fmi

Documentation

Index

• Variables
• type FMIndex
  • func NewFMIndex() *FMIndex
  • func (fmi *FMIndex) Last2First(i int) int
  • func (fmi *FMIndex) Locate(query []byte, mismatches int) ([]int, error)
  • func (fmi *FMIndex) Match(query []byte, mismatches int) (bool, error)
  • func (fmi *FMIndex) String() string
  • func (fmi *FMIndex) Transform(s []byte) ([]byte, error)
• type Stack
  • func (s Stack) Empty() bool
  • func (s Stack) Peek() sMatch
  • func (s *Stack) Pop() sMatch
  • func (s *Stack) Put(i sMatch)

Variables

var FasterLocating = true

FasterLocating can further accelerate Locate in cost of extra memory (size of reference).

Types

type FMIndex

type FMIndex struct {
	// EndSymbol
	EndSymbol byte

	// SuffixArray
	SuffixArray []int

	// Burrows-Wheeler Transform
	BWT []byte

	// First column of BWM
	F []byte

	// Alphabet in the BWT
	Alphabet []byte

	// Count of Letters in Alphabet.
	// CountOfLetters map[byte]int
	CountOfLetters []int // slice is faster han map

	// C[c] is a table that, for each character c in the alphabet,
	// contains the number of occurrences of lexically smaller characters
	// in the text.
	// C map[byte]int
	C []int // slice is faster han map

	// Occ(c, k) is the number of occurrences of character c in the
	// prefix L[1..k], k is 0-based.
	// Occ map[byte]*[]int32
	Occ []*[]int32 // slice is faster han map
	// contains filtered or unexported fields
}

FMIndex is Burrows-Wheeler Index

func NewFMIndex

func NewFMIndex() *FMIndex

NewFMIndex is constructor of FMIndex

func (*FMIndex) Last2First

func (fmi *FMIndex) Last2First(i int) int

Last2First mapping

func (*FMIndex) Locate

func (fmi *FMIndex) Locate(query []byte, mismatches int) ([]int, error)

Locate locates the pattern

func (*FMIndex) Match

func (fmi *FMIndex) Match(query []byte, mismatches int) (bool, error)

Match is a simple version of Locate, which returns immediately for a match.

func (*FMIndex) String

func (fmi *FMIndex) String() string

func (*FMIndex) Transform

func (fmi *FMIndex) Transform(s []byte) ([]byte, error)

Transform return Burrows-Wheeler-Transform of s

type Stack

type Stack []sMatch

Stack struct

func (Stack) Empty

func (s Stack) Empty() bool

Empty tell if it is empty

func (Stack) Peek

func (s Stack) Peek() sMatch

Peek return the last element

func (*Stack) Pop

func (s *Stack) Pop() sMatch

Pop pops element from the stack

func (*Stack) Put

func (s *Stack) Put(i sMatch)

Put puts element to stack