lexicmap utils reindex-seeds

Usage

$ lexicmap utils reindex-seeds -h
Recreate the primary indexes of seeds data.

The seeds files are not changed. Different seeds files are processed in
parallel using -j/--threads, and --partitions controls the number of anchor
partitions in each primary index.

The partition count must be a power of 4 and at least 4. The mask prefix length
plus log4(partitions) must not exceed the k-mer size; equality is allowed.

This command writes single-level .idx files and removes their corresponding
.idx15 files afterward. Use "lexicmap utils reindex-seeds2" to create adaptive
two-level indexes that can reduce seed-matching time for large primary-prefix
blocks.

Each primary index is replaced only after its new file has been written and
closed successfully. A failed rebuild leaves that chunk's old index intact.

Usage:
  lexicmap utils reindex-seeds [flags]

Flags:
  -h, --help             help for reindex-seeds
  -d, --index string     ► Index directory created by "lexicmap index".
      --partitions int   ► Number of anchor partitions in each primary seed index. Must be a power of
                         4 and at least 4; mask prefix length + log4(value) must not exceed the k-mer
                         size. (default 4096)

Global Flags:
      --force-gzip-output    ► Gzip-compress result output regardless of the filename, including stdout.
  -X, --infile-list string   ► File of input file list (one file per line). If given, they are
                             appended to files from CLI arguments.
      --log string           ► Log file.
      --quiet                ► Do not print any verbose information. But you can write them to a file
                             with --log.
  -j, --threads int          ► Number of CPU cores to use. By default, it uses all available cores.
                             (default 16)

Examples

$ lexicmap utils reindex-seeds -d demo.lmi/ --partitions 1024
10:20:29.150 [INFO] recreating seed indexes with 1024 partitions for: demo.lmi/
processed files:  16 / 16 [======================================] ETA: 0s. done
10:20:29.166 [INFO] update index information file: demo.lmi/info.toml
10:20:29.166 [INFO] finished updating the index information file: demo.lmi/info.toml
10:20:29.166 [INFO]
10:20:29.166 [INFO] elapsed time: 15.981266ms
10:20:29.166 [INFO]