Open vkkodali opened 1 year ago
Oh, 2bp intron. Smells like a bug. I will have a look later.
Actually it occurs to me that -J
should be larger than -F
; otherwise a frameshift will always may be aligned as an intron. You may try to reduce frameshift penalty -F
. However, with an excessively small -F
, you will get more frameshifts in alignment.
Actually it occurs to me that
-J
should be larger than-F
Thanks! Looks like at some point in the past, the default value for -F
was set to 17 (see manual). I will try reducing it to 20 and test.
Didn't realize the manpage was that old. Now updated to v0.9.
I noticed this when testing for #33. In the example shown below, the
cs:Z:
tag uses the following to represent an intron:~gt-1ag
. Is this expected?