parameterize-skips - Branch - sourmash-bio/sourmash

WIP: skipmer improvements

#3415Merged

Comparing

parameterize-skips

(

28781bc

) with

try-skipmers

(

d7f59cf

)

-1%

Improvements: 0

Regressions: 0

Untouched: 21

New: 0

Dropped: 0

Ignored: 0

Benchmarks

Passed

intersection

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

20.3 µs

20.2 µs

large intersection_size btree

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

19 ms

abund0_ani_ci1

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

736.9 µs

736.6 µs

abund1_ani_ci1

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

960.2 µs

959.8 µs

abund1_ani_ci0

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

938.7 µs

938.4 µs

abund0_ani_ci0

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

717.1 µs

716.9 µs

intersection_size

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

18.3 µs

large intersection

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

10.6 ms

large intersection btree

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

19.4 ms

large intersection_size

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

9.3 ms

load nodegraph

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

187.3 µs

save nodegraph

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

93.2 µs

save compressed nodegraph

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

-2%

1.4 ms

valid

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

-3%

14.1 ms

14.5 ms

force with valid kmers

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

-3%

14.1 ms

14.5 ms

lowercase

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

-3%

14.1 ms

14.5 ms

invalid kmers

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

-3%

10.5 ms

10.8 ms

invalid kmers

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

-3%

401.1 ms

415 ms

force with valid kmers

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

-3%

400.7 ms

414.5 ms

lowercase

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

-3%

400.5 ms

414.4 ms

valid

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

-3%

400.6 ms

414.5 ms

Commits

Click on a commit to change the comparison range

Base

try-skipmers

d7f59cf

-50%

init ReadingFrames

2ba40b0

1 month ago

by bluegenes

+15%

actual fix dna validation; almost there

82ff63e

26 days ago

by bluegenes

apply lint suggestion; add back indexing comment

6c18180

26 days ago

by bluegenes

+33%

fix uppercasing + validation

af2af55

25 days ago

by bluegenes

clippy fixes; rm comment

28781bc

25 days ago

by bluegenes

Home Terms Privacy Docs