repart

kmtricks repart

kmtricks repart is the first module of kmtricks. It allows to compute configuration and minimizer repartition. Since all kmtricks's computations are based on repartition, this module must be executed before the others and sets definitively some parameters, to change them you must recompute a repartition.

The computed repartition is dumped at kmtricks_dir/repartition_gatb/repartition.minimRepart. To use it see kmtricks repartition API.

Usage

kmtricks repart v1.0.0

DESCRIPTION
  Compute minimizer repartition.

USAGE
  kmtricks repart --file <FILE> [--run-dir <DIR>] [--kmer-size <INT>] [--minimizer-size <INT>] 
                  [--minimizer-type <INT>] [--repartition-type <INT>] 
                  [--nb-partitions <INT>] [--bloom-size <INT>] [-t/--threads <INT>] 
                  [-v/--verbose <STR>] [-h/--help] [--version] 

OPTIONS
  [global]
     --file      - kmtricks input file, see README.md. 
     --run-dir   - kmtricks runtime directory. {km_dir}
     --kmer-size - size of a k-mer. [8, 127] {31}

  [advanced performance tweaks]
     --minimizer-size   - size of minimizers. [4, 15] {10}
     --minimizer-type   - minimizer type (0=lexi, 1=freq). {0}
     --repartition-type - minimizer repartition (0=unordered, 1=ordered). {0}
     --nb-partitions    - number of partitions (0=auto). {0}
     --bloom-size       - bloom filter size {10000000}

  [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}