Heng Li
Heng Li
You are probably right. Have you tried that? One thing I haven't thought through is whether this would lead to out-of-bound access to `qr[]`.
The input sequences should all have different names.
When I googled "infix", I found this issue. Then I realized that I have missed this question for 3 years. Sorry. It is non-trivial to implement infix alignment with the...
I wonder with reduced index size if the shared memory mode is still much needed. Also, as I remember, someone proposed a better way to implement shared memory mode but...
In the asm/ggs mode, minigraph by default only aligns through gaps shorter than 100kb. Is the gap longer than 100kb?
> Can you suggest reasons for why this segment didn't split during graph construction? How do you know this? Probably this region is not used for graph construction.
These L-lines don't show whether that 251kb region is used in graph construction. > what would be the possible reasons for a large region like this to not be used...
Duplicate of #1. Minigraph is more for mapping to a reference graph. I don't think a reference graph should allow overlaps. Also, it is tricky to work with overlaps. It...
Sorry for misreading your question. My initial intention was to require CIGAR because L-lines may have tags. Making CIGAR optional will complicate tags. In addition, `0M` doesn't waste much space...
This is probably a bug. You can take it as uncalled `.` for now.