Command Reference

kmhelpers commands cover the full k-mer index lifecycle: build indices from raw sequences, then query them. Most workflows only need three top-level commands - design, build, and query. Click on any command below to see its full options, inputs/outputs, examples, and additional information.

Main Pipeline

Command	Description
`design`	Discover samples, profile them, and compose index definitions (steps: `list` → `profile` → `compose`)
`build`	Validate paths and build indices (steps: `plan` → `apply`)
`query`	Query indices with FASTA/FASTQ sequences
`compress`	Compress an index managed in a registry (under development)

Design (manual steps)

Steps run internally by design:

Command	Description
`list`	Step 1 - scan a directory and count k-mers
`profile`	Step 2 - compute Bloom-filter distribution
`compose`	Step 3 - generate index definition files

Build (manual steps)

Steps run internally by build:

Command	Description
`plan`	Step 1 - validate paths and preview the build plan
`apply`	Step 2 - build k-mer indices

Utilities

Command	Description
`manage`	Manage k-mer index registries (under development)
`pipeline`	Run a sequence of commands defined in a YAML pipeline file

Global Options

These options are available on the root kmhelpers command and apply to all subcommands:

-C, --config FILE         YAML config file for default values  [env var:
                          KMHELPERS_CONFIG]
-v, --verbose             Increase verbosity: -v for DEBUG
-q, --quiet               Decrease verbosity: -q for WARNING, -qq for ERROR,
                          -qqq for CRITICAL
-NF, --no-log-formatting  Disable log formatter  [env var:
                          KMHELPERS_NO_LOG_FORMATTING]
-L, --log-file FILE       Path to log file (logs will be written in addition
                          to console output)  [env var: KMHELPERS_LOG_FILE]
--chdir DIRECTORY         Change to directory before initialization  [env
                          var: KMHELPERS_RUN_DIR]
-y, --yes                 Automatically answer yes to all confirmation
                          prompts.  [env var: KMHELPERS_SKIP_CONFIRMATION]

Also honors KMHELPERS_LOG_LEVEL: default log level 0-4 (0=CRITICAL, 4=DEBUG) before -v/-q adjustments. Default: 3 (INFO).