cmd

Documentation

Index

• Variables
• func Execute()
• func ParseByteSize(val string) (int, error)
• type Options

Variables

var BufferSize = 65536 //os.Getpagesize()

BufferSize is size of buffer

var RootCmd = &cobra.Command{
	Use:   "unikmer",
	Short: "Unique-Kmer Toolkit",
	Long: fmt.Sprintf(`unikmer - Unique-Kmer Toolkit

unikmer is a toolkit for nucleic acid k-mer analysis, providing functions
including set operation on k-mers optional with TaxIds but without count
information.

K-mers are either encoded (k<=32) or hashed (arbitrary k) into 'uint64',
and serialized in binary file with extension '.unik'.

TaxIds can be assigned when counting k-mers from genome sequences,
and LCA (Lowest Common Ancestor) is computed during set opertions
including computing union, intersection, set difference, unique and
repeated k-mers.

Version: v%s

Author: Wei Shen <shenwei356@gmail.com>

Documents  : https://shenwei356.github.io/unikmer
Source code: https://github.com/shenwei356/unikmer

Dataset (optional):

  Manipulating k-mers with TaxIds needs taxonomy file from e.g., 
  NCBI Taxonomy database, please extract "nodes.dmp", "names.dmp",
  "delnodes.dmp" and "merged.dmp" from link below into ~/.unikmer/ ,
  ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz , 
  or some other directory, and later you can refer to using flag
  --data-dir or environment variable UNIKMER_DB.

  For GTDB, use https://github.com/nick-youngblut/gtdb_to_taxdump 
  for taxonomy conversion.

  Note that TaxIds are represented using uint32 and stored in 4 or
  less bytes, all TaxIds should be in range of [1, %d]

`, VERSION, maxUint32),
}

RootCmd represents the base command when called without any subcommands

var VERSION = "0.17.2"

VERSION is the version

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 ParseByteSize

func ParseByteSize(val string) (int, error)

ParseByteSize parses byte size from string.

Types

type Options

type Options struct {
	NumCPUs          int
	Verbose          bool
	Compress         bool
	Compact          bool
	CompressionLevel int
	MaxTaxid         uint32
	IgnoreTaxid      bool
	DataDir          string
	NodesFile        string
	CacheLCA         bool

	NoCheckFile bool
}

Options contains the global flags