Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We鈥檒l occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[MRG] Fix containment calculation for nodegraphs #1862

Merged
merged 2 commits into from
Mar 5, 2022
Merged

[MRG] Fix containment calculation for nodegraphs #1862

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
39fb8f0
fix containment calculation for nodegraphs
luizirber Mar 4, 2022
1c363da
add a containment test
luizirber Mar 5, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
20 changes: 19 additions & 1 deletion src/core/src/sketch/nodegraph.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -309,7 +309,7 @@ impl Nodegraph {
.zip(&other.bs)
.map(|(bs, bs_other)| bs.intersection(bs_other).count())
.sum();
let size: usize = self.bs.iter().map(|bs| bs.len()).sum();
let size: usize = self.bs.iter().map(|bs| bs.count_ones(..)).sum();
result as f64 / size as f64
}
}
Expand Down Expand Up @@ -435,6 +435,24 @@ mod test {
assert_eq!(ng.unique_kmers(), 1);
}

#[test]
fn containment() {
let mut ng1: Nodegraph = Nodegraph::new(&[31], 3);
let mut ng2: Nodegraph = Nodegraph::new(&[31], 3);

(0..20).for_each(|i| {
if i % 2 == 0 {
ng1.count(i);
};
ng2.count(i);
});

assert_eq!(ng1.containment(&ng2), 1.0);
assert_eq!(ng1.similarity(&ng2), 0.5);
assert_eq!(ng1.unique_kmers(), 10);
assert_eq!(ng2.unique_kmers(), 20);
}

Comment on lines +438 to +455
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

there you go @ctb

#[test]
fn load_save_nodegraph() {
let mut datadir = PathBuf::from(env!("CARGO_MANIFEST_DIR"));
Expand Down