seismic migrate

Purpose

seismic migrate updates a SEISMIC-RNA output directory produced by an older version so that it works with the current version. The current migration handles version 0.24 → 0.25, which renamed two steps:

relate/ directories and files → idmut/
mask/ directories and files → filter/

and updated the JSON fields in report files to match renamed options.

The input directory is never modified. seismic migrate copies the entire output tree and updates the copy.

Inputs

Output directory from SEISMIC-RNA 0.24: Pass the top-level output directory (the one whose immediate children are per-sample directories). Exactly one path may be supplied.

Outputs

A full copy of the input tree, with all renames and JSON field updates applied. Written to --out-dir (default ./out). The output directory must not exist before running the command.

Quick example

Migrate the output directory out/ into a new directory out-0.25/:

seismic migrate out -o out-0.25

After the command succeeds, use out-0.25 in place of out.

Options

--out-dir DIR (-o): Path for the migrated output (must not exist; default ./out).
--num-cpus N: Parallel workers; one per sample directory (default: all CPUs).

The auto-generated Command Line Reference lists every option with its current default.

Caveats

The output directory must not exist before the command runs.
The output path must differ from the input path.
Only the 0.24 → 0.25 migration is supported. Outputs from 0.23 or earlier may not migrate correctly.
If idmut/{ref}/refseq.brickle is missing for a reference, all masked positions are attributed to G (the U list is left empty).

Common errors

seismic migrate can process 1 directory at a time, but got N: You supplied more than one positional argument.
<dir> contains no sample directories: You passed a sample directory or project root instead of the top-level output directory.
the output directory must not exist: Delete or rename the existing directory, or choose a different path.