index

kmtricks index is basically a wrapper around HowDeSBT. It allows to compute an HowDeSBT's index from kmtricks's Bloom filters. It can be run only after a complete run of kmtricks in hash mode. See examples.

Usage

DESCRIPTION
  Build HowDeSBT index.

USAGE
  kmtricks index --run-dir <DIR> [--bits <INT>] [--cull <FLOAT>] [-t/--threads <INT>] [-v/--verbose <STR>] 
                 [--keep-all-nodes] [--howde] [--allsome] [--determined] [--determined-brief] 
                 [--uncompressed] [--rrr] [--roar] [-h/--help] [--version] 

OPTIONS
  [global]
     --run-dir - kmtricks runtime directory 

  [Clustering options]
     --bits           - Number of bits to use from each filter. {100000}
     --cull           - Remove nodes for which saturation of determined is less than cull {0.2}
     --keep-all-nodes - keep all node of the binary tree. [⚑]

  [Build options]
     --howde            - equivalent to --determined,brief --rrr [⚑]
     --allsome          - create tree nodes as all/some bloom filters [⚑]
     --determined       - create tree nodes as determined/how bloom filters [⚑]
     --determined-brief - create tree nodes as determined/how, but only store  active bits [⚑]
     --uncompressed     - create the nodes as uncompressed bit vector(s) [⚑]
     --rrr              - create the nodes as rrr-compressed bit vector(s) [⚑]
     --roar             - create the nodes as roar-compressed bit vector(s) [⚑]

  [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}