Are SA tags lifted?

[DanielNaro]

Hello,
The documentation does not list the SA flag as lifted, and from reading the code I think that it is indeed not the case. Could you confirm this?
Is this a development you are considering? I guess the logic would be fairly similar to ChainMap::lift_segment, would it not?
Thanks and best regards,
Daniel Naro

[milkschen]

Hi Daniel,

We don't have a short-term plan to lift the SA flag due to limited bandwidth. The CIGAR information in SA:z is a bit tricky to deal with, though still doable.

As you mentioned, most SAM fields are lifted in ChainMap::lift_segment() for the ChainMap mode. The NM:i and MD:z tags are lifted in void read_and_lift() if the -m optional flag is toggled.

Nae-Chyun