Skip to content

feat: Allow use of bookmark in examples/haploid_wright_fisher #479

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’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Mar 16, 2023
Merged

feat: Allow use of bookmark in examples/haploid_wright_fisher #479

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
35 changes: 32 additions & 3 deletions examples/haploid_wright_fisher.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,30 @@ use proptest::prelude::*;
use rand::distributions::Distribution;
use rand::SeedableRng;

fn rotate_edges(bookmark: &tskit::types::Bookmark, tables: &mut tskit::TableCollection) {
let num_edges = tables.edges().num_rows().as_usize();
let left =
unsafe { std::slice::from_raw_parts_mut((*tables.as_mut_ptr()).edges.left, num_edges) };
let right =
unsafe { std::slice::from_raw_parts_mut((*tables.as_mut_ptr()).edges.right, num_edges) };
let parent =
unsafe { std::slice::from_raw_parts_mut((*tables.as_mut_ptr()).edges.parent, num_edges) };
let child =
unsafe { std::slice::from_raw_parts_mut((*tables.as_mut_ptr()).edges.child, num_edges) };
let mid = bookmark.edges().as_usize();
left.rotate_left(mid);
right.rotate_left(mid);
parent.rotate_left(mid);
child.rotate_left(mid);
}

// ANCHOR: haploid_wright_fisher
fn simulate(
seed: u64,
popsize: usize,
num_generations: i32,
simplify_interval: i32,
update_bookmark: bool,
) -> Result<tskit::TreeSequence> {
if popsize == 0 {
return Err(anyhow::Error::msg("popsize must be > 0"));
Expand Down Expand Up @@ -46,6 +64,7 @@ fn simulate(
let parent_picker = rand::distributions::Uniform::new(0, popsize);
let breakpoint_generator = rand::distributions::Uniform::new(0.0, 1.0);
let mut rng = rand::rngs::StdRng::seed_from_u64(seed);
let mut bookmark = tskit::types::Bookmark::new();

for birth_time in (0..num_generations).rev() {
for c in children.iter_mut() {
Expand All @@ -64,7 +83,10 @@ fn simulate(
}

if birth_time % simplify_interval == 0 {
tables.full_sort(tskit::TableSortOptions::default())?;
tables.sort(&bookmark, tskit::TableSortOptions::default())?;
if update_bookmark {
rotate_edges(&bookmark, &mut tables);
}
if let Some(idmap) =
tables.simplify(children, tskit::SimplificationOptions::default(), true)?
{
Expand All @@ -73,6 +95,9 @@ fn simulate(
*o = idmap[usize::try_from(*o)?];
}
}
if update_bookmark {
bookmark.set_edges(tables.edges().num_rows());
}
}
std::mem::swap(&mut parents, &mut children);
}
Expand All @@ -91,6 +116,8 @@ struct SimParams {
num_generations: i32,
simplify_interval: i32,
treefile: Option<String>,
#[clap(short, long, help = "Use bookmark to avoid sorting entire edge table.")]
bookmark: bool,
}

fn main() -> Result<()> {
Expand All @@ -100,6 +127,7 @@ fn main() -> Result<()> {
params.popsize,
params.num_generations,
params.simplify_interval,
params.bookmark,
)?;

if let Some(treefile) = &params.treefile {
Expand All @@ -114,8 +142,9 @@ proptest! {
#[test]
fn test_simulate_proptest(seed in any::<u64>(),
num_generations in 50..100i32,
simplify_interval in 1..100i32) {
let ts = simulate(seed, 100, num_generations, simplify_interval).unwrap();
simplify_interval in 1..100i32,
bookmark in proptest::bool::ANY) {
let ts = simulate(seed, 100, num_generations, simplify_interval, bookmark).unwrap();

// stress test the branch length fn b/c it is not a trivial
// wrapper around the C API.
Expand Down