dna

Documentation

Index

• func AllToLower(bases []Base)
• func AllToUpper(bases []Base)
• func BaseToRune(base Base) rune
• func BasesToString(bases []Base) string
• func CompareSeqsCaseSensitive(alpha []Base, beta []Base) int
• func CompareSeqsIgnoreCase(alpha []Base, beta []Base) int
• func Count(seq []Base) (ACount int, CCount int, GCount int, TCount int, NCount int, aCount int, ...)
• func CountGaps(seq []Base) int
• func CountMask(seq []Base) (unmaskedCount int, maskedCount int, gapCount int)
• func RangeToLower(bases []Base, start int, end int)
• func RangeToUpper(bases []Base, start int, end int)
• func ReverseComplement(bases []Base)
• type Base
  • func StringToBases(s string) ([]Base, error)
  • func ToLower(b Base) Base
  • func ToUpper(b Base) Base

Functions

func AllToLower

func AllToLower(bases []Base)

func AllToUpper

func AllToUpper(bases []Base)

func BaseToRune

func BaseToRune(base Base) rune

func BasesToString

func BasesToString(bases []Base) string

func CompareSeqsCaseSensitive

func CompareSeqsCaseSensitive(alpha []Base, beta []Base) int

func CompareSeqsIgnoreCase

func CompareSeqsIgnoreCase(alpha []Base, beta []Base) int

func Count

func Count(seq []Base) (ACount int, CCount int, GCount int, TCount int, NCount int, aCount int, cCount int, gCount int, tCount int, nCount int, gapCount int)

func CountGaps

func CountGaps(seq []Base) int

func CountMask

func CountMask(seq []Base) (unmaskedCount int, maskedCount int, gapCount int)

func RangeToLower

func RangeToLower(bases []Base, start int, end int)

start is closed, end is open, both are zero-based

func RangeToUpper

func RangeToUpper(bases []Base, start int, end int)

start is closed, end is open, both are zero-based

func ReverseComplement

func ReverseComplement(bases []Base)

Types

type Base

type Base byte

const (
	A Base = 0
	C Base = 1
	G Base = 2
	T Base = 3
	N Base = 4

	Gap Base = 10
)

TODO: change these names so that all variables can be seen from outside. Maybe BaseA, Basea, etc

func StringToBases

func StringToBases(s string) ([]Base, error)

func ToLower

func ToLower(b Base) Base

func ToUpper

func ToUpper(b Base) Base