cmd

Documentation

Index

• Variables
• func Execute()
• func MD5(s []byte) string
• type BedFeature
  • func ReadBedFeatures(file string) ([]BedFeature, error)
• type LocationChunk
• type LocationInfo

Variables

var RootCmd = &cobra.Command{
	Use:   "fakit",
	Short: "Swiss army knife of FASTA format",
	Long: `fakit -- Swiss army knife of FASTA format

Version: 0.1.6

Author: Wei Shen <shenwei356@gmail.com>

Documents  : http://shenwei356.github.io/fakit
Source code: https://github.com/shenwei356/fakit

`,
}

RootCmd represents the base command when called without any subcommands

var Threads = runtime.NumCPU()

Threads for bread.NewBufferedReader()

Functions

func Execute

func Execute()

Execute adds all child commands to the root command sets flags appropriately. This is called by main.main(). It only needs to happen once to the rootCmd.

func MD5

func MD5(s []byte) string

MD5 of a slice

Types

type BedFeature

type BedFeature struct {
	Chr    string
	Start  int // 1based
	End    int // end included
	Name   *string
	Strand *string
}

BedFeature is the gff BedFeature struct

func ReadBedFeatures

func ReadBedFeatures(file string) ([]BedFeature, error)

ReadBedFeatures returns gtf BedFeatures of a file

type LocationChunk

type LocationChunk struct {
	ID   uint64
	Data []LocationInfo
}

LocationChunk is LocationChunk

type LocationInfo

type LocationInfo struct {
	Record      *fasta.FastaRecord
	PatternName string
	Strand      string
	Locations   [][]int
}

LocationInfo is LocationInfo