List of all items

Structs

• bbcache::client::BBClient
• bbcache::client::BBClientBuilder
• bbcache::utils::ResourcePrint
• core::models::Fragment
• core::models::Interval
• core::models::Region
• core::models::RegionSet
• core::models::bed_set::BedSet
• core::models::bed_set::BedSetIterator
• core::models::fragments::Fragment
• core::models::interval::Interval
• core::models::region::Region
• core::models::region_set::RegionSet
• core::models::region_set::RegionSetIterator
• core::utils::FileInfo
• fragsplit::BarcodeToClusterMap
• fragsplit::map::BarcodeToClusterMap
• igd::create::ctg_t
• igd::create::gdata0_t
• igd::create::gdata_t
• igd::create::igd_t
• igd::create::tile_t
• igd::search::igd_t_from_disk
• igd::search::info_t
• io::GTokWriter
• io::gtok::GTokWriter
• overlaprs::AIList
• overlaprs::Bits
• overlaprs::Interval
• overlaprs::ailist::AIList
• overlaprs::ailist::IterFind
• overlaprs::bits::Bits
• overlaprs::bits::IterBits
• overlaprs::bits::IterFind
• overlaprs::multi_chrom_overlapper::IterFindOverlaps
• overlaprs::multi_chrom_overlapper::MultiChromOverlapper
• overlaprs::traits::Interval
• refget::Alphabet
• refget::AlphabetGuesser
• refget::FaiMetadata
• refget::FaiRecord
• refget::FastaStreamHasher
• refget::ParseOptions
• refget::SeqColDigestLvl1
• refget::SequenceCollection
• refget::SequenceCollectionMetadata
• refget::SequenceEncoder
• refget::SequenceMetadata
• refget::collection::FaiMetadata
• refget::collection::SeqColDigestLvl1
• refget::collection::SequenceCollection
• refget::collection::SequenceCollectionMetadata
• refget::collection::SequenceMetadata
• refget::digest::Alphabet
• refget::digest::AlphabetGuesser
• refget::digest::AutoDecompressWriter
• refget::digest::FaiMetadata
• refget::digest::FastaStreamHasher
• refget::digest::ParseOptions
• refget::digest::SeqColDigestLvl1
• refget::digest::SequenceCollection
• refget::digest::SequenceCollectionMetadata
• refget::digest::SequenceEncoder
• refget::digest::SequenceMetadata
• refget::digest::alphabet::Alphabet
• refget::digest::alphabet::AlphabetGuesser
• refget::digest::auto_decompress::AutoDecompressWriter
• refget::digest::encoder::SequenceEncoder
• refget::digest::fasta::ParseOptions
• refget::digest::stream::FastaStreamHasher
• refget::digest::types::FaiMetadata
• refget::digest::types::SeqColDigestLvl1
• refget::digest::types::SequenceCollection
• refget::digest::types::SequenceCollectionMetadata
• refget::digest::types::SequenceMetadata
• refget::fasta::FaiRecord
• refget::fasta::ParseOptions
• refget::store::RefgetStore
• refget::store::RetrievedSequence
• refget::store::StoreStats
• refget::store::SubstringsFromRegions
• scoring::ConsensusSet
• scoring::CountMatrix
• scoring::FragmentFileGlob
• scoring::OverlapResult
• scoring::RowIterator
• scoring::counts::CountMatrix
• scoring::counts::RowIterator
• scoring::files::ConsensusSet
• scoring::files::FragmentFileGlob
• scoring::files::OverlapResult
• tokenizers::BatchEncoding
• tokenizers::Encoding
• tokenizers::Token
• tokenizers::Tokenizer
• tokenizers::Universe
• tokenizers::config::SpecialTokenAssignment
• tokenizers::config::TokenizerConfig
• tokenizers::encoding::BatchEncoding
• tokenizers::encoding::Encoding
• tokenizers::tokenizer::Token
• tokenizers::tokenizer::Tokenizer
• tokenizers::universe::Universe
• tokenizers::utils::special_tokens::SpecialTokens
• uniwig::utils::Chromosome

Enums

• core::errors::RegionSetError
• core::utils::FileType
• igd::create::ParseBedResult
• io::TokenSize
• io::gtok::TokenSize
• overlaprs::OverlapperType
• overlaprs::multi_chrom_overlapper::MultiChromOverlapperError
• refget::AlphabetType
• refget::SequenceCollectionRecord
• refget::SequenceRecord
• refget::collection::SequenceCollectionRecord
• refget::collection::SequenceRecord
• refget::digest::AlphabetType
• refget::digest::SequenceCollectionRecord
• refget::digest::SequenceRecord
• refget::digest::alphabet::AlphabetType
• refget::digest::types::SequenceCollectionRecord
• refget::digest::types::SequenceRecord
• refget::store::StorageMode
• scoring::ScoringMode
• scoring::scoring_modes::ScoringMode
• tokenizers::TokenizerError
• tokenizers::UniverseError
• tokenizers::config::SpecialToken
• tokenizers::config::TokenizerConfigError
• tokenizers::config::TokenizerInputFileType
• tokenizers::config::TokenizerType
• tokenizers::error::TokenizerError
• tokenizers::universe::UniverseError
• tokenizers::universe::utils::UniverseFileType
• uniwig::counting::BAMRecordError

