fastx_sequence_scan.hpp File Reference

#include <cstdint>
#include <string>
#include <string_view>
#include <utility>
#include <vector>
#include <cusbf/Alphabet.cuh>
#include <cusbf/detail/fastx_buffer_reader.hpp>

Include dependency graph for fastx_sequence_scan.hpp:

Go to the source code of this file.

Classes
struct	cusbf::detail::fastx_sequence_extent
	A contiguous run of sequence bytes (record header lines excluded). More...
struct	cusbf::detail::fastx_sequence_span
	One parallel scan span of the combined FASTA sequence stream. More...

Namespaces
namespace	cusbf
namespace	cusbf::detail

Functions
constexpr bool	cusbf::detail::fastx_is_sequence_whitespace (char ch) noexcept
	True for bytes that FASTA sequence consumers conventionally skip between bases.
std::vector< fastx_sequence_extent >	cusbf::detail::fastx_fasta_extents (std::string_view data)
	Collects the sequence extents of every FASTA record in data.
std::vector< fastx_sequence_span >	cusbf::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.