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MRG: fix sketch downsampling across the plugin, incl fastmultigather
, manysearch
, and multisearch
#504
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ctb
changed the title
WIP: fix scaled stuff
WIP: fix sketch downsampling in both Nov 10, 2024
fastmultigather
implementations
ctb
changed the title
WIP: fix sketch downsampling in both
WIP: fix sketch downsampling across the plugin, incl Nov 11, 2024
fastmultigather
implementationsfastmultigather
, manysearch
, and multisearch
ctb
changed the title
WIP: fix sketch downsampling across the plugin, incl
MRG: fix sketch downsampling across the plugin, incl Nov 11, 2024
fastmultigather
, manysearch
, and multisearch
fastmultigather
, manysearch
, and multisearch
Merging without review so I can cut a new release. |
This was referenced Nov 11, 2024
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Tackles #505, and maybe fixes #483.
This PR adds tests and short-term fixes for a myriad of downsampling problems, largely caused by sourmash-bio/sourmash#3384, in which
Collection:sig_from_record
does not downsample the loaded sketch.Specifically this PR:
fastmultigather
to downsample the query properly;fasmultigather
on a RocksDB to properly handle scaled, includig downsampling the query, and also checking the max scaled on the RocksDB;manysearch
to downsample both the queries (viaMultiCollection
) and database sketches, as well as output scaled, ksize, and moltype;manysearch
against RocksDB to downsample the query, as well as check the max scaled on the RocksDB and output scaled, ksize, and moltype;multisearch
andpairwise
to downsample queries and against, as well as output scaled, ksize, and moltype;MultiCollection::load_sketches
to downsample them to the provided selection (as used inmanysearch
;I'm doing a patchfix release with this because it's returning incorrect results ;(. At some point we will want to revisit the code and clean it up more - see #510.