diff --git a/Cargo.lock b/Cargo.lock index 0fdf6422..5366747b 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -409,19 +409,6 @@ version = "0.3.31" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "953ec861398dccce10c670dfeaf3ec4911ca479e9c02154b3a215178c5f566f2" -[[package]] -name = "popgen" -version = "0.1.0" -dependencies = [ - "itertools 0.14.0", - "noodles", - "noodles-core", - "rand", - "thiserror 2.0.12", - "triangle_matrix", - "tskit", -] - [[package]] name = "ppv-lite86" version = "0.2.20" @@ -648,6 +635,19 @@ version = "1.0.17" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "00e2473a93778eb0bad35909dff6a10d28e63f792f16ed15e404fca9d5eeedbe" +[[package]] +name = "varistat" +version = "0.1.0" +dependencies = [ + "itertools 0.14.0", + "noodles", + "noodles-core", + "rand", + "thiserror 2.0.12", + "triangle_matrix", + "tskit", +] + [[package]] name = "wasi" version = "0.13.3+wasi-0.2.2" diff --git a/Cargo.toml b/Cargo.toml index a9feed77..90569a9c 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -1,5 +1,5 @@ [package] -name = "popgen" +name = "varistat" version = "0.1.0" edition = "2021" diff --git a/examples/from_tskit.rs b/examples/from_tskit.rs index 87992d10..1e760332 100644 --- a/examples/from_tskit.rs +++ b/examples/from_tskit.rs @@ -1,6 +1,6 @@ use std::env; -use popgen::MultiSiteCounts; +use varistat::MultiSiteCounts; fn process_ts(ts: &tskit::TreeSequence) { let counts = MultiSiteCounts::try_from_tree_sequence(ts, None).unwrap(); diff --git a/examples/from_vcf.rs b/examples/from_vcf.rs index 58d8794b..c49e26b6 100644 --- a/examples/from_vcf.rs +++ b/examples/from_vcf.rs @@ -1,5 +1,5 @@ use noodles::vcf; -use popgen::{adapter::vcf::record_to_genotypes_adapter, MultiSiteCounts}; +use varistat::{adapter::vcf::record_to_genotypes_adapter, MultiSiteCounts}; static VCF_FILE: &str = r#"##fileformat=VCFv4.5 ##FORMAT= diff --git a/src/adapter.rs b/src/adapter.rs index 362c3f96..ba4694f0 100644 --- a/src/adapter.rs +++ b/src/adapter.rs @@ -1,6 +1,6 @@ #[cfg(feature = "noodles")] pub mod vcf { - use crate::{AlleleID, PopgenResult}; + use crate::{AlleleID, VaristatResult}; use noodles::vcf::variant::record::samples::keys::key; use noodles::vcf::variant::record::samples::series::Value; use noodles::vcf::variant::record::samples::Sample; @@ -13,7 +13,7 @@ pub mod vcf { record: Record, num_samples: usize, ploidy: usize, - ) -> PopgenResult>> { + ) -> VaristatResult>> { let mut genotypes = Vec::with_capacity(ploidy * num_samples); for sample in record.samples().iter() { diff --git a/src/from_tree_sequence.rs b/src/from_tree_sequence.rs index bc7219e9..dc6f38dc 100644 --- a/src/from_tree_sequence.rs +++ b/src/from_tree_sequence.rs @@ -1,4 +1,4 @@ -use crate::{MultiSiteCounts, PopgenResult}; +use crate::{MultiSiteCounts, VaristatResult}; // NOTES: // 1. tskit could use Add for all id types! @@ -42,7 +42,7 @@ fn update_right( pub fn try_from_tree_sequence( ts: &tskit::TreeSequence, _parameters: Option, -) -> PopgenResult { +) -> VaristatResult { let mut counts = MultiSiteCounts::default(); let mut left = 0.0; // NOTE: we need TreeSequence to be able to provide these diff --git a/src/lib.rs b/src/lib.rs index 29695a3b..cf51efde 100644 --- a/src/lib.rs +++ b/src/lib.rs @@ -11,7 +11,7 @@ pub mod stats; mod test; pub(crate) mod util; -pub type PopgenResult = Result; +pub type VaristatResult = Result; #[cfg(feature = "tskit")] pub use tskit; @@ -21,7 +21,7 @@ pub use from_tree_sequence::FromTreeSequenceOptions; #[non_exhaustive] #[derive(Debug, thiserror::Error)] -pub enum PopgenError { +pub enum VaristatError { #[cfg(feature = "noodles")] #[error("couldn't handle VCF: {0}")] NoodlesVCF(#[from] std::io::Error), @@ -95,7 +95,7 @@ impl MultiSiteCounts { pub fn try_from_tree_sequence( ts: &tskit::TreeSequence, options: Option, - ) -> Result { + ) -> Result { from_tree_sequence::try_from_tree_sequence(ts, options) } diff --git a/src/test.rs b/src/test.rs index d4e42ee6..878e92b7 100644 --- a/src/test.rs +++ b/src/test.rs @@ -16,7 +16,7 @@ mod tests { #[cfg(feature = "noodles")] mod vcf { use crate::adapter::vcf::record_to_genotypes_adapter; - use crate::{AlleleID, MultiSiteCounts, PopgenResult}; + use crate::{AlleleID, MultiSiteCounts, VaristatResult}; use noodles::vcf::header::record::value::map::{Contig, Format}; use noodles::vcf::header::record::value::Map; use noodles::vcf::variant::io::Write; @@ -168,7 +168,7 @@ mod tests { .records() .map(Result::unwrap) .map(|rec| record_to_genotypes_adapter(&header, rec, num_samples, ploidy)) - .collect::>>() + .collect::>>() .unwrap(); let counts = MultiSiteCounts::from_tabular(all_alleles.iter().cloned()); (all_alleles, counts) diff --git a/tests/test_try_from_tree_sequence.rs b/tests/test_try_from_tree_sequence.rs index 85469ca0..f588b1c4 100644 --- a/tests/test_try_from_tree_sequence.rs +++ b/tests/test_try_from_tree_sequence.rs @@ -1,8 +1,8 @@ // NOTE: these tests require compiling // with the tskit feature -use popgen::tskit; -use popgen::tskit::prelude::StreamingIterator; +use varistat::tskit; +use varistat::tskit::prelude::StreamingIterator; #[cfg(test)] struct MutationData { @@ -63,7 +63,7 @@ struct SiteCountContents { } #[cfg(test)] -fn validate_site_counts(counts: &popgen::iter::SiteCounts, expected: SiteCountContents) { +fn validate_site_counts(counts: &varistat::iter::SiteCounts, expected: SiteCountContents) { let num_alleles = expected .derived .iter() @@ -246,7 +246,7 @@ mod naive_details { #[cfg(test)] fn generate_expected_site_counts_naive( ts: &tskit::TreeSequence, - options: Option, + options: Option, ) -> Vec { let mut expected = vec![]; // We have no code depending on options yet @@ -645,9 +645,9 @@ where #[cfg(test)] fn generate_counts_and_validate( ts: &tskit::TreeSequence, - options: Option, + options: Option, ) { - let counts = popgen::MultiSiteCounts::try_from_tree_sequence(ts, None).unwrap(); + let counts = varistat::MultiSiteCounts::try_from_tree_sequence(ts, None).unwrap(); let expected = generate_expected_site_counts_naive(ts, options); assert_eq!(counts.len(), expected.len()); for (obs, exp) in counts.iter().zip(expected.into_iter()) {