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todo: Improve --regions-overlap variant #1746

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pd3 opened this issue Feb 9, 2024 · 0 comments
Open

todo: Improve --regions-overlap variant #1746

pd3 opened this issue Feb 9, 2024 · 0 comments

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pd3 commented Feb 9, 2024

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.
pd3 added a commit to samtools/bcftools that referenced this issue Feb 12, 2024
@pd3
Add new --regions-overlap option
d25e3f1 
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
@pd3 pd3 mentioned this issue Feb 12, 2024
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