Namespace noLZSS

Namespaces

• Namespace noLZSS::detail

Classes

• Struct Factor

• Struct FactorFileFooter

• Struct FastaFactorizationResult

• Struct FastaParseResult

• Struct FastaPerSequenceCountResult

• Struct FastaPerSequenceFactorizationResult

• Struct FastaReferenceTargetResult

• Struct PreparedSequenceResult

• Struct ThreadContext

• Class ParallelFactorizer

Enums

• Enum FastaDnaSanitizationMode

Functions

• Function noLZSS::complement

• Function noLZSS::count_factors

• Function noLZSS::count_factors_dna_w_rc

• Function noLZSS::count_factors_fasta_dna_no_rc_per_sequence

• Function noLZSS::count_factors_fasta_dna_w_rc_per_sequence

• Function noLZSS::count_factors_file

• Function noLZSS::count_factors_file_dna_w_rc

• Function noLZSS::count_factors_file_multiple_dna_w_rc

• Function noLZSS::count_factors_multiple_dna_w_rc

• Function noLZSS::factorize

• Function noLZSS::factorize_dna_rc_w_ref_fasta_files

• Function noLZSS::factorize_dna_w_rc

• Function noLZSS::factorize_dna_w_reference_seq

• Function noLZSS::factorize_dna_w_reference_seq_file

• Function noLZSS::factorize_fasta_dna_no_rc_per_sequence

• Function noLZSS::factorize_fasta_dna_w_rc_per_sequence

• Function noLZSS::factorize_fasta_multiple_dna_no_rc

• Function noLZSS::factorize_fasta_multiple_dna_w_rc

• Function noLZSS::factorize_file

• Function noLZSS::factorize_file_dna_w_rc

• Function noLZSS::factorize_file_multiple_dna_w_rc

• Template Function noLZSS::factorize_file_stream

• Template Function noLZSS::factorize_file_stream_dna_w_rc

• Template Function noLZSS::factorize_file_stream_multiple_dna_w_rc

• Function noLZSS::factorize_multiple_dna_w_rc

• Template Function noLZSS::factorize_stream

• Template Function noLZSS::factorize_stream_dna_w_rc

• Template Function noLZSS::factorize_stream_multiple_dna_w_rc

• Function noLZSS::factorize_w_reference

• Function noLZSS::factorize_w_reference_file

• Function noLZSS::identify_sentinel_factors

• Function noLZSS::is_canonical_dna

• Function noLZSS::is_rc

• Function noLZSS::lcp

• Function noLZSS::next_leaf

• Function noLZSS::parallel_factorize_dna_w_rc_to_file(std::string_view, const std::string&, size_t)

• Function noLZSS::parallel_factorize_dna_w_rc_to_file(::std::string_view, const ::std::string&, size_t)

• Function noLZSS::parallel_factorize_file_dna_w_rc_to_file(const std::string&, const std::string&, size_t)

• Function noLZSS::parallel_factorize_file_dna_w_rc_to_file(const ::std::string&, const ::std::string&, size_t)

• Function noLZSS::parallel_factorize_file_to_file(const std::string&, const std::string&, size_t, size_t)

• Function noLZSS::parallel_factorize_file_to_file(const ::std::string&, const ::std::string&, size_t, size_t)

• Function noLZSS::parallel_factorize_to_file(std::string_view, const std::string&, size_t, size_t)

• Function noLZSS::parallel_factorize_to_file(::std::string_view, const ::std::string&, size_t, size_t)

• Function noLZSS::parallel_write_factors_binary_file_fasta_dna_no_rc_per_sequence

• Function noLZSS::parallel_write_factors_binary_file_fasta_dna_w_rc_per_sequence

• Function noLZSS::parallel_write_factors_binary_file_fasta_multiple_dna_no_rc

• Function noLZSS::parallel_write_factors_binary_file_fasta_multiple_dna_w_rc

• Function noLZSS::parallel_write_factors_dna_w_reference_fasta_files_to_binary

• Function noLZSS::parse_fasta_sequences_and_ids

• Function noLZSS::prepare_multiple_dna_sequences_no_rc

• Function noLZSS::prepare_multiple_dna_sequences_w_rc

• Function noLZSS::prepare_ref_target_dna_no_rc_from_fasta

• Function noLZSS::prepare_ref_target_dna_w_rc_from_fasta

• Function noLZSS::rc_end

• Function noLZSS::revcomp

• Function noLZSS::sanitize_filename

• Function noLZSS::to_upper_ascii

• Function noLZSS::write_factors_binary_file

• Function noLZSS::write_factors_binary_file_dna_w_rc

• Function noLZSS::write_factors_binary_file_fasta_dna_no_rc_per_sequence

• Function noLZSS::write_factors_binary_file_fasta_dna_w_rc_per_sequence

• Function noLZSS::write_factors_binary_file_fasta_multiple_dna_no_rc

• Function noLZSS::write_factors_binary_file_fasta_multiple_dna_w_rc

• Function noLZSS::write_factors_binary_file_multiple_dna_w_rc

• Function noLZSS::write_factors_dna_w_reference_fasta_files_to_binary

• Function noLZSS::write_fasta_metadata

• Function noLZSS::write_single_sequence_factors

Typedefs

• Typedef noLZSS::cst_t

Variables

• Variable noLZSS::RC_MASK