespace	cusbf
namespace	cusbf::detail

Concepts
concept	cusbf::RecordQueryConsumer
	Callable invoked once per record by Filter::query_record_batch overloads that take a callback.
concept	cusbf::FastxRecordConsumer
	Callable invoked once per record by Filter::query_fastx_records and related FASTX streaming query APIs.

Enumerations
enum class	cusbf::detail::FastxFormat : uint8_t { cusbf::detail::unknown , cusbf::detail::fasta , cusbf::detail::fastq }
	Detected file format for a FASTA/FASTQ stream. More...

Functions
void	cusbf::detail::trimTrailingCarriageReturn (std::string &line)
	Removes a trailing carriage return from line if present (Windows line endings).
uint32_t	cusbf::detail::fastx_column_at (std::string_view line, size_t byte_index)
	1-based column at byte_index within line (clamped to the line end).
uint32_t	cusbf::detail::fastx_quality_excess_column (uint64_t quality_length, uint64_t expected_length, std::string_view line)
	1-based column of the first quality byte that exceeds expected_length.
uint32_t	cusbf::detail::fastx_quality_short_column (std::string_view line)
	1-based column where a quality run ends too short (position after the last byte).
Result< std::unique_ptr< std::istream > >	cusbf::detail::openFastxFile (const std::filesystem::path &path)
	Opens a FASTA/FASTQ file for reading.