Update submodule racon

Author: rvaser

src/graph.cpp

@@ -50,7 +50,7 @@ Graph::Node::Node(Node* begin, Node* end)
     }
   }
   if (begin != end) {
-    data += end->sequence->Inflate();
+    data += end->sequence->InflateData();
     count += end->count;
   }
 
@@ -818,7 +818,7 @@ void Graph::Construct(std::vector<std::unique_ptr<biosoup::NucleicAcid>>& sequen
 
       auto sequence = biosoup::NucleicAcid{
           sequences[it->id()]->name,
-          sequences[it->id()]->Inflate(it->begin(), it->end() - it->begin())};
+          sequences[it->id()]->InflateData(it->begin(), it->end() - it->begin())};  // NOLINT
 
       sequence_to_node[it->id()] = Node::num_objects;
 
@@ -1116,7 +1116,7 @@ std::uint32_t Graph::RemoveBubbles(const ram::MinimizerEngine& minimizer_engine)
         }
       }
     }
-    data += path.back()->sequence->Inflate();
+    data += path.back()->sequence->InflateData();
     return std::unique_ptr<biosoup::NucleicAcid>(
         new biosoup::NucleicAcid("", data));
   };
@@ -1638,9 +1638,28 @@ void Graph::Polish(
 
   piles_.clear();  // save memory
 
+  double avg_q = 0.;
+  for (const auto& it : sequences) {
+    if (it->block_quality.empty()) {
+      continue;
+    }
+    double q = std::accumulate(
+        it->block_quality.begin(),
+        it->block_quality.end(),
+        0.);
+    avg_q += q / it->block_quality.size();
+  }
+  if (avg_q == 0.) {  // when all values equal to '!'
+    for (const auto& it : sequences) {
+      it->block_quality.clear();
+    }
+  } else {
+    avg_q /= sequences.size();
+  }
+
   auto polisher = racon::Polisher::Create(
       thread_pool_,
-      1ULL << 34,  // 16GB
+      avg_q,
       0.3,
       500,
       true,
@@ -1840,7 +1859,9 @@ std::vector<std::unique_ptr<biosoup::NucleicAcid>> Graph::GetUnitigs(
         " RC:i:" + std::to_string(it->count) +
         " XO:i:" + std::to_string(it->is_circular);
 
-    dst.emplace_back(new biosoup::NucleicAcid(name, it->sequence->Inflate()));
+    dst.emplace_back(new biosoup::NucleicAcid(
+        name,
+        it->sequence->InflateData()));
   }
 
   return dst;
@@ -2026,7 +2047,7 @@ void Graph::PrintGfa(const std::string& path) const {
       continue;
     }
     os << "S\t" << it->sequence->name
-       << "\t"  << it->sequence->Inflate()
+       << "\t"  << it->sequence->InflateData()
        << "\tLN:i:" << it->sequence->inflated_len
        << "\tRC:i:" << it->count
        << std::endl;

src/graph.hpp

@@ -31,7 +31,9 @@ void serialize(Archive& archive, NucleicAcid& sequence) {  // NOLINT
       sequence.id,
       sequence.name,
       sequence.deflated_data,
-      sequence.inflated_len);
+      sequence.block_quality,
+      sequence.inflated_len,
+      sequence.is_reverse_complement);
 }
 
 }  // namespace biosoup
@@ -230,7 +232,7 @@ class Graph {
 
     std::string Label() const {
       // return tail->data.substr(0, length);
-      return tail->sequence->Inflate(0, length);
+      return tail->sequence->InflateData(0, length);
     }
 
     template<class Archive>

src/main.cpp

@@ -244,7 +244,7 @@ int main(int argc, char** argv) {
 
   for (const auto& it : graph.GetUnitigs(num_polishing_rounds > 0)) {
     std::cout << ">" << it->name << std::endl;
-    std::cout << it->Inflate() << std::endl;
+    std::cout << it->InflateData() << std::endl;
   }
 
   timer.Stop();

test/raven_test.cpp

@@ -49,7 +49,7 @@ TEST_F(RavenTest, Assemble) {
   g.Polish(s, 3, -5, -4, 0, false, 0, 2);
   auto u = std::move(g.GetUnitigs(true).front());
   u->ReverseAndComplement();
-  EXPECT_EQ(1312, EditDistance(u->Inflate(), r->Inflate()));
+  EXPECT_EQ(1137, EditDistance(u->InflateData(), r->InflateData()));
 }
 
 TEST_F(RavenTest, Checkpoints) {