fasta_parser.hpp File Reference

#include <cuda/std/cstdint>
#include <memory>
#include <optional>
#include <string>
#include <string_view>
#include <thread>
#include <utility>
#include <vector>
#include <cuddl/detail/dna.hpp>
#include <cuddl/detail/fastx_sequence_file.hpp>
#include <cuddl/error.hpp>

Include dependency graph for fasta_parser.hpp:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Classes
struct	cuddl::detail::fasta_parse_result
	Result of parsing one FASTA/FASTQ file into packed canonical k-mers. More...
struct	cuddl::detail::fastx_sequence_span
	One parallel scan span of the combined FASTA sequence stream. More...
struct	cuddl::detail::span_result
	One worker's rolling-window state and output. More...

Namespaces
namespace	cuddl
	Batch operations over contiguous device rows.
namespace	cuddl::detail

Functions
constexpr uint64_t	cuddl::detail::reverse_complement (uint64_t packed, uint32_t k) noexcept
	Reverse-complements a packed k-mer (2 bits per base) with bit-parallel reversal.
std::vector< fastx_sequence_span >	cuddl::detail::fastx_split_sequence_spans (std::vector< fastx_sequence_extent > const &extents, uint32_t seed_bases, uint32_t count)
	Splits the combined FASTA sequence stream into count contiguous spans.
void	cuddl::detail::consume_byte (char ch, uint32_t k, uint64_t mask, span_result &result, uint64_t &window, uint32_t &window_len)
	Feeds one byte of sequence through the DDL rolling-window extraction.
Result< fasta_parse_result >	cuddl::detail::parse_fasta (std::string const &path, uint32_t k, unsigned threads=std::thread::hardware_concurrency())
	Parses a FASTA/FASTQ file's sequence bases into packed canonical k-mers of length k.