List of all items
Structs
- core::align::concat::AlignmentConcatenation
- core::align::convert::AlignmentConversion
- core::align::filter::AlignmentFiltering
- core::align::partition::PartitionConverter
- core::align::split::AlignmentSplitting
- core::align::summarize::AlignmentSummary
- core::contig::summarize::ContigSummaryHandler
- core::read::summarize::GenomicReadSummary
- core::sequence::extract::SequenceExtraction
- core::sequence::filter::SequenceFiltering
- core::sequence::id::IdRecords
- core::sequence::id::SequenceID
- core::sequence::remove::SequenceRemoval
- core::sequence::rename::SequenceRenaming
- core::sequence::rename::SequenceRenamingDry
- core::sequence::translate::SequenceTranslation
- helper::concat::Concat
- helper::concat::ConcatParams
- helper::finder::ContigFileFinder
- helper::finder::IDs
- helper::finder::SeqFileFinder
- helper::finder::SeqReadFinder
- helper::logger::AlignSeqLogger
- helper::logger::ContigLogger
- helper::logger::ReadLogger
- helper::sequence::SeqCheck
- helper::sequence::SeqParser
- helper::translation::NcbiTables
- helper::translation::STD_CODE_MAP
- helper::types::Header
- helper::types::Partition
- helper::types::TaxonRecords
- parser::fasta::Fasta
- parser::fasta::FastaReader
- parser::fasta::Records
- parser::nexus::Nexus
- parser::partition::PartitionParser
- parser::phylip::Phylip
- parser::qscores::QScoreParser
- stats::common::CommonStats
- stats::common::NStats
- stats::common::StreamStats
- stats::contigs::ContigSummary
- stats::fastq::FastqMappedRead
- stats::fastq::FastqSummary
- stats::fastq::FastqSummaryMin
- stats::qscores::ReadQScore
- stats::read::ReadRecord
- stats::read::ReadSummary
- stats::sequence::CharMatrix
- stats::sequence::CharSummary
- stats::sequence::Chars
- stats::sequence::Completeness
- stats::sequence::SiteSummary
- stats::sequence::Sites
- stats::sequence::Taxa
- writer::archive::Archive
- writer::contigs::ContigSummaryWriter
- writer::partition::PartWriter
- writer::read::ReadPosSummaryWriter
- writer::read::ReadSummaryWriter
- writer::sequences::SeqWriter
- writer::summary::CsvWriter
- writer::summary::SummaryWriter
- writer::text::IdWriter
Enums
- core::align::filter::FilteringParameters
- core::sequence::extract::SeqExtractionParameters
- core::sequence::filter::SeqFilteringParameters
- core::sequence::remove::SeqRemovalParameters
- core::sequence::rename::SeqRenamingParameters
- helper::types::ContigFmt
- helper::types::DataType
- helper::types::GeneticCodes
- helper::types::InputFmt
- helper::types::OutputFmt
- helper::types::PartitionFmt
- helper::types::SeqReadFmt
- helper::types::SummaryMode
- helper::types::SummaryOutput
Functions
- cli::parse_cli
- helper::alphabet::check_valid_dna
- helper::alphabet::check_valid_seq
- helper::alphabet::is_valid_aa
- helper::alphabet::is_valid_dna
- helper::files::create_output_fname
- helper::files::create_output_fname_for_text
- helper::files::create_output_fname_from_path
- helper::files::decode_gzip
- helper::files::open_file
- helper::logger::init_file_logger
- helper::logger::init_logger
- helper::logger::log_input_partition
- helper::logger::strip_color
- helper::partition::construct_partition_path
- helper::types::infer_contig_fmt_auto
- helper::types::infer_input_auto
- helper::types::infer_raw_input_auto
- helper::utils::fmt_num
- helper::utils::get_crate_version
- helper::utils::parse_duration
- helper::utils::print_divider
- helper::utils::print_execution_time
- helper::utils::print_welcome_text
- helper::utils::set_spinner
- parser::delimited::parse_delimited_text
- parser::fasta::parse_only_id
- parser::txt::parse_text_file
- stats::sequence::get_pars_inf