Mutation "chunks"

Cargo.toml

@@ -10,6 +10,7 @@ forrustts = {version = "0.3.0-alpha.0", git = "https://github.com/ForwardSimulat
 rand = "0.8.5"
 rand_distr = "0.4.3"
 clap = { version = "4.2.1", features = ["derive"] }
+rclite = "0.2.2"
 
 [dev-dependencies]
 proptest = "1.1.0"

src/genome_dynamic_chunks.rs

@@ -0,0 +1,68 @@
+use forrustts::genetics::GenerateBreakpoints;
+use forrustts::genetics::GeneticMap;
+use forrustts::prelude::*;
+
+use crate::common::DiploidGenome;
+use crate::common::Mutation;
+
+struct Chunk {
+    mutations: Vec<usize>,
+    num_mutations: usize,
+    count: u32,
+}
+
+#[derive(Default, Clone)]
+struct Genome {
+    chunks: Vec<usize>,
+}
+
+pub struct DiploidPopulation {
+    chunk_length: usize,
+    chunks: Vec<Chunk>,
+    mutations: Vec<Mutation>,
+    mutation_counts: Vec<u32>,
+    individuals: Vec<DiploidGenome>,
+    genomes: Vec<Genome>,
+}
+
+impl DiploidPopulation {
+    pub fn new(size: usize, chunk_length: usize) -> Self {
+        let genomes = vec![Genome::default(); 2 * size];
+        let individuals = vec![
+            DiploidGenome {
+                first: 0,
+                second: 0
+            };
+            size
+        ];
+
+        Self {
+            chunk_length,
+            genomes,
+            individuals,
+            mutations: vec![],
+            mutation_counts: vec![],
+            chunks: vec![],
+        }
+    }
+}
+
+fn crossover(
+    genome1: usize,
+    genome2: usize,
+    mutations: &Vec<Mutation>,
+    crossover_position: Vec<Position>,
+    new_mutations: Vec<usize>,
+    genomes: &mut Vec<Genome>,
+    chunks: &mut Vec<Chunk>,
+) -> Genome {
+    let mut current_genome = genome1;
+    let mut current_genome_index = 0_usize;
+    let mut current_genome_index_position = 0_usize;
+
+    let mut new_chunks = Vec::<usize>::default();
+
+    todo!("not done");
+
+    Genome { chunks: new_chunks }
+}

src/lib.rs

@@ -2,6 +2,7 @@ mod common;
 
 pub mod fwdpp_copy;
 pub mod genome_array;
+pub mod genome_dynamic_chunks;
 
 // Public "API" for examples
 pub use common::SimParams;