Traits

• fragsplit::ClusterCount
• fragsplit::ClusterLookup
• fragsplit::map::ClusterCount
• fragsplit::map::ClusterLookup
• overlaprs::Overlapper
• overlaprs::multi_chrom_overlapper::IntoMultiChromOverlapper
• overlaprs::traits::Overlapper
• refget::SequenceCollectionExt
• refget::SequenceCollectionRecordExt
• refget::SequenceMetadataExt
• refget::SequenceRecordExt
• refget::collection::SequenceCollectionExt
• refget::collection::SequenceCollectionRecordExt
• refget::collection::SequenceMetadataExt
• refget::collection::SequenceRecordExt
• scoring::FindOverlaps
• scoring::files::FindOverlaps

Functions

• bbcache::utils::get_default_bedbase_api
• bbcache::utils::get_default_cache_folder
• bbcache::utils::print_resources
• core::utils::generate_id_to_region_map
• core::utils::generate_id_to_region_string_map
• core::utils::generate_ordering_map_for_universe_regions
• core::utils::generate_region_string_to_id_map
• core::utils::generate_region_to_id_map
• core::utils::get_chrom_sizes
• core::utils::get_dynamic_reader
• core::utils::get_dynamic_reader_w_stdin
• core::utils::get_file_info
• core::utils::parse_bedlike_file
• core::utils::read_bedset_file
• core::utils::remove_all_extensions
• fragsplit::pseudobulk_fragment_files
• fragsplit::split::pseudobulk_fragment_files
• igd::create::create_igd_f
• igd::create::igd_add
• igd::create::igd_saveT
• igd::create::igd_save_db
• igd::create::parse_bed
• igd::search::getOverlaps
• igd::search::get_file_info_tsv
• igd::search::get_igd_info
• igd::search::get_tsv_path
• igd::search::igd_search
• io::append_tokens_to_gtok_file
• io::gtok::append_tokens_to_gtok_file
• io::gtok::init_gtok_file
• io::gtok::read_tokens_from_gtok
• io::gtok::write_tokens_to_gtok
• io::init_gtok_file
• io::read_tokens_from_gtok
• io::write_tokens_to_gtok
• refget::canonicalize_json
• refget::collection::digest_sequence
• refget::collection::digest_sequence_with_description
• refget::collection::parse_rgsi_line
• refget::collection::read_rgsi_file
• refget::compute_fai
• refget::decode_string_from_bytes
• refget::decode_substring_from_bytes
• refget::digest::algorithms::canonicalize_json
• refget::digest::algorithms::md5
• refget::digest::algorithms::sha512t24u
• refget::digest::alphabet::guess_alphabet
• refget::digest::alphabet::guess_alphabet_fast
• refget::digest::alphabet::lookup_alphabet
• refget::digest::canonicalize_json
• refget::digest::decode_string_from_bytes
• refget::digest::decode_substring_from_bytes
• refget::digest::digest_fasta_bytes
• refget::digest::digest_sequence
• refget::digest::digest_sequence_with_description
• refget::digest::encode_sequence
• refget::digest::encoder::decode_string_from_bytes
• refget::digest::encoder::decode_substring_from_bytes
• refget::digest::encoder::encode_sequence
• refget::digest::fasta::digest_fasta_bytes
• refget::digest::fasta::load_fasta_bytes
• refget::digest::fasta::parse_fasta_header
• refget::digest::guess_alphabet
• refget::digest::load_fasta_bytes
• refget::digest::lookup_alphabet
• refget::digest::md5
• refget::digest::parse_fasta_header
• refget::digest::parse_rgsi_line
• refget::digest::sha512t24u
• refget::digest::types::digest_sequence
• refget::digest::types::digest_sequence_with_description
• refget::digest::types::parse_rgsi_line
• refget::digest_fasta
• refget::digest_fasta_bytes
• refget::digest_sequence
• refget::digest_sequence_with_description
• refget::encode_sequence
• refget::fasta::compute_fai
• refget::fasta::digest_fasta
• refget::fasta::load_fasta
• refget::fasta::parse_fasta_header
• refget::guess_alphabet
• refget::load_fasta
• refget::load_fasta_bytes
• refget::lookup_alphabet
• refget::md5
• refget::parse_fasta_header
• refget::parse_rgsi_line
• refget::read_rgsi_file
• refget::sha512t24u
• scoring::barcode_scoring_from_fragments
• scoring::fragment_scoring::barcode_scoring_from_fragments
• scoring::fragment_scoring::region_scoring_from_fragments
• scoring::matrix_market::write_sparse_counts_to_mtx
• scoring::region_scoring_from_fragments
• scoring::write_sparse_counts_to_mtx
• tokenizers::count_fragments_by_barcode
• tokenizers::create_tokenize_core_from_universe
• tokenizers::prepare_universe_and_special_tokens
• tokenizers::tokenize_fragment_file
• tokenizers::utils::count_fragments_by_barcode
• tokenizers::utils::create_tokenize_core_from_universe
• tokenizers::utils::fragments::count_fragments_by_barcode
• tokenizers::utils::fragments::tokenize_fragment_file
• tokenizers::utils::prepare_universe_and_special_tokens
• tokenizers::utils::tokenize_fragment_file
• uniwig::counting::bam_to_bed_no_counts
• uniwig::counting::core_counts
• uniwig::counting::fixed_core_counts_bam_to_bw
• uniwig::counting::fixed_start_end_counts_bam
• uniwig::counting::fixed_start_end_counts_bam_to_bw
• uniwig::counting::get_shifted_pos
• uniwig::counting::start_end_counts
• uniwig::counting::variable_core_counts_bam_to_bw
• uniwig::counting::variable_shifted_bam_to_bw
• uniwig::counting::variable_start_end_counts_bam_to_bw
• uniwig::create_bw_writer
• uniwig::reading::create_chrom_vec_default_score
• uniwig::reading::create_chrom_vec_scores
• uniwig::reading::parse_bedlike_file_with_scores
• uniwig::reading::read_bam_header
• uniwig::reading::read_chromosome_sizes
• uniwig::uniwig_main
• uniwig::utils::clamped_start_position
• uniwig::utils::clamped_start_position_zero_pos
• uniwig::utils::compress_counts
• uniwig::utils::get_final_chromosomes
• uniwig::utils::npy_to_wig
• uniwig::utils::read_u32_npy
• uniwig::utils::version_sort
• uniwig::writing::write_bw_files
• uniwig::writing::write_combined_files
• uniwig::writing::write_to_bed_graph_file
• uniwig::writing::write_to_npy_file
• uniwig::writing::write_to_wig_file
• uniwig::writing::write_to_wig_file_variable

