Comparing
try-skipmers
(e077599
) withlatest
(b69c960
)-1%
- Improvements
- 0
- Regressions
- 0
- Untouched
- 21
- New
- 0
- Dropped
- 0
- Ignored
- 0
Benchmarks
Passed
intersection_size
src/core/benches/minhash.rs::minhash::intersection::minhash::intersection_size0%
18.3 µs
18.3 µs
save nodegraph
src/core/benches/nodegraph.rs::nodegraph::save_load::nodegraph::save nodegraph0%
93.3 µs
93.2 µs
abund1_ani_ci1
src/core/benches/gather.rs::gather::gather_stats_benchmarks::gather_stats::abund1_ani_ci10%
959.9 µs
959.6 µs
abund1_ani_ci0
src/core/benches/gather.rs::gather::gather_stats_benchmarks::gather_stats::abund1_ani_ci00%
938.5 µs
938.2 µs
abund0_ani_ci1
src/core/benches/gather.rs::gather::gather_stats_benchmarks::gather_stats::abund0_ani_ci10%
736.5 µs
736.4 µs
abund0_ani_ci0
src/core/benches/gather.rs::gather::gather_stats_benchmarks::gather_stats::abund0_ani_ci00%
716.9 µs
716.8 µs
save compressed nodegraph
src/core/benches/nodegraph.rs::nodegraph::save_load::nodegraph::save compressed nodegraph0%
1.4 ms
1.4 ms
large intersection
src/core/benches/minhash.rs::minhash::intersection::minhash::large intersection0%
10.6 ms
10.6 ms
intersection
src/core/benches/minhash.rs::minhash::intersection::minhash::intersection0%
20.2 µs
20.2 µs
large intersection btree
src/core/benches/minhash.rs::minhash::intersection::minhash::large intersection btree0%
19.4 ms
19.4 ms
large intersection_size btree
src/core/benches/minhash.rs::minhash::intersection::minhash::large intersection_size btree0%
19 ms
19 ms
large intersection_size
src/core/benches/minhash.rs::minhash::intersection::minhash::large intersection_size0%
9.3 ms
9.3 ms
load nodegraph
src/core/benches/nodegraph.rs::nodegraph::save_load::nodegraph::load nodegraph0%
187.3 µs
187.4 µs
valid
src/core/benches/compute.rs::compute::add_sequence::add_sequence::valid-2%
14.2 ms
14.5 ms
lowercase
src/core/benches/compute.rs::compute::add_sequence::add_sequence::lowercase-2%
14.2 ms
14.5 ms
force with valid kmers
src/core/benches/compute.rs::compute::add_sequence::add_sequence::force with valid kmers-2%
14.2 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
valid
src/core/benches/compute.rs::compute::add_sequence_protein::add_sequence_protein::valid-3%
402 ms
414.5 ms
invalid kmers
src/core/benches/compute.rs::compute::add_sequence_protein::add_sequence_protein::invalid kmers-3%
402.4 ms
415 ms
force with valid kmers
src/core/benches/compute.rs::compute::add_sequence_protein::add_sequence_protein::force with valid kmers-3%
402 ms
414.5 ms
lowercase
src/core/benches/compute.rs::compute::add_sequence_protein::add_sequence_protein::lowercase-3%
401.9 ms
414.4 ms
Commits
Click on a commit to change the comparison rangeBase
latest
b69c960
-55%
Merge branch 'latest' into try-skipmers
117cd0d
3 months ago
by bluegenes+55%
use hash fn encoding instead; init testing
2bac5fd
3 months ago
by bluegenes0%
fix test
fdd1a44
3 months ago
by bluegenes0%
Merge branch 'latest' into try-skipmers
55435d1
3 months ago
by bluegenes0%
cont
ff33f7b
2 months ago
by bluegenes0%
test
11978ed
2 months ago
by bluegenes0%
skipmers must be at least ksize 3
2de520e
2 months ago
by bluegenes0%
Merge branch 'latest' into try-skipmers
cb2e7e1
2 months ago
by bluegenes0%
clippy fix
d4a6200
2 months ago
by bluegenes0%
Merge branch 'latest' into try-skipmers
d7f59cf
2 months ago
by bluegenes-1%
WIP: skipmer improvements (#3415)
Make skipmers robust, but keep #3395 functional in the meantime.
This PR:
- enables second skipmer types, so we have m1n3 in addition to m2n3
- switches to a reading frame approach for both translation + skipmers,
which means we first build the reading frame, then kmerize, rather than
building kmers + translating/skipping on the fly
- avoids "extended length" needed for skipping on the fly
Since this changes the `SeqToHashes` strategy a bit, there's one python
test where we now see a different error.
Future thoughts:
- with the new structure, it would be straightforward to add validation
to exclude protein k-mers with invalid amino acids (`X`). I guess I'm
not entirely sure what happens to those atm...
96aea47
2 months ago
by bluegenes0%
Merge branch 'latest' into try-skipmers
25a16ae
2 months ago
by bluegenes0%
try fix branchwater incompat
6359e16
2 months ago
by bluegenes0%
roll back web-sys too
43e069c
2 months ago
by bluegenes0%
add js-sys, web-sys to dependabot ignore
6008646
2 months ago
by bluegenes0%
add more tests
b20479c
1 month ago
by bluegenes0%
more tests
e5ea8af
1 month ago
by bluegenes0%
test protein rf display
8a0600d
1 month ago
by bluegenes0%
Merge branch 'latest' into try-skipmers
8cb0bea
1 month ago
by bluegenes0%
Merge branch 'latest' into try-skipmers
81bab97
1 month ago
by bluegenes0%
seqtohashes errors instead of panic for frame errors (#3445)
e077599
1 month ago
by bluegenes