Seqhash is a struct that contains the Seqhash algorithm sequence types.

Each alignment is a single line of a SAM file, representing a linear alignment of a segment, consisting of 11 or more tab delimited fields. The 11 fie

Alphabet is a struct that holds a list of symbols and a map of symbols to their index in the list.

AminoAcid holds information for an amino acid and related codons in a struct

****************************************************************************** Higher level assembly Practically speakin

BaseCount is a struct that holds the base counts for a sequence.

BasePairType is a type to hold information of the type of a base pair. The chosen numbers denote where the energy paramater values can be found for th

* These interfaces are here to satisfy the `SequenceFolder` interface, which looks like this: type SequenceFolder interface { Fold(sequence strin

Change is a change to a given DNA sequence. A list of changes is given as the output of Cds.

Describes different types of citations. Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.

Codon holds information for a codon triplet in a struct

Describes a cofactor.

Describes different types of general annotations. Equivalent to the flat file CC-line.

Describes the authors of a citation when these are represented by a consortium. Equivalent to the flat file RG-line.

DBReference represents a database reference

DanglingEndsModel specifies the model of dangling ends to use in the free energy calculations. Dangling ends are bases adjacent to helices in free end

****************************************************************************** Aug 30, 2023 Lower level interfaces *********************************

May be one of Swiss-Prot, TrEMBL

Describes a database cross-reference. Equivalent to the flat file DR-line.

Decoder decodes XML elements2

May be one of left-to-right, right-to-left

DnaSuggestion is a suggestion of a fixer, generated by a problematicSequenceFunc. Bias must be `NA`, `GC`, or `AT`, with `NA` representing a neutral s

DualBarcode contains a forward and reverse barcode.

****************************************************************************** Feb 12, 2024 Dual barcodes When using Nano

EnergyParams contains all the energy parameters needed for the free energy calculations. The order of entries to access theses matrices always uses t

EnergyParamsSet is used to specify the set of RNA free energy paramaters to parse.

Entry represents a UniRef entry

Enzyme is a struct that represents restriction enzymes.

Enzyme represents a single enzyme within the Rebase database

Error is an error type that is returned when a symbol is not in the alphabet.

Describes the type of events that cause alternative products.

Describes the evidence for an annotation. No flat file equivalent.

Feature holds the information for a feature in a Genbank file and other annotated sequence files.

Describes different types of sequence annotations. Equivalent to the flat file FT-line.

Format is a enum of different parser formats.

Fragment is a struct that represents linear DNA sequences with sticky ends.

May be one of single, multiple

Genbank is the main struct for the Genbank file format.

Describes non-nuclear gene locations (organelles and plasmids). Equivalent to the flat file OG-line.

Describes different types of gene designations. Equivalent to the flat file GN-line.

Describes a gene. Equivalent to the flat file GN-line.

A Group is a collection of goroutines working on subtasks that are part of the same overall task. A zero Group is valid, has no limit on the number o

Hairpin contains all the information needed to denote a hairpin loop in a RNA's secondary structure. It consists of a `Stem` and a single stranded reg

Hash2MetadataKey is a key for a seqhash v2 single letter metadata tag.

Header is an empty struct since UniRef files don't have headers

Header is a blank struct, needed for compatibility with bio parsers. It contains nothing.

****************************************************************************** Oct 10, 2021 slow5 parser begins here. Specification below: https://ha

Header is a blank struct, needed for compatibility with bio parsers. It contains nothing.

Header is a blank struct, needed for compatibility with bio parsers. It contains nothing.

Header is a blank struct, needed for compatibility with bio parsers. It contains nothing.

Header is a blank struct, needed for compatibility with bio parsers. It contains nothing.

32kB is a magic number often used by the Go stdlib for parsing. We multiply it by two. Each header in a SAM file begins with an @ followed by a two le

HeaderTypes defines the possible header types returned by every parser.

Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.

Describes isoforms in 'alternative products' annotations.

KmerOverlap represents the overlap between two fragments indicative of a ligation event.

The following functions help test for writing with a limit in order to get that sweet sweet test coverage. LimitedWriter wraps another io.Writer and r

Pileup struct is a single position in a pileup file. Pileup files "pile" a bunch of separate bam/sam alignments into something more readable at a per

Location is a struct that holds the location of a feature.

Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not

Locus holds Locus information in a Meta struct.

murmur3 is a fast non-cryptographic hash algorithm that was also used in the original papers-> https://github.com/shenwei356/go-hashing-kmer-bench Mas

Match contains the identifier and score of a potential match to the searched sequence.