structures

Documentation

Overview

Package structures is a basic package to hold basic structures, methods, and functions for tile libraries and genomes. Most important is the TileVariant structure, which holds all the necessary data to represent a tile variant. Equality on TileVariants is defined by hash. In addition, the default number of paths in a genome is provided here for convenience.

Index

• Constants
• type TileVariant
  • func (t TileVariant) Equals(t2 TileVariant) bool
• type VariantHash

Constants

const Paths int = 863 // Constant because we know that the number of paths is always the same.

Paths is the number of paths a genome has, for convenience.

Types

type TileVariant

type TileVariant struct {
	Hash             VariantHash // The hash of the tile variant's bases.
	Length           int         // The length (span) of the tile
	Annotation       string      // Any notes about this tile (by default, no comments)
	LookupReference  int64       // The lookup reference for the bases of this variant in the text file for the corresponding library.
	Complete         bool        // Tells if this variant is complete or not (complete meaning no nocalls). Mostly for genomes, to quickly tell which tiles are complete and which are not.
	ReferenceLibrary interface{} // A way of referencing the library this variant is from. (Will be a *Library).
}

TileVariant is a struct for representing a tile variant using the hash, length, and any annotation(s) on the variant. In this case, a tile variant is a set of a bases that could exist in between two tags on the genome, spanning any number of steps. We use the hash of the bases as a standin for the actual bases, to save space. We also keep the span of the tile, since it tells us how many steps are in the path of the genome. The Annotation field holds a string for any notes about this tile. The LookupReference field tells at what location in the reference text file that this tile can be found. This is majorly for the use of the tilelibrary package. Complete is a field that determines whether the tile variant contains nocalls or not. Used for convenience in both the genome and tilelibrary packages. ReferenceLibrary is a field that holds a *Library, used in package tilelibrary. It is an interface{} to avoid circular imports. Putting any other type into ReferenceLibrary may result in errors. Note: no explicit TileVariant constructor is provided. However, all fields are exported, so other packages can construct and modify TileVariants freely.

func (TileVariant) Equals

func (t TileVariant) Equals(t2 TileVariant) bool

Equals checks for equality of variants based on hash. This works based on the assumption that no two tile variants in the same path and step have the same hash.

type VariantHash

type VariantHash [md5.Size]byte

VariantHash is a type hash for the bases of a tile variant. Currently, the hash algorithm is MD5.