Felix Bemm

Above code is actually fine, the issue appears somewhere else.

Guess it is `genomicMSA.cc` `if ((completeName[i] == '-') || (completeName[i] == '.'))` Changing it to: `if ((completeName[i] == '.'))` Test running.

@MarioStanke Remove '-' fixes this but I am not sure if '-' is actually there for a good reason.

@cjw85 Would it be possible to stick to Major.Minor instead of MajorMinorPatch for `_`?

minimap2 shows the same behaviour when running chromosomes vs. chromosomes with one of the "asmX" presets. Just starts to consume memory after it reports on distinct minimizer. Same happens if...

@lh3 does miniasm have a upper limitation of what it can actually read? I am trying to assemble a gzipped 4Tb PAF file and it looks there is a hard...

@mr--white set `-m` to something between 1000-2000 during your minimap2 overlap. Resulting PAF file should much smaller and miniasm run through.

That I know but almost no other annotation (tool) does produce such a format. Plus, putting the prefixes there is redundant with the feature column of the GFF format specification....

The latter might be a short term fix but one has to remove `gene:` or `transcript:` from the annotated VCF in the end again or has to live with the...

+1 1.04 is not there yet.