Swap #

[[step]]
    action = "Swap"
    segment_a = "read1"
    segment_b = "read2"
    if_tag = "mytag"

Swaps exactly two segments.

Arguments segment_a/segment_b are only necessary if there are more than two segments defined in the input.

Optionally only applies if a tag is truthy via if_tag.

Conditional swaps forget location tags #

A location tag records where in a segment some bytes live, so it is tied to one segment. An unconditional swap moves both segments as whole units, so location tags survive — they simply follow their segment.

A conditional swap (if_tag set) swaps reads one at a time, so after it runs a single location tag would point into two different segments depending on the read. Loctations are limted to a single segment, so a conditional Swap forgets every location tag on the two swapped segments. Referring to such a tag (or its location_… / initial_location_… companion) after the swap is a configuration error.

If you need to keep the data across a conditional swap, snapshot the tag to a plain string before the swap with ConcatTags; string tags are not segment-bound and are unaffected by the swap.