hhfilter(1) on Linux
The text bddb06b9a289, as Debian 9 (Stretch) shipped it.
filter an alignment by maximum sequence identity of match states and minimum coverage
Flags it lists
-
-M -
-a -
-cov -
-diff -
-i -
-id -
-neff -
-o -
-qid -
-qsc -
-v