cmd

package
v0.2.3 Latest Latest
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This package is not in the latest version of its module.

 Go to latest Published: May 6, 2016 License: MIT Imports: 30 Imported by: 0

Documentation

Index

Constants

This section is empty.

Variables

View Source 
var RootCmd = &cobra.Command{
	Use:   "fakit",
	Short: "a cross-platform and efficient suit for FASTA/Q file manipulation",
	Long: `fakit -- a cross-platform and efficient suit for FASTA/Q file manipulation

Version: 0.2.3

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

View Source 
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 added in v0.1.4 

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

BedFeature is the gff BedFeature struct

func ReadBedFeatures added in v0.1.4 

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

ReadBedFeatures returns gtf BedFeatures of a file

func ReadBedFilteredFeatures added in v0.1.8 

func ReadBedFilteredFeatures(file string, chrs []string) ([]BedFeature, error)

ReadBedFilteredFeatures returns gtf BedFeatures of selected chrs from file

type Config added in v0.1.7 

type Config struct {
	Alphabet               *seq.Alphabet
	ChunkSize              int
	BufferSize             int
	Threads                int
	LineWidth              int
	IDRegexp               string
	IDNCBI                 bool
	OutFile                string
	Quiet                  bool
	AlphabetGuessSeqLength int
	ValidateSeqLength      int
}

Config is the global falgs

type LocationChunk 

type LocationChunk struct {
	ID   uint64
	Data []LocationInfo
}

LocationChunk is LocationChunk

type LocationInfo 

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

LocationInfo is LocationInfo

Source Files

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