Swap order of rescues

ksahlin · Feb 28, 2024 · ae4fe29 · ae4fe29
1 parent 1960bef
commit ae4fe29
Showing 1 changed file with 8 additions and 9 deletions.
diff --git a/src/aln.cpp b/src/aln.cpp
@@ -973,17 +973,17 @@ void align_or_map_paired(
         Timer nam_timer;
         auto [nonrepetitive_fraction, nams] = find_nams(query_randstrobes, index);
 
-        if (nams.empty()) {
-            query_randstrobes = randstrobes_query_rescue(record.seq, index_parameters);
-            std::tie(nonrepetitive_fraction, nams) = find_nams(query_randstrobes, index);
-        }
         statistics.tot_find_nams += nam_timer.duration();
 
         if (map_param.rescue_level > 1) {
             Timer rescue_timer;
             if (nams.empty() || nonrepetitive_fraction < 0.7) {
                 nams = find_nams_rescue(query_randstrobes, index, map_param.rescue_cutoff);
                 details[is_revcomp].nam_rescue = true;
+                if (nams.empty()) {
+                    query_randstrobes = randstrobes_query_rescue(record.seq, index_parameters);
+                    std::tie(nonrepetitive_fraction, nams) = find_nams(query_randstrobes, index);
+                }
             }
             statistics.tot_time_rescue += rescue_timer.duration();
         }
@@ -1098,18 +1098,17 @@ void align_or_map_single(
     Timer nam_timer;
     auto [nonrepetitive_fraction, nams] = find_nams(query_randstrobes, index);
 
-    if (nams.empty()) {
-        query_randstrobes = randstrobes_query_rescue(record.seq, index_parameters);
-        std::tie(nonrepetitive_fraction, nams) = find_nams(query_randstrobes, index);
-    }
-
     statistics.tot_find_nams += nam_timer.duration();
 
     if (map_param.rescue_level > 1) {
         Timer rescue_timer;
         if (nams.empty() || nonrepetitive_fraction < 0.7) {
             details.nam_rescue = true;
             nams = find_nams_rescue(query_randstrobes, index, map_param.rescue_cutoff);
+            if (nams.empty()) {
+                query_randstrobes = randstrobes_query_rescue(record.seq, index_parameters);
+                std::tie(nonrepetitive_fraction, nams) = find_nams(query_randstrobes, index);
+            }
         }
         statistics.tot_time_rescue += rescue_timer.duration();
     }