Eric T. Dawson

This adds the functions needed to generate the anchor chains from a list of overlaps, assuming the overlap list has not been previously filtered (though masking using the select_mask is...

Notes from #422 : - Refactor `rescue_overlap_ends` to use a helper function such as `extend_overlap_by_similarity(Overlap& overlap, const std::string_view query_sequence, const std::string_view target_sequence, const std::int32_t extension)`. This should make testing and...

Hey @indraniel , The documentation on variant calling has gotten pretty fragmented as we've experimented with new patterns. In brief, there are two calling pipelines: 1. `vg call`, which does...

I think these two issues are related but maybe not duplicates. The issue isn't the graph structure but its format in this case. I have a graph with no overlaps...

> Making CIGAR optional will complicate tags Yes - I can file an issue on the spec to clarify whether "CIGAR optional" means no field present or CIGAR field ==...

Hi all, Has there been any more work on this? Both tools are absolutely fantastic and I'd be happy to follow suit in making [yet another MinHash classifier](https://github.com/edawson/rkmh) compatible with...

Particularly problematic are the population-specific allele frequencies (AFR, AMR, EUR, EX, etc.). MEINFO throws a different error: ``` --------------------------------------------------------------------------- RemoteTraceback Traceback (most recent call last) RemoteTraceback: """ Traceback (most recent...

I agree these shouldn't be fixed to specific versions and should eventually be a range, but can we use a ">=" semantic instead as a start? Very much looking forward...