cmd

var BufferSize = 65536 //os.Getpagesize()

var RootCmd = &cobra.Command{
	Use:   "unikmer",
	Short: "Toolkit for k-mer with taxonomic information",
	Long: fmt.Sprintf(`unikmer - Toolkit for k-mer with taxonomic information

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://bioinf.shenwei.me/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 'taxonkit create-taxdump' to create NCBI-style
  taxonomy dump files, or download from:
    https://github.com/shenwei356/gtdb-taxonomy

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

`, VERSION, maxUint32),
}

var VERSION = "0.19.1"