Merge

In addition to registering multiple indexes, compatible sub-indexes (i.e. sharing the parameters: k-mer size, Bloom filter size, number of partitions) can also be merged. This way, the indexes are physically extended resulting in optimal query times.

Options

kmindex merge v0.5.2

DESCRIPTION
  Merge sub-indexes.

USAGE
  kmindex merge -i/--index <STR> -n/--new-name <STR> -p/--new-path <STR> -m/--to-merge <LIST[STR]>
                [-r/--rename <STR>] [-t/--threads <INT>] [-v/--verbose <STR>]
                [-d/--delete-old] [-h/--help] [--version]

OPTIONS
  [global]
    -i --index      - Global index path.
    -n --new-name   - Name of the new index.
    -p --new-path   - Output path.
    -m --to-merge   - Sub-indexes to merge, comma separated.
    -d --delete-old - Delete old sub-index files. [⚑]
    -r --rename     - Rename sample ids.
                      - A sub-index cannot contain samples with similar identifiers.
                        Sub-indexes containing identical identifiers cannot be merged, the
                        identifiers must be renamed.
                      - Renaming can be done in three different ways:

                        1. Using identifier files (one per line).
                           For example, if you want to merge three sub-indexes:
                             '-r f:id1.txt,id2.txt,id3.txt'

                        2. Using a format string ('{}' is replaced by an integer in [0, nb_samples)).
                             '-r "s:id_{}"'

                        3. Manually (not recommended).
                           Identifiers can be changed in 'kmtricks.fof' files in sub-index directories.

  [common]
    -t --threads - Number of threads. {12}
    -h --help    - Show this message and exit. [⚑]
       --version - Show version and exit. [⚑]
    -v --verbose - Verbosity level [debug|info|warning|error]. {info}