manage

Synopsis

Manage k-mer index registries.

USAGE

kmhelpers manage [OPTIONS] COMMAND [ARGS]...

Argument	Description
-r, --registry-path DIR	Path to kmindex registry (default: current directory)

I/O

Input: kmindex registry (-r), subcommand-specific arguments
Output: updated registry state (create, add, remove, rename, relink) or printed info (list, info, check)

Subcommands

Subcommand	Description
create	Initialise a registry and optionally register existing indices
add	Register existing kmtricks indices in an existing registry
list	List all indices in a registry
info	Show detailed information about an index
check	Validate registry consistency and index structures
remove	Remove one or more indices from the registry
rename	Rename an index
relink	Recreate links after moving index files

Subcommand Options

create

Option	Description
-i, --input-dir DIR	Directory containing existing kmtricks indices to register
-n, --index-ids TEXT	Specific index IDs to register (default: all found)

add

Option	Description
-i, --input-dir DIR	Directory containing kmtricks indices to add (required)
-n, --index-ids TEXT	Specific index IDs to register (default: all found)

info

Option	Description
-n, --index-id TEXT	Index ID to show information for (required)
--json	Output as JSON

remove

Option	Description
-n, --index-ids TEXT	Index ID(s) to remove (required, repeatable)
-d, --delete-files	Also delete index files from disk
-y, --yes	Skip confirmation prompt

rename

Option	Description
-f, --from TEXT	Current index ID (required)
-t, --to TEXT	New index ID (required)

relink

Option	Description
-i, --input-dir DIR	Directory containing the moved index files (required)
-n, --index-id TEXT	Index ID to relink (default: all registered indices)

Examples

# Create a registry in the current directory
kmhelpers manage create

# Create a registry and register indices from a directory
kmhelpers manage create -i /data/indices

# List all registered indices
kmhelpers manage list
kmhelpers manage -r /path/to/registry list

# Add indices from a directory to an existing registry
kmhelpers manage add -i /data/new_indices

# Show info for a specific index
kmhelpers manage info -n my_index

# Show info as JSON
kmhelpers manage info -n my_index --json

# Check consistency
kmhelpers manage check

# Remove an index (keep files)
kmhelpers manage remove -n my_index

# Remove an index and delete files from disk
kmhelpers manage remove -n my_index -d

# Remove multiple indices without confirmation
kmhelpers manage remove -n idx1 -n idx2 -y

# Rename an index
kmhelpers manage rename -f old_name -t new_name

# Relink all indices from a new directory
kmhelpers manage relink -i /new/location

# Relink a specific index
kmhelpers manage relink -i /new/location -n my_index