Fixed bug with signif / subset not outputting sequence

src/depth_table.h

@@ -30,11 +30,11 @@ struct Marker {
         output_file << "\n";
     }
 
-    void output_fasta(std::ofstream& output_file, uint16_t min_depth) const {
+    void output_fasta(std::ofstream& output_file, uint min_depth) const {
 
         output_file << ">" << this->id;
         for (auto group: this->groups) output_file << "_" << group.first << ":" << group.second;
-        output_file << "_mindepth:" << min_depth << "_p:" << this->p << "\n" << this->sequence << "\n";
+        output_file << "_p:" << this->p << "_mindepth:" << min_depth << "\n" << this->sequence << "\n";
     }
 
 };

src/signif.cpp

@@ -23,7 +23,7 @@ void signif(Parameters& parameters) {
     MarkersQueue markers_queue;
     std::mutex queue_mutex;
 
-    std::thread parsing_thread(table_parser, std::ref(parameters), std::ref(popmap), std::ref(markers_queue), std::ref(queue_mutex), std::ref(header), std::ref(parsing_ended), true, false);
+    std::thread parsing_thread(table_parser, std::ref(parameters), std::ref(popmap), std::ref(markers_queue), std::ref(queue_mutex), std::ref(header), std::ref(parsing_ended), false, false);
     std::thread processing_thread(processor, std::ref(markers_queue), std::ref(popmap), std::ref(parameters), std::ref(queue_mutex), std::ref(candidate_markers), std::ref(n_markers), std::ref(parsing_ended), BATCH_SIZE);
 
     parsing_thread.join();
@@ -76,7 +76,7 @@ void processor(MarkersQueue& markers_queue, Popmap& popmap, Parameters& paramete
 
                     ++n_markers;  // Increment total number of markers for Bonferroni correction
                     chi_squared = get_chi_squared(marker.groups[parameters.group1], marker.groups[parameters.group2], popmap.counts[parameters.group1], popmap.counts[parameters.group2]);
-                    marker.p = get_chi_squared_p(chi_squared);
+                    marker.p = static_cast<float>(get_chi_squared_p(chi_squared));
                     // First pass: filter markers with non-corrected p < 0.05
                     if (static_cast<float>(marker.p) < parameters.signif_threshold) candidate_markers.push_back(marker);
 

src/subset.cpp

@@ -17,7 +17,7 @@ void subset(Parameters& parameters) {
 
     std::ofstream output_file = open_output(parameters.output_file_path);
 
-    std::thread parsing_thread(table_parser, std::ref(parameters), std::ref(popmap), std::ref(markers_queue), std::ref(queue_mutex), std::ref(header), std::ref(parsing_ended), true, false);
+    std::thread parsing_thread(table_parser, std::ref(parameters), std::ref(popmap), std::ref(markers_queue), std::ref(queue_mutex), std::ref(header), std::ref(parsing_ended), false, false);
     std::thread processing_thread(processor, std::ref(markers_queue), std::ref(popmap), std::ref(parameters), std::ref(queue_mutex), std::ref(output_file), std::ref(parsing_ended), BATCH_SIZE);
 
     parsing_thread.join();