Options #

There is a small set of runtime knobs exposed under [options].

Most workflows can rely on the defaults.

[options]
    threads = 10
    max_blocks_in_flight = 100
    block_size = 10000
    buffer_size = 102400
    accept_duplicate_files = false
    spot_check_read_pairing = true

Key	Default	Description
`threads`	(auto)	Worker threads for transformations. See threading.
`max_blocks_in_flight`	`100`	How many blocks may be concurrently being processed. Lowering this limits RAM usage.
`block_size`	`10000`	Number of fragments pulled per batch. Increase for very large runs when IO is abundant; decrease to reduce peak memory use.
`buffer_size`	`102400`	Initial bytes reserved per block. The allocator grows buffers on demand, so tuning is rarely necessary.
`accept_duplicate_files`	`false`	Permit the same path to appear multiple times across segments. Useful for fixtures or synthetic tests; keep disabled to catch accidental copy/paste errors.
`spot_check_read_pairing`	`true`	Sample every 1000th fragment to ensure paired reads still share a name prefix; disable when names are intentionally divergent or rely on `ValidateName` to customise the separator.

Changing these knobs can affect memory pressure and concurrency behavior.

Measure before and after if you deviate from defaults.