Jordan Eizenga

For my part, I've done: - Max gap length determined on a per-alignment basis rather than per-aligner - Bug fix to dynamic programming - Bug fix to the full length...

I agree, that's probably true about documenting the quality-adjusted scores. I'll try to summarize here. Basically, you have a separate score matrix for each Phred score, which are typically included...

There's now a wiki page that describes our most mature variant calling workflow: https://github.com/vgteam/vg/wiki/Whole-genome-calling-and-genotyping

In https://github.com/vgteam/GetBlunted Ryan and I output a text-based translation table that identifies each node with the original sequence(s) that contributed to them. The tables look something like this: ``` #blunted_seq_name...

Can you provide the command line call that you ran into this error on?

@adamnovak This looks to me like it's running into a problem in the named-node stuff you implemented. Could you take a look?

If the sequences are mostly related by simple mutations (e.g. small indels, substitutions), you could also generate a multiple sequence alignment with an external tools and then use it to...

I think you are correct that the current state-of-the-art is to annotate the genomes individually. There are prototype annotation systems implemented in `vg annotate`, but they are far from mature....

I imagine this is probably actually a bug in libvgio: https://github.com/vgteam/libvgio/blob/6a8b7fa6f8f848c587536cd6e501eb7bc81b2c1d/include/vg/io/alignment_io.hpp#L60-L73

Can you share the inputs to recreate this crash? Otherwise, there's not a lot for us to go on. The primary maintainer of this subcommand is @ekg, but I suspect...