CLI reference

Auto-generated from the helixforge click app by scripts/gen_cli_reference.py. Do not edit by hand, run the script (or let the pre-commit/CI drift gate regenerate it). Each command's description, options, and examples come straight from its docstring and epilog, so this reference cannot drift from the code.

HelixForge v3: isoform-aware refinement of Helixer annotations.

Command	Description
helixforge confidence	Inspect (read-only): score genes against the Helixer HDF5 confidence track.
helixforge doctor	Preflight: validate inputs + resolve external tools before a run.
helixforge evidence	Inspect (read-only): score any GFF3 against RNA-seq + protein evidence.
helixforge parallel aggregate	Collect per-chunk outputs by pattern → one annotation; verify + fail closed.
helixforge parallel example-sbatch	Write a copy-paste SBATCH wrapper that runs a tasks file on one node.
helixforge parallel plan	Partition the genome (v1 strategies) + reserve disjoint HFG ranges → plan.json.
helixforge parallel suggest	Recommend chunk count + per-chunk resources (heuristic; prints trade-offs).
helixforge parallel tasks	Expand a command template over the plan → an executor-agnostic task file.
helixforge reconcile	Reconcile Helixer models with evidence → tiered GFF3 + per-gene report.
helixforge stats	Inspect (read-only): before/after table of a Helixer vs HelixForge GFF3.
helixforge utils align	Run miniprot protein-to-genome alignment.
helixforge utils convert	GFF3 <-> GTF format conversion.
helixforge utils extract-proteins	Translate CDS from GFF3 + genome to protein FASTA.
helixforge utils fetch-db	Download, decompress, and Diamond-format reference protein databases.
helixforge utils filter	Tiered output filtering by confidence/evidence/biotype.
helixforge utils qc	Genome-wide QC report (HTML/JSON/TSV).
helixforge utils summarize	Annotation statistics table.
helixforge viz	Render per-locus plots, interactive pages, or browser tracks for a run.