List of all items

Structs

• QualOpts
• cli::Args
• coverage::CoverageHistogram
• merge_ska_array::KmerIter
• merge_ska_array::MergeSkaArray
• merge_ska_dict::MergeSkaDict
• ska_dict::SkaDict
• ska_dict::bloom_filter::KmerFilter
• ska_dict::nthash::NtHashIterator
• ska_dict::split_kmer::SplitKmer
• ska_ref::RefKmer
• ska_ref::RefSka
• ska_ref::aln_writer::AlnWriter
• ska_ref::idx_check::IdxCheck
• ska_ref::idx_check::IdxCheckIter
• skalo::read_graph::PathState
• skalo::utils::Config
• skalo::utils::DataInfo
• skalo::utils::DnaSequence
• skalo::utils::VariantInfo

Enums

• QualFilter
• cli::Commands
• cli::FileType
• cli::FilterType
• cli::ValidMinKmer

Traits

• ska_dict::bit_encoding::UInt

Functions

• cli::check_threads
• cli::cli_args
• generic_modes::align
• generic_modes::apply_filters
• generic_modes::delete
• generic_modes::distance
• generic_modes::map
• generic_modes::merge
• generic_modes::save_skf
• generic_modes::skalo
• generic_modes::weed
• io_utils::any_fastq
• io_utils::count_fastq
• io_utils::get_2_fastq_path
• io_utils::get_input_list
• io_utils::kmer_min_cutoff
• io_utils::load_array
• io_utils::read_input_fastas
• io_utils::set_ostream
• merge_ska_dict::build_and_merge
• ska_dict::bit_encoding::base_to_prob
• ska_dict::bit_encoding::decode_base
• ska_dict::bit_encoding::decode_kmer
• ska_dict::bit_encoding::encode_base
• ska_dict::bit_encoding::is_ambiguous
• ska_dict::bit_encoding::rc_base
• ska_dict::bit_encoding::valid_base
• skalo::extremities::identify_good_kmers
• skalo::input::build_graph
• skalo::process_indels::process_indels
• skalo::read_graph::build_variant_groups
• skalo::utils::rev_compl

Type Aliases

• merge_ska_dict::InputFastx

Statics

• skalo::utils::CONFIG
• skalo::utils::DATA_INFO

Constants

• cli::DEFAULT_AMBIGMASK
• cli::DEFAULT_AMBIGMISSING
• cli::DEFAULT_CONSTGAPS
• cli::DEFAULT_KMER
• cli::DEFAULT_MAX_INDEL_KMERS
• cli::DEFAULT_MAX_PATHDEPTH
• cli::DEFAULT_MINCOUNT
• cli::DEFAULT_MINFREQ
• cli::DEFAULT_MINQUAL
• cli::DEFAULT_MISSING_SKALO
• cli::DEFAULT_PROPORTION_READS
• cli::DEFAULT_QUALFILTER
• cli::DEFAULT_REPEATMASK
• cli::DEFAULT_STRAND
• ska_dict::bit_encoding::IUPAC
• ska_dict::bit_encoding::RC_IUPAC