Minor fix

ksahlin · Feb 26, 2024 · 8c32350 · 8c32350
1 parent 383515d
commit 8c32350
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 11 deletions.
diff --git a/src/aln.cpp b/src/aln.cpp
@@ -936,21 +936,21 @@ inline void get_best_map_location(
                                         std::make_pair(std::cref(nams2), read2_len) }) {
             size_t best_score = 0;
             // We loop twice because we need to count the number of NAMs with best score
-            for (auto &t : nams) {
-                if (t.score == nams[0].score){
+            for (auto &nam : nams) {
+                if (nam.score == nams[0].score){
                     ++best_score;
                 } else {
                     break;
                 }
             }
-            for (auto &t: nams) {
-                if (t.ref_start < 0) {
+            for (auto &nam: nams) {
+                if (nam.ref_start < 0) {
                     continue;
                 }
-                if (t.score != nams[0].score){
+                if (nam.score != nams[0].score){
                     break;
                 }
-                abundances[t.ref_id] += float(read_len) / float(best_score);
+                abundances[nam.ref_id] += float(read_len) / float(best_score);
             }
         }
     }
@@ -1181,14 +1181,14 @@ void align_or_map_single(
                     }
                 }
 
-                for (auto &t: nams) {
-                    if (t.ref_start < 0) {
+                for (auto &nam: nams) {
+                    if (nam.ref_start < 0) {
                         continue;
                     }
-                    if (t.score != nams[0].score){
+                    if (nam.score != nams[0].score){
                         break;
                     }
-                    abundances[t.ref_id] += float(record.seq.length()) / float(n_best);
+                    abundances[nam.ref_id] += float(record.seq.length()) / float(n_best);
                 }
             }
         }

diff --git a/src/main.cpp b/src/main.cpp
@@ -105,7 +105,7 @@ InputBuffer get_input_buffer(const CommandLineOptions& opt) {
     }
 }
 
-void output_abundance(std::vector<double> abundances, References references){
+void output_abundance(const std::vector<double> abundances, const References references){
         for (size_t i = 0; i < references.size(); ++i) {
             std::cout << references.names[i] << '\t' << std::fixed << std::setprecision(6) << abundances[i] / double(references.sequences[i].size()) << std::endl;
         }