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| constexpr bool | cuddl::detail::fastx_is_sequence_whitespace (char ch) noexcept |
| | True for bytes that FASTA sequence consumers conventionally skip between bases.
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| size_t | cuddl::detail::fastx_line_end_scalar (std::string_view data, size_t position) |
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| fastx_line_end_fn | cuddl::detail::resolve_fastx_line_end () |
| | Selects the fastest line-end scanner the host supports.
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| size_t | cuddl::detail::fastx_line_end (std::string_view data, size_t position) |
| | First line-end position at or after position using the resolved scanner.
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| uint32_t | cuddl::detail::pack_bases16_portable (char const *bases, size_t count, uint32_t &word) |
| | Packs up to sixteen bases into a two-bit word, base j in bits 2j and 2j+1.
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| uint64_t | cuddl::detail::pack_bases_pieces (char const *bases, size_t count, uint32_t *words, size_t width) |
| | Packs width bases from sixteen-base pieces, for a tail shorter than a full step.
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| uint64_t | cuddl::detail::pack_bases_portable (char const *bases, size_t count, uint32_t *words) |
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| bases_packer | cuddl::detail::resolve_bases_packer () |
| | Selects the widest base packer the host supports.
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| void | cuddl::detail::pack_fastx_sequence_file (fastx_sequence_file &result, uint32_t k) |
| | Packs a parsed file's records in place into two-bit words, run by run.
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| libdeflate_result | cuddl::detail::decompress_gzip_member (libdeflate_decompressor *decoder, std::string_view input, char *output, size_t capacity, size_t &consumed, size_t &produced) |
| | Decodes one gzip member, checking structure and ISIZE but not checksums.
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| Result< void > | cuddl::detail::gunzip_members_into (std::string_view input, std::string &output, std::string const &path) |
| | Decompresses gzip members from a mapped buffer into output, appending.
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| Result< size_t > | cuddl::detail::gunzip_members_direct (std::string_view input, decompression_target target, bool &insufficient, std::string const &path) |
| | Decompresses gzip members straight into a caller's buffer.
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| uint64_t | cuddl::detail::gzip_decompressed_size (std::string const &path) |
| | Uncompressed size the gzip trailer advertises, or 0 when it cannot be read.
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| size_t | cuddl::detail::gzip_size_hint (std::string_view input) |
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| compact_shuffle_table const & | cuddl::detail::compact_impl::compact_shuffle () noexcept |
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| char * | cuddl::detail::compact_sequence_whitespace (char const *first, char const *last, char *out) |
| | Copies bases from [first, last) to out, dropping sequence whitespace.
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| char const * | cuddl::detail::fasta_next_header (char const *first, char const *last) |
| | First '>' in [first, last) that starts a line, or last.
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| char * | cuddl::detail::fasta_sequence_compact (char const *first, char const *last, char *out, char const *&stop) |
| | Compacts one FASTA record's sequence from first to out, stopping at the next header.
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| std::vector< fastx_sequence_extent > | cuddl::detail::fastx_fasta_compact_extents (std::string_view data, char *out) |
| | Collects FASTA sequence extents with whitespace compacted out, in one pass over data.
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| void | cuddl::detail::compact_fastx_sequence_extents (fastx_sequence_file &result) |
| | Compacts sequence whitespace in place, leaving every extent a run of bases.
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| Result< void > | cuddl::detail::parse_fastx_sequence_file (fastx_sequence_file &result, std::string const &path) |
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| Result< void > | cuddl::detail::pack_fasta_chunks (fastx_sequence_file &result, std::string_view data, char *out, uint32_t k, std::string const &path) |
| | Compact and pack one cache-sized block at a time, without a genome-sized ASCII write.
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| Result< std::unique_ptr< fastx_sequence_file > > | cuddl::detail::finish_fastx_sequence_file (std::unique_ptr< fastx_sequence_file > result, std::string_view data, std::string const &path, bool defer_fasta, uint32_t pack_k) |
| | Parses, packs or defers the bytes data of a loaded file, which result holds.
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| Result< std::optional< std::string_view > > | cuddl::detail::inflate_and_pack (fastx_sequence_file &result, std::string_view input, std::string const &path, decompression_source source, uint32_t k) |
| | Inflates gzip input in this thread's reusable heap buffer and, for FASTA, packs it there and moves only the packed words into a buffer from source.
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| Result< std::unique_ptr< fastx_sequence_file > > | cuddl::detail::decode_fastx_sequence_file (std::unique_ptr< fastx_mapped_file > file, std::string const &path, decompression_source source, bool defer_fasta, uint32_t pack_k=0) |
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| Result< std::unique_ptr< fastx_sequence_file > > | cuddl::detail::load_fastx_sequence_file (std::string const &path, decompression_source source={}, bool defer_fasta=false, bool read=false, uint32_t pack_k=0) |
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