refactor_rs_downsample - Branch - sourmash-bio/sourmash

MRG: improve downsampling behavior on `KmerMinHash`; fix `RevIndex::gather` bug around `scaled`.

#3342Merged

Comparing

refactor_rs_downsample

(

80c3404

) with

latest

(

1a6312b

)

-17%

Regressions: 4

Untouched: 17

Benchmarks

Failed

abund0_ani_ci1Regression

src/core/benches/gather.rs::gather::gather_stats_benchmarks::gather_stats::abund0_ani_ci1

-16%

581.4 µs692.9 µs

abund1_ani_ci0Regression

src/core/benches/gather.rs::gather::gather_stats_benchmarks::gather_stats::abund1_ani_ci0

-12%

787.2 µs898.7 µs

abund0_ani_ci0Regression

src/core/benches/gather.rs::gather::gather_stats_benchmarks::gather_stats::abund0_ani_ci0

-17%

560.6 µs672.2 µs

abund1_ani_ci1Regression

src/core/benches/gather.rs::gather::gather_stats_benchmarks::gather_stats::abund1_ani_ci1

-12%

809.7 µs921.2 µs

Passed

intersection

src/core/benches/minhash.rs::minhash::intersection::minhash::intersection

18.2 µs18.2 µs

load nodegraph

src/core/benches/nodegraph.rs::nodegraph::save_load::nodegraph::load nodegraph

187.1 µs187.1 µs

force with valid kmers

src/core/benches/compute.rs::compute::add_sequence_protein::add_sequence_protein::force with valid kmers

399.2 ms399.2 ms

invalid kmers

src/core/benches/compute.rs::compute::add_sequence_protein::add_sequence_protein::invalid kmers

399.6 ms399.6 ms

lowercase

src/core/benches/compute.rs::compute::add_sequence_protein::add_sequence_protein::lowercase

399.1 ms399.1 ms

valid

src/core/benches/compute.rs::compute::add_sequence_protein::add_sequence_protein::valid

399.2 ms399.2 ms

save nodegraph

src/core/benches/nodegraph.rs::nodegraph::save_load::nodegraph::save nodegraph

93.1 µs93.1 µs

large intersection

src/core/benches/minhash.rs::minhash::intersection::minhash::large intersection

9.1 ms9.1 ms

intersection_size

src/core/benches/minhash.rs::minhash::intersection::minhash::intersection_size

15.4 µs15.4 µs

large intersection_size

src/core/benches/minhash.rs::minhash::intersection::minhash::large intersection_size

7.5 ms7.5 ms

large intersection_size btree

src/core/benches/minhash.rs::minhash::intersection::minhash::large intersection_size btree

18.2 ms18.2 ms

save compressed nodegraph

src/core/benches/nodegraph.rs::nodegraph::save_load::nodegraph::save compressed nodegraph

1.4 ms1.4 ms

large intersection btree

src/core/benches/minhash.rs::minhash::intersection::minhash::large intersection btree

18.3 ms18.3 ms

valid

src/core/benches/compute.rs::compute::add_sequence::add_sequence::valid

14 ms14 ms

lowercase

src/core/benches/compute.rs::compute::add_sequence::add_sequence::lowercase

14 ms14 ms

force with valid kmers

src/core/benches/compute.rs::compute::add_sequence::add_sequence::force with valid kmers

14 ms14 ms

invalid kmers

src/core/benches/compute.rs::compute::add_sequence::add_sequence::invalid kmers

10.4 ms10.4 ms

Commits

Click on a commit to change the comparison range

Base

latest

1a6312b

+0.01%

implement downsample_max_hash in terms of downsample_scaled

d9eeafd

1 year ago

by ctb

adjust references & use clone too much

4ab87e4

1 year ago

by ctb

switch to using scaled; avoid unnecessary clones?

ffa9683

1 year ago

by ctb

update to fix? scaled=0 situation

5f70fcc

11 months ago

by ctb

+0.07%

define new error

ffd8ffe

11 months ago

by ctb

-0.01%

bump sourmash core to 0.16.0 b/c of API change

b67fc04

11 months ago

by ctb

update include/sourmash.h

9b9fc5a

11 months ago

by ctb

rename error type; test specific error type

79e7b7d

11 months ago

by ctb

-16.67%

Merge branch 'latest' into refactor_rs_downsample

c5d3623

11 months ago

by ctb

Merge branch 'latest' into refactor_rs_downsample

80c3404

11 months ago

by ctb

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