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when I first implemented the LCA stuff, I was young and foolish and thought there was a point to allowing flexibility in removing identifier versions - e.g. converting GCF_000422665.1 into GCF_000422665 for purposes of lineage mapping.
But, in practice, this is really not used and just massively complicated the code base.
I think we should remove it completely and just standardize on identifiers for LCA and taxonomy being the first space-separated value in the signature name. We could even make it a SourmashSignature property, .ident. 🤔
A responsible way to do this would:
for sourmash v5, make --keep-identifier-versions=True the default everywhere; this would be a breaking change;
for sourmash v6, make remove support for keep-identifier-versions altogether.
This musing is occasioned by #1808 where the implementation of LCA_SqliteDatabase is made more confusing by this identifier stuff.
The text was updated successfully, but these errors were encountered:
when I first implemented the LCA stuff, I was young and foolish and thought there was a point to allowing flexibility in removing identifier versions - e.g. converting
GCF_000422665.1
intoGCF_000422665
for purposes of lineage mapping.But, in practice, this is really not used and just massively complicated the code base.
I think we should remove it completely and just standardize on identifiers for LCA and taxonomy being the first space-separated value in the signature name. We could even make it a
SourmashSignature
property,.ident
. 🤔A responsible way to do this would:
--keep-identifier-versions=True
the default everywhere; this would be a breaking change;keep-identifier-versions
altogether.This musing is occasioned by #1808 where the implementation of
LCA_SqliteDatabase
is made more confusing by this identifier stuff.The text was updated successfully, but these errors were encountered: