You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
In #1808, we are adding LCA_SqliteDatabase, which supports on-disk LCA databases.
The "standard" way of creating these is to use sourmash lca index ... -F sql, which has the disadvantage of first creating an LCA_Database in memory, and only then saving it to disk. This is unnecessarily memory intensive.
An alternative would be to directly support creation and update of an LCA database on disk in lca index, perhaps through the implementation of an insert on LCA_SqliteDatabase. This would be much lower memory.
Right now, you can do this by combining sourmash sig cat ... -o lca.sqldb (to create a SqliteIndex) then sourmash tax prepare -t <tax> -o lca.sqldb (to add a LineageDB_Sqlite table), but this skips all of the
consistency checking that sourmash lca index does.
The text was updated successfully, but these errors were encountered:
In #1808, we are adding
LCA_SqliteDatabase
, which supports on-disk LCA databases.The "standard" way of creating these is to use
sourmash lca index ... -F sql
, which has the disadvantage of first creating anLCA_Database
in memory, and only then saving it to disk. This is unnecessarily memory intensive.An alternative would be to directly support creation and update of an LCA database on disk in
lca index
, perhaps through the implementation of aninsert
onLCA_SqliteDatabase
. This would be much lower memory.Right now, you can do this by combining
sourmash sig cat ... -o lca.sqldb
(to create aSqliteIndex
) thensourmash tax prepare -t <tax> -o lca.sqldb
(to add aLineageDB_Sqlite
table), but this skips all of theconsistency checking that
sourmash lca index
does.The text was updated successfully, but these errors were encountered: