kmtricks socks interface

The binary kmtricks-socks provides socks interface.

kmtricks-socks v1.0.0

DESCRIPTION
  kmtricks socks interface

USAGE
  kmtricks-socks [build|lookup-kmer]

COMMANDS
  build       - Build index.
  lookup-kmer - Lookup k-mers.

Build index

kmtricks-socks build ./kmtricks.fof ./index --kmer-size 31 --abundance-min 2 --bloom-size 10000000

Complete usage

kmtricks-socks build v1.0.0

DESCRIPTION
  Build index.

USAGE
  kmtricks-socks build [-k/--kmer-size <INT>] [-m/--abundance-min <INT>] [-b/--bloom-size <INT>] 
                       [--nb-partitions <INT>] [-t/--threads <INT>] [-v/--verbose <STR>] 
                       [-h/--help] [--version] <input> <output>

POSITIONALS
  <input> : kmtricks fof
  <output> : output directory

OPTIONS
  [global]
    -k --kmer-size     - size of k-mers. {31}
    -m --abundance-min - Min abundance for solid k-mers. {1}
    -b --bloom-size    - size of k-mers. {100000000}
       --nb-partitions - number of partitions (0=auto). {0}

  [common]
    -t --threads - number of threads. {8}
    -h --help    - show this message and exit. [⚑]
       --version - show version and exit. [⚑]
    -v --verbose - verbosity level [debug|info|warning|error]. {info}

Query

kmtricks-socks lookup-kmer ./query.fasta -i ./index

Complete usage

kmtricks-socks lookup-kmer v1.0.0

DESCRIPTION
  Lookup k-mers.

USAGE
  kmtricks-socks lookup-kmer -i/--index-dir <DIR> [-t/--threshold <FLOAT>] [-o/--output-type <STR>] [-t/--threads <INT>] 
                             [-v/--verbose <STR>] [-h/--help] [--version] <query>

POSITIONALS
  A query file in fasta format

OPTIONS
  [global]
    -i --index-dir   - Index directory. 
    -t --threshold   - Threshold. {0.7}
    -o --output-type - output type. [vector|list] {vector}

  [common]
    -t --threads - number of threads. {8}
    -h --help    - show this message and exit. [⚑]
       --version - show version and exit. [⚑]
    -v --verbose - verbosity level [debug|info|warning|error]. {info}