mutations

Documentation

Overview

package mutations provides data structures & functions for counting mutations given an alignment of ancestral and tips sequences

Index

• type Mutation
• type MutationList
  • func CountMutations(t *tree.Tree, a align.Alignment) (mutations *MutationList, err error)
  • func NewMutationList() (mutations *MutationList)
  • func (m *MutationList) Append(mapp *MutationList) (err error)

Types

type Mutation

type Mutation struct {
	AlignmentSite             int    // Index of the site of the alignment
	BranchIndex               int    // Index of the branch
	ChildNodeName             string // Name of the parent of the clade
	ParentCharacter           uint8  // Parent character
	ChildCharacter            uint8  // Child character
	NumTips                   int    // Total number of descendent tips
	NumTipsWithChildCharacter int    // Number of descendent tips that have the child character
}

type MutationList

type MutationList struct {
	Mutations map[string]Mutation // Key: "AlignmentSite-BranchIndex-ParentCharacter-ChildCharacter"
}

func CountMutations

func CountMutations(t *tree.Tree, a align.Alignment) (mutations *MutationList, err error)

func NewMutationList

func NewMutationList() (mutations *MutationList)

func (*MutationList) Append

func (m *MutationList) Append(mapp *MutationList) (err error)