Type Aliases

• tokenizers::config::TokenizerConfigResult

Constants

• bbcache::consts::BBCLIENT_CACHE_ENV
• bbcache::consts::BEDBASE_API_ENV
• bbcache::consts::DEFAULT_BEDFILE_EXT
• bbcache::consts::DEFAULT_BEDFILE_SUBFOLDER
• bbcache::consts::DEFAULT_BEDSET_EXT
• bbcache::consts::DEFAULT_BEDSET_SUBFOLDER
• core::consts::BAM_FILE_EXTENSION
• core::consts::BED_FILE_EXTENSION
• core::consts::CHR_COL_NAME
• core::consts::DELIMITER
• core::consts::END_COL_NAME
• core::consts::GTOK_EXT
• core::consts::GZ_FILE_EXTENSION
• core::consts::IGD_FILE_EXTENSION
• core::consts::START_COL_NAME
• fragsplit::consts::DEFAULT_OUT
• fragsplit::consts::FRAGSPLIT_CMD
• igd::create::MAX_CHROM_NAME_LEN
• igd::create::maxCount
• io::GTOK_HEADER
• io::GTOK_U16_FLAG
• io::GTOK_U32_FLAG
• io::consts::GTOK_HEADER
• io::consts::GTOK_U16_FLAG
• io::consts::GTOK_U32_FLAG
• overlaprs::consts::OVERLAP_CMD
• refget::ASCII_ALPHABET
• refget::DNA_2BIT_ALPHABET
• refget::DNA_3BIT_ALPHABET
• refget::DNA_IUPAC_ALPHABET
• refget::PROTEIN_ALPHABET
• refget::digest::ASCII_ALPHABET
• refget::digest::DNA_2BIT_ALPHABET
• refget::digest::DNA_3BIT_ALPHABET
• refget::digest::DNA_IUPAC_ALPHABET
• refget::digest::PROTEIN_ALPHABET
• refget::digest::alphabet::ASCII_ALPHABET
• refget::digest::alphabet::DNA_2BIT_ALPHABET
• refget::digest::alphabet::DNA_3BIT_ALPHABET
• refget::digest::alphabet::DNA_IUPAC_ALPHABET
• refget::digest::alphabet::PROTEIN_ALPHABET
• scoring::consts::END_SHIFT
• scoring::consts::START_SHIFT
• tokenizers::DEFAULT_UNIVERSE_FILENAME
• tokenizers::consts::TOKENIZERS_CMD
• tokenizers::tokenizer::DEFAULT_UNIVERSE_FILENAME