Gordon Gremme comments

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                                            Gordon Gremme

translation code and ambiguity handling

Sounds like a good appoach. Maybe issue a warning, too.

make compact ulong store dynamic

If it would be possible to remove the bitpackstring code that would be great. The automatically generated code is very hard to maintain.

gt gff3 -sort doesn't work on some gff files in one go

Thanks for the report, I'll look into it! Might take a while, though...

extractfeat: -matchdescstart should probably be set by default

No, it's not common to use MD5 IDs in GFF3 files. But I think the tight coupling between annotations and sequences this produces prevents many errors further down the line....

extractfeat: -matchdescstart should probably be set by default

That sounds like a good approach to me. I would prefer allowing both in one file, if that is feasible. Otherwise deciding in the beginning should be good enough.

extractfeat: -matchdescstart should probably be set by default

Sounds reasonable. Who wants to tackle it?