update reference results for default per-base mutation

update reference results for default per-base mutation

fix tag parser

handle overlap/indel incompatibilities

Merge branch 'dev'

update reference results

for new functionality definition

update reference results

for cdr3 splitting in vsearch

Merge branch 'dev'

Conflicts:
	manual.md

(re-) add explicit cdr3 length clustering prefilter

fix gldir reference