working on improving error-handling

src/aldknni.rs

@@ -685,17 +685,17 @@ impl GenotypesAndPhenotypes {
             // Instantiate output file
             let mae_intermediate = match sensible_round(sum_mae / n_missing, 4) {
                 Ok(x) => x,
-                Err(e) => return Err(ImputefError {
-                    code: 114,
-                    message: "Error printing the MAE for the intermediate file: ".to_owned() +
-                    &fname_intermediate_file
-                })
+                Err(e) => {
+                    return Err(ImputefError {
+                        code: 114,
+                        message: "Error printing the MAE for the intermediate file: ".to_owned()
+                            + &fname_intermediate_file,
+                    })
+                }
             };
             println!(
                 "--> {}: Writing out intermediate file with expected MAE of {}: {}",
-                i,
-                mae_intermediate,
-                &fname_intermediate_file
+                i, mae_intermediate, &fname_intermediate_file
             );
             let mut file_out = match OpenOptions::new()
                 .create_new(true)
@@ -820,11 +820,13 @@ impl GenotypesAndPhenotypes {
         }
         let mae = match sensible_round(sum_mae / n_missing, 4) {
             Ok(x) => x,
-            Err(e) => return Err(ImputefError {
-                code: 122,
-                message: "Error in adaptive_ld_knn_imputation() method | ".to_owned() +
-                &e.message
-            })
+            Err(e) => {
+                return Err(ImputefError {
+                    code: 122,
+                    message: "Error in adaptive_ld_knn_imputation() method | ".to_owned()
+                        + &e.message,
+                })
+            }
         };
         Ok((vec_fname_intermediate_files_and_mae[0].0.to_owned(), mae))
     }

src/filter_missing.rs

@@ -11,11 +11,13 @@ impl GenotypesAndPhenotypes {
     ) -> Result<&mut Self, ImputefError> {
         match self.check() {
             Ok(x) => x,
-            Err(e) => return Err(ImputefError{
+            Err(e) => return Err(ImputefError {
                 code: 201,
-                message: "Error checking GenotypesAndPhenotypes in the method set_missing_by_depth() | ".to_owned() +
-                &e.message
-            })
+                message:
+                    "Error checking GenotypesAndPhenotypes in the method set_missing_by_depth() | "
+                        .to_owned()
+                        + &e.message,
+            }),
         };
         let (n, _p) = self.intercept_and_allele_frequencies.dim();
         let (_n, l) = self.coverages.dim();
@@ -37,11 +39,13 @@ impl GenotypesAndPhenotypes {
         }
         match self.check() {
             Ok(x) => x,
-            Err(e) => return Err(ImputefError{
+            Err(e) => return Err(ImputefError {
                 code: 202,
-                message: "Error checking GenotypesAndPhenotypes in the method set_missing_by_depth() | ".to_owned() +
-                &e.message
-            })
+                message:
+                    "Error checking GenotypesAndPhenotypes in the method set_missing_by_depth() | "
+                        .to_owned()
+                        + &e.message,
+            }),
         };
         Ok(self)
     }
@@ -87,9 +91,10 @@ impl GenotypesAndPhenotypes {
             missingness_per_pool.fold(0.0, |sum, &x| if x > 0.0 { sum + 1.0 } else { sum });
         let n_after_filtering = n - (n_missing * frac_top_missing_pools).ceil() as usize;
         if n_after_filtering == 0 {
-            return Err(ImputefError{
+            return Err(ImputefError {
                 code: 204,
-                message: "No pools left after filtering, please reduce 'frac_top_missing_pools'".to_owned(),
+                message: "No pools left after filtering, please reduce 'frac_top_missing_pools'"
+                    .to_owned(),
             });
         }
         // Sort by increasing missingness
@@ -187,7 +192,8 @@ impl GenotypesAndPhenotypes {
         if l_after_filtering == 0 {
             return Err(ImputefError {
                 code: 207,
-                message: "No loci left after filtering, please reduce 'frac_top_missing_loci'".to_owned(),
+                message: "No loci left after filtering, please reduce 'frac_top_missing_loci'"
+                    .to_owned(),
             });
         }
         // Sort by increasing missingness

src/geno.rs

@@ -13,8 +13,8 @@ impl Parse<LocusFrequencies> for String {
         if self.as_bytes()[0] == 35_u8 {
             return Err(ImputefError {
                 code: 301,
-                message: "Commented out line: ".to_owned() + &self
-            })
+                message: "Commented out line: ".to_owned() + &self,
+            });
         }
         let vec_line: Vec<&str> = self.split('\t').collect();
         let vec_line: Vec<&str> = if vec_line.len() == 1 {
@@ -36,7 +36,9 @@ impl Parse<LocusFrequencies> for String {
             Err(_) => {
                 return Err(ImputefError {
                     code: 302,
-                    message: "Please check format of the file: position is not and integer: ".to_owned() + &self
+                    message: "Please check format of the file: position is not and integer: "
+                        .to_owned()
+                        + &self,
                 })
             }
         };
@@ -143,12 +145,12 @@ impl LoadAll for FileGeno {
                 Err(x) => match x {
                     ImputefError => continue,
                     _ => {
-                        return Err(ImputefError{
+                        return Err(ImputefError {
                             code: 308,
                             message: "T_T Input sync file error, i.e. '".to_owned()
-                            + &fname
-                            + "' at line with the first 20 characters as: "
-                            + &line
+                                + &fname
+                                + "' at line with the first 20 characters as: "
+                                + &line,
                         })
                     }
                 },
@@ -213,11 +215,15 @@ impl LoadAll for FileGeno {
         for thread in thread_objects {
             match thread.join() {
                 Ok(x) => x,
-                Err(_) => return Err(ImputefError{
-                    code: 310,
-                    message: "Unknown thread error occured in load() method for FileGeno struct: ".to_owned() +
-                    &fname
-                })
+                Err(_) => {
+                    return Err(ImputefError {
+                        code: 310,
+                        message:
+                            "Unknown thread error occured in load() method for FileGeno struct: "
+                                .to_owned()
+                                + &fname,
+                    })
+                }
             };
         }
         // Extract output filenames from each thread into a vector and sort them
@@ -423,21 +429,25 @@ pub fn load_geno<'a, 'b>(
     // Extract pool names from the txt file
     let file: File = File::open(fname).expect("Error reading the allele frequency table file.");
     let reader = io::BufReader::new(file);
-    let mut header: String = match reader
-        .lines()
-        .next() {
-            Some(x) => match x {
-                Ok(y) => y,
-                Err(_) => return Err(ImputefError {
+    let mut header: String = match reader.lines().next() {
+        Some(x) => match x {
+            Ok(y) => y,
+            Err(_) => {
+                return Err(ImputefError {
                     code: 316,
-                    message: "Error reading the allele frequency table file: ".to_owned() + &fname
+                    message: "Error reading the allele frequency table file: ".to_owned() + &fname,
                 })
-            },
-            None => return Err(ImputefError{
+            }
+        },
+        None => {
+            return Err(ImputefError {
                 code: 317,
-                message: "Please check the format of the allele frequency table text file: ".to_owned() + &fname
+                message: "Please check the format of the allele frequency table text file: "
+                    .to_owned()
+                    + &fname,
             })
-        };
+        }
+    };
     if header.ends_with('\n') {
         header.pop();
         if header.ends_with('\r') {
@@ -475,23 +485,31 @@ pub fn load_geno<'a, 'b>(
         true => (),
         false => return Err(ImputefError {
             code: 319,
-            message: "Error in the number of pools and the pool sizes do not match in the input file: ".to_owned() +
-            &fname
+            message:
+                "Error in the number of pools and the pool sizes do not match in the input file: "
+                    .to_owned()
+                    + &fname,
         }),
     };
     let file_geno = FileGeno {
         filename: fname.to_owned(),
     };
-    let genotypes_and_phenotypes = match file_geno
-    .convert_into_genotypes_and_phenotypes(filter_stats, false, n_threads) {
+    let genotypes_and_phenotypes = match file_geno.convert_into_genotypes_and_phenotypes(
+        filter_stats,
+        false,
+        n_threads,
+    ) {
         Ok(x) => x,
         Err(e) => return Err(ImputefError {
             code: 320,
-            message: "Error parsing the genotype data (extracted from allele frequency table text file: ".to_owned() + &fname + ") via convert_into_genotypes_and_phenotypes() method within impute()."
-        })
+            message:
+                "Error parsing the genotype data (extracted from allele frequency table text file: "
+                    .to_owned()
+                    + &fname
+                    + ") via convert_into_genotypes_and_phenotypes() method within impute().",
+        }),
     };
-    Ok((genotypes_and_phenotypes, 
-        filter_stats))
+    Ok((genotypes_and_phenotypes, filter_stats))
 }
 
 #[cfg(test)]

src/helpers.rs

@@ -52,10 +52,14 @@ pub fn define_chunks(
     let vec_idx_loci_idx_fin: Vec<usize> = vec_idx_all[1..n_chunks].to_owned();
     match vec_idx_loci_idx_ini.len() == vec_idx_loci_idx_fin.len() {
         true => (),
-        false => return Err(ImputefError {
-            code: 401,
-            message: "Error defining chunks: the number of initial and final indices are different.".to_owned()
-        })
+        false => {
+            return Err(ImputefError {
+                code: 401,
+                message:
+                    "Error defining chunks: the number of initial and final indices are different."
+                        .to_owned(),
+            })
+        }
     };
     Ok((vec_idx_loci_idx_ini, vec_idx_loci_idx_fin))
 }
@@ -73,10 +77,12 @@ pub fn find_file_splits(fname: &str, n_threads: &usize) -> Result<Vec<u64>, Impu
     let mut reader = BufReader::new(file);
     let end = match reader.stream_position() {
         Ok(x) => x,
-        Err(_) => return Err(ImputefError {
-            code: 403,
-            message: "Error navigating file: ".to_owned() + fname
-        })
+        Err(_) => {
+            return Err(ImputefError {
+                code: 403,
+                message: "Error navigating file: ".to_owned() + fname,
+            })
+        }
     };
     let mut out = (0..end)
         .step_by((end as usize) / n_threads)
@@ -91,14 +97,15 @@ pub fn find_file_splits(fname: &str, n_threads: &usize) -> Result<Vec<u64>, Impu
 
 /// Round-up an `f64` to `n_digits` decimal points
 pub fn sensible_round(x: f64, n_digits: usize) -> Result<f64, ImputefError> {
-    let factor = match ("1e".to_owned() + &n_digits.to_string())
-        .parse::<f64>() {
-            Ok(x) => x,
-            Err(_) => return Err(ImputefError{
+    let factor = match ("1e".to_owned() + &n_digits.to_string()).parse::<f64>() {
+        Ok(x) => x,
+        Err(_) => {
+            return Err(ImputefError {
                 code: 404,
-                message: "Error parsing String into f64: ".to_owned() + &x.to_string()
+                message: "Error parsing String into f64: ".to_owned() + &x.to_string(),
             })
-        };
+        }
+    };
     Ok((x * factor).round() / factor)
 }
 
@@ -110,10 +117,10 @@ pub fn parse_f64_roundup_and_own(x: f64, n_digits: usize) -> Result<String, Impu
     }
     match sensible_round(x, n_digits) {
         Ok(x) => Ok(x.to_string()),
-        Err(e) => Err(ImputefError{
+        Err(e) => Err(ImputefError {
             code: 405,
-            message: "Error in parse_f64_roundup_and_own() | ".to_owned() + &e.message
-        })
+            message: "Error in parse_f64_roundup_and_own() | ".to_owned() + &e.message,
+        }),
     }
 }
 
@@ -246,11 +253,13 @@ pub fn pearsons_correlation_pairwise_complete(
     };
     let r = match sensible_round(r, 7) {
         Ok(x) => x,
-        Err(e) => return Err(ImputefError{
-            code: 410,
-            message: "Error in pearsons_correlation_pairwise_complete() | ".to_owned() +
-            &e.message
-        })
+        Err(e) => {
+            return Err(ImputefError {
+                code: 410,
+                message: "Error in pearsons_correlation_pairwise_complete() | ".to_owned()
+                    + &e.message,
+            })
+        }
     };
     Ok((r, pval))
 }