better patch to get correct sparsity for tsv input but removing break…

… when populating coverages matrix while counting loci with less than 1 allele shown

src/filter_missing.rs

@@ -51,31 +51,15 @@ impl GenotypesAndPhenotypes {
     }
 
     pub fn missing_rate(&mut self) -> Result<f64, ImputefError> {
-        let (n, p) = self.intercept_and_allele_frequencies.dim();
+        let (n, _p) = self.intercept_and_allele_frequencies.dim();
         let (_n, l) = self.coverages.dim();
-        // Count missing data based on coverages
-        let sum_cov: f64 = self.coverages.fold(0.00, |sum, &x| {
+        let sum: f64 = self.coverages.fold(0.00, |sum, &x| {
             if (x.is_nan()) || (x == 0.0) {
                 sum + 1.00
             } else {
                 sum
             }
         });
-        // Count missing data based on missing frequencies
-        let mut sum_freq: f64 = self.intercept_and_allele_frequencies.fold(0.00, |sum, &x| {
-            if x.is_nan() {
-                sum + 1.00
-            } else {
-                sum
-            }
-        });
-        sum_freq = sum_freq / (p as f64 / l as f64); // correct by the number of alleles per locus
-        // Use the larger and more precise missing count
-        let sum: f64 = if sum_cov > sum_freq {
-            sum_cov
-        } else {
-            sum_freq
-        };
         sensible_round(sum * 100.0 / ((n * l) as f64), 5)
     }
 

src/geno.rs

@@ -347,11 +347,13 @@ impl LoadAll for FileGeno {
                     coverages[(i, j)] = f64::NAN;
                 }
                 if mat.slice(s![i, idx_ini..idx_fin]).sum() < 1.0 {
-                    freq_sum_less_than_one = true;
-                    break;
+                    freq_sum_less_than_one = if !freq_sum_less_than_one {
+                        true
+                    } else {
+                        freq_sum_less_than_one
+                    };
                 }
             }
-            // if (n_alleles == 1) || freq_sum_less_than_one {
             if freq_sum_less_than_one {
                 p += 1;
             }