Merge pull request #15 from jeffersonfparil/dev

adding additional inner-loop-break-condition when the last 3 consecut…

src/rust/src/aldknni.rs

@@ -307,11 +307,13 @@ impl GenotypesAndPhenotypes {
                     n_non_missing
                 };
                 // Select randomly non-missing pools to impute and estimate imputation error from
-                let mut rng = rand::thread_rng();
+                let mut rng: rand::rngs::ThreadRng = rand::thread_rng();
                 let idx_random_pools: Vec<usize> = (0..vec_q.len()).filter(|&idx| !vec_q[idx].is_nan()).choose_multiple(&mut rng, n_reps);
-                let mut optimum_mae = 1.0;
-                let mut optimum_min_loci_corr = vec_min_loci_corr[0];
-                let mut optimum_max_pool_dist = vec_max_pool_dist[0];
+                // Optimum mae, and parameters
+                let mut optimum_mae: f64 = 1.0;
+                let mut optimum_min_loci_corr: f64 = vec_min_loci_corr[0];
+                let mut optimum_max_pool_dist: f64 = vec_max_pool_dist[0];
+                let mut recent_3_maes: Vec<f64> = vec![0.0, 0.5, 1.0];
                 // Find the optimal min_loci_corr and max_pool_dist which minimise imputation error (MAE: mean absolute error)
                 // Across minimum loci correlation thresholds
                 for min_loci_corr in vec_min_loci_corr.iter() {
@@ -347,7 +349,15 @@ impl GenotypesAndPhenotypes {
                             ).abs();
                         }
                         mae /= n_reps as f64;
-                        if (mae <= f64::EPSILON) | (mae > optimum_mae) {
+                        // The most recent 3 MAEs
+                        recent_3_maes[2] = recent_3_maes[1];
+                        recent_3_maes[1] = recent_3_maes[0];
+                        recent_3_maes[0] = mae;
+                        // Inner loop break conditions
+                        if (mae <= f64::EPSILON) |
+                           (mae > optimum_mae) |
+                           (((recent_3_maes[0]-recent_3_maes[1]).abs() <= f64::EPSILON) &
+                            ((recent_3_maes[0]-recent_3_maes[2]).abs() <= f64::EPSILON)) {
                             break;
                         }
                         if mae < optimum_mae {

src/rust/src/lib.rs

@@ -45,7 +45,7 @@ fn impute(
     // 2) sync - intermediate richness and most preferred (*.sync)
     // 3) geno - least detailed - tab-delimited: chr,pos,allele,sample-1,sample-2,some-name-@#@#$%^&*(+)}:<'?"-with-a-bunch-of-asci-characters,... (*.txt)
     let extension_name: &str = fname
-        .split(".")
+        .split('.')
         .collect::<Vec<&str>>()
         .last()
         .expect("Error extracting the last character of the input filename in impute().");
@@ -216,7 +216,7 @@ fn impute(
             vec_header
         };
         let vec_header: Vec<&str> = if vec_header.len() == 1 {
-            header.split(";").collect()
+            header.split(';').collect()
         } else {
             vec_header
         };
@@ -297,7 +297,7 @@ fn impute(
     } else {
         fname_out_prefix.to_owned() + "-" + &rand_id + "-IMPUTED.csv"
     };
-    let _ = if &imputation_method == &"mean".to_owned() {
+    let _ = if imputation_method == *"mean" {
         println!("###################################################################################################");
         println!("mvi: mean value imputation");
         println!("###################################################################################################");

src/rust/src/vcf.rs

@@ -414,7 +414,7 @@ impl ChunkyReadAnalyseWrite<VcfLine, fn(&mut VcfLine, &FilterStats) -> Option<St
         // Find the positions where to split the file into n_threads pieces
         let chunks = find_file_splits(&fname, n_threads).expect("Error calling find_file_splits() within the read_analyse_write() method for FileVcf struct.");
         let n_threads = chunks.len() - 1;
-        let outname_ndigits = chunks[n_threads].to_string().len();
+        let n_digits = chunks[n_threads].to_string().len();
         println!("Chunks: {:?}", chunks);
         // Tuple arguments of vcf2sync_chunks
         // Instantiate thread object for parallel execution
@@ -428,7 +428,7 @@ impl ChunkyReadAnalyseWrite<VcfLine, fn(&mut VcfLine, &FilterStats) -> Option<St
             let self_clone = self.clone();
             let start = chunks[i];
             let end = chunks[i + 1];
-            let outname_ndigits = outname_ndigits;
+            let outname_ndigits = n_digits;
             let filter_stats = filter_stats.clone();
             let thread_ouputs_clone = thread_ouputs.clone(); // Mutated within the current thread worker
             let thread = std::thread::spawn(move || {

tests/tests.R

@@ -26,22 +26,22 @@ test_that(
 )
 
 test_that(
-    "aldknni_optim", {
-        print("aldknni_optim:")
-        vcf = fn_extract_missing(aldknni(fname=fname_vcf))
-        sync = fn_extract_missing(aldknni(fname=fname_sync))
-        csv = fn_extract_missing(aldknni(fname=fname_csv)) - c(0, 0, 0, 0, 1, 0)
+    "aldknni_fixed", {
+        print("aldknni_fixed:")
+        vcf = fn_extract_missing(aldknni(fname=fname_vcf, min_loci_corr=0.9, max_pool_dist=0.1))
+        sync = fn_extract_missing(aldknni(fname=fname_sync, min_loci_corr=0.9, max_pool_dist=0.1))
+        csv = fn_extract_missing(aldknni(fname=fname_csv, min_loci_corr=0.9, max_pool_dist=0.1)) - c(0, 0, 0, 0, 1, 0)
         expect_equal(vcf, sync, tolerance=0.1)
         expect_equal(vcf, csv, tolerance=0.1)
     }
 )
 
 test_that(
-    "aldknni_fixed", {
-        print("aldknni_fixed:")
-        vcf = fn_extract_missing(aldknni(fname=fname_vcf, min_loci_corr=0.9, max_pool_dist=0.1))
-        sync = fn_extract_missing(aldknni(fname=fname_sync, min_loci_corr=0.9, max_pool_dist=0.1))
-        csv = fn_extract_missing(aldknni(fname=fname_csv, min_loci_corr=0.9, max_pool_dist=0.1)) - c(0, 0, 0, 0, 1, 0)
+    "aldknni_optim", {
+        print("aldknni_optim:")
+        vcf = fn_extract_missing(aldknni(fname=fname_vcf))
+        sync = fn_extract_missing(aldknni(fname=fname_sync))
+        csv = fn_extract_missing(aldknni(fname=fname_csv)) - c(0, 0, 0, 0, 1, 0)
         expect_equal(vcf, sync, tolerance=0.1)
         expect_equal(vcf, csv, tolerance=0.1)
     }