-
Notifications
You must be signed in to change notification settings - Fork 447
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
todo: Improve --regions-overlap variant
#1746
Comments
pd3
added a commit
to samtools/bcftools
that referenced
this issue
Feb 12, 2024
Add new --regions-overlap option which allows to take into account overlapping deletions that start out of the fasta file target region. Note this will need to be updated if the issue samtools/htslib#1746 is resolved. Resolves #2091
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
The mode
--regions-overlap variant|2
is supposed to recognize the actual bases affected by the variant. This is trickier than currently implemented in https://github.com/samtools/htslib/blob/develop/synced_bcf_reader.c#L569.The existing code trims variants from the left, but does not take into account cases like
ACGA > A--A
, which can be trimmed from both ends.In addition, the API does not give the choice to trim from the left or right in ambiguous cases. For many use cases, the desired behavior is to trim in such a way to prevent spurious overlaps. Alternatively, a new mode
3
can be added which acts the opposite way and reports an overlap whenever possible.The text was updated successfully, but these errors were encountered: