-
Notifications
You must be signed in to change notification settings - Fork 398
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Order of operations in CIGAR #1118
Labels
Comments
P.S.: This might be related to #502? |
Yes, related but not the same. We may move |
Can it not be resolved by linear time postprocessing? Something like anochoring the (mis)matches in the CIGAR string, and then sorting-and-merging any other CIGAR operations between (mis)match anchors? |
No, can't. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
I found that Minimap2 sometimes generates an unusual order of CIGAR opertations; with some
N
s, followed by someI
s then followed by moreN
s instead of the more expected order of having all theN
s combined together.Here is an example that produces this result:
You can see that after the first exon,
101S61M2I99M2D1M1I9M1D24M
, there are183N
skip, followed by437I
insertion, followed by another skip of131864N
.The text was updated successfully, but these errors were encountered: