Shuffle NAMs even for paired ends

ksahlin · Nov 16, 2023 · 57fe7df · 57fe7df
1 parent 2ecdd00
commit 57fe7df
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/src/aln.cpp b/src/aln.cpp
@@ -986,7 +986,8 @@ void align_PE_read(
     const MappingParameters &map_param,
     const IndexParameters& index_parameters,
     const References& references,
-    const StrobemerIndex& index
+    const StrobemerIndex& index,
+    std::minstd_rand& random_engine
 ) {
     std::array<Details, 2> details;
     std::array<std::vector<Nam>, 2> nams_pair;
@@ -1014,6 +1015,7 @@ void align_PE_read(
         details[is_revcomp].nams = nams.size();
         Timer nam_sort_timer;
         std::sort(nams.begin(), nams.end(), by_score<Nam>);
+        shuffle_top_nams(nams, random_engine);
         statistics.tot_sort_nams += nam_sort_timer.duration();
         nams_pair[is_revcomp] = nams;
     }

diff --git a/src/aln.hpp b/src/aln.hpp
@@ -100,7 +100,8 @@ void align_PE_read(
     const MappingParameters& map_param,
     const IndexParameters& index_parameters,
     const References& references,
-    const StrobemerIndex& index
+    const StrobemerIndex& index,
+    std::minstd_rand& random_engine
 );
 
 void align_SE_read(

diff --git a/src/pc.cpp b/src/pc.cpp
@@ -170,7 +170,7 @@ void perform_task(
             to_uppercase(record1.seq);
             to_uppercase(record2.seq);
             align_PE_read(record1, record2, sam, sam_out, statistics, isize_est, aligner,
-                        map_param, index_parameters, references, index);
+                        map_param, index_parameters, references, index, random_engine);
             statistics.n_reads += 2;
         }
         for (size_t i = 0; i < records3.size(); ++i) {