LRA Handling of Ambiguity

[zhemingfan]

We were wondering how LRA handles ambiguity in the alignment as there are no secondary alignment outputs.

[mchaisso]

--PrintNumAln can output additional alignments, however when the alignments are ambiguous the mapping quality is low.

…

On Wed, Apr 7, 2021 at 6:47 PM zhemingfan ***@***.***> wrote: We were wondering how LRA handles ambiguity in the alignment as there are no secondary alignment outputs. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#15>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAKPGPXAY2PTC6G7PU4W4UTTHUDJTANCNFSM42R4BRXQ> .

[oneillkza]

Thanks @mchaisso

We were also curious about the TP tag mentioned in the readme. As far as I can tell, this is not included in the output sam by default. Is this populated when --PrintNumAln is used?