Gap character can be changed

CMakeLists.txt

@@ -4,7 +4,10 @@ project(spoa VERSION 4.1.4
              LANGUAGES CXX
              DESCRIPTION "Spoa is a c++ library (and tool) for SIMD vectorized partial order alignment.")
 
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic")
+if(NOT MSVC)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic")
+endif()
+
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)

include/spoa/graph.hpp

@@ -161,8 +161,7 @@ class Graph {
       const char* sequence, std::uint32_t sequence_len,
       const char* quality, std::uint32_t quality_len);
 
-  std::vector<std::string> GenerateMultipleSequenceAlignment(
-      bool include_consensus = false);
+  std::vector<std::string> GenerateMultipleSequenceAlignment(bool include_consensus = false, char gap='-');
 
   std::string GenerateConsensus();
 

src/graph.cpp

@@ -336,14 +336,13 @@ std::vector<std::uint32_t> Graph::InitializeMultipleSequenceAlignment(
   return dst;
 }
 
-std::vector<std::string> Graph::GenerateMultipleSequenceAlignment(
-    bool include_consensus) {
+std::vector<std::string> Graph::GenerateMultipleSequenceAlignment(bool include_consensus, char gap) {
   std::uint32_t row_size = 0;
   auto node_id_to_column = InitializeMultipleSequenceAlignment(&row_size);
 
   std::vector<std::string> dst;
   for (std::uint32_t i = 0; i < sequences_.size(); ++i) {
-    std::string row(row_size, '-');
+    std::string row(row_size, gap);
     auto it = sequences_[i];
     while (true) {
       row[node_id_to_column[it->id]] = decoder_[it->code];
@@ -355,7 +354,7 @@ std::vector<std::string> Graph::GenerateMultipleSequenceAlignment(
   }
   if (include_consensus) {
     TraverseHeaviestBundle();
-    std::string row(row_size, '-');
+    std::string row(row_size, gap);
     for (const auto& it : consensus_) {
       row[node_id_to_column[it->id]] = decoder_[it->code];
     }