enabled chained gap closing

AntonBankevich · Nov 27, 2024 · e923824 · e923824
1 parent a8eee0e
commit e923824
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/src/projects/dbg/graph_modification.hpp b/src/projects/dbg/graph_modification.hpp
@@ -12,10 +12,10 @@ namespace dbg {
 
     class Connection {
     public:
-        EdgeId tip1;
-        EdgeId tip2;
+        VertexId tip1;
+        VertexId tip2;
         AlignmentForm al;
 
-        Connection(Edge &tip1, Edge &tip2, AlignmentForm al) : tip1(tip1.getId()), tip2(tip2.getId()), al(std::move(al)) {}
+        Connection(Edge &tip1, Edge &tip2, AlignmentForm al) : tip1(tip1.getFinish().getId()), tip2(tip2.getFinish().getId()), al(std::move(al)) {}
     };
 }
diff --git a/src/projects/error_correction/gap_closing.cpp b/src/projects/error_correction/gap_closing.cpp
@@ -101,6 +101,8 @@ namespace dbg {
         return std::move(res);
     }
 
+//    TODO: split gap closing operation into seuence correction and adding new edge.
+//    TODO: make it work with a chain of isolated edges
     void GapCloserPipeline(logging::Logger &logger, size_t threads, dbg::SparseDBG &dbg) {
         GapCloser gap_closer(700, 10000, 311, 0.05);
         std::vector<dbg::Connection> patches = gap_closer.GapPatches(logger, dbg, threads);
@@ -109,7 +111,7 @@ namespace dbg {
         }
         omp_set_num_threads(threads);
         for(Connection &connection : patches) {
-            dbg.mergeTipsToEdge(*connection.tip1, connection.tip2->rc(), std::move(connection.al));
+            dbg.mergeTipsToEdge(connection.tip1->rc().front().rc(), connection.tip2->rc().front(), std::move(connection.al));
         }
     }
 }