StoreTagBackInSequence #

[[step]]
    action = "StoreTagBackInSequence"
    in_label = "mytag"
    on_lost = "Complain" # Ignore|Complain

This transformation stores a tag’s value back into the sequence, replacing the original sequence at that location.

This only works if either the tag’s length is unchanged, or it’s a single region tag, since for a multi-region tag it would be undefined where to add or remove bases.

If reads have been manipulated in away that this tag’s bases are (even partially lost), the on_lost handling comes to pass. By default, a run-time error is raised. Set it to ‘Ignore’ to instead leave the reads unchanged.

This is useful for example after you have applied Lowercase to a tag, to lowercase precise regions in a read.

Compare with StoreTagInSequence which stores one tag’s values in another tag’s location.