From 192ba0e3257430af813d697f20a0e38dc1b80f06 Mon Sep 17 00:00:00 2001
From: Anton Bankevich <anton.bankevich@gmail.com>
Date: Mon, 25 Nov 2024 02:54:59 -0500
Subject: [PATCH] Fix in parallel assignement of sequences to vertices and fix
 in primitive bulge corrector.

---
 src/projects/assembly_graph/assembly_graph_base.hpp    |  5 ++++-
 .../error_correction/tournament_correction.cpp         | 10 +++++++---
 2 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/src/projects/assembly_graph/assembly_graph_base.hpp b/src/projects/assembly_graph/assembly_graph_base.hpp
index cdd7117..40684da 100644
--- a/src/projects/assembly_graph/assembly_graph_base.hpp
+++ b/src/projects/assembly_graph/assembly_graph_base.hpp
@@ -623,10 +623,13 @@ namespace ag {
         VERIFY(isCanonical() == _seq.isCanonical());
         if (getSeq().empty()) {
             seq = std::move(_seq);
+            Sequence rc_seq = seq.rc();
             unlock();
             if(rc_ != nullptr) {
                 rc_->lock();
-                rc_->seq = !getSeq();
+                if(rc_->getSeq().empty()) {
+                    rc_->seq = std::move(rc_seq);
+                }
                 rc_->unlock();
             }
         } else {
diff --git a/src/projects/error_correction/tournament_correction.cpp b/src/projects/error_correction/tournament_correction.cpp
index d9642af..f529957 100644
--- a/src/projects/error_correction/tournament_correction.cpp
+++ b/src/projects/error_correction/tournament_correction.cpp
@@ -266,10 +266,11 @@ namespace dbg {
     }
 
     std::string PrimitiveBulgeCorrector::correctRead(dbg::GraphPath &path) {
-        std::stringstream ss;
         size_t corrected = 0;
+        GraphPath result;
         for (PathPosition pos = path.firstPosition(); pos != path.lastPosition(); ++pos) {
             Edge &edge = pos.nextEdge();
+            result += edge;
             if (path.getSegment(pos) != Segment<Edge>(edge, 0, edge.truncSize())) {
                 continue;
             }
@@ -286,14 +287,17 @@ namespace dbg {
             if (edge.getCoverage() > alt.getCoverage()) {
                 continue;
             }
-            Edge &rcEdge = edge.rc();
             if (edge.getCoverage() + alt.getCoverage() > threshold || edge.getCoverage() > alt.getCoverage()) {
                 continue;
             }
             corrected++;
-            path.reroute(pos, pos + 1, dbg::GraphPath(alt));
+            result.pop_back();
+            result += alt;
         }
         if (corrected > 0) {
+            result.setCutLeft(path.leftCut());
+            result.setCutRight(path.rightCut());
+            path = std::move(result);
             return itos(corrected);
         } else {
             return "";