Brian Abernathy

It seems important to differentiate between reads lacking an alignment due to no minimizers and too many minimizers. If sub-sampling to reduce the search space is not feasible, it may...

@adamnovak I'm primarily interested in reads that do not contain an alignment in the graph regardless of computational complexity. I'm not particularly interested in the MAPQ 0 alignments themselves. Any...

Thanks for the detailed diagnosis, I was able to manually index the graph. It seems that `vg autoindex` could benefit from an option to select sequence-based or vcf-based graph input....

Thanks for the info, I understand why you wouldn't want to assume "*" = 0 overlap. Have you considered adding an option to explicitly set the "*" overlap value? I...

I'm primarily working with vg, which was used to produce the GFAs in question. Of course, the * overlap GFAs produced by vg work fine with all vg tools. I...