Corrects issue with no colours being included in merged graph

samhorsfield96 · Jan 23, 2025 · c6d1119 · c6d1119
1 parent f9d5dfd
commit c6d1119
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Showing 3 changed files with 31 additions and 16 deletions.
diff --git a/src/graph.cpp b/src/graph.cpp
@@ -202,7 +202,6 @@ GraphTuple Graph::update (const std::string& graphfile,
         // read in 1st graph
         ColoredCDBG<> ccdbg_a;
         ccdbg_a.read(graphfile, coloursfile, num_threads);
-        // need to add to  _ref_paths, _read_paths
 
         //set local variables
         kmer = ccdbg_a.getK();
@@ -212,7 +211,10 @@ GraphTuple Graph::update (const std::string& graphfile,
         nb_colours_a = ccdbg_a.getNbColors();
         // get colour names
         input_colours_a = ccdbg_a.getColorNames();
-
+        for (const auto& entry : input_colours_a)
+        {
+            _ref_paths.push_back(entry);
+        }
 
         if (infile2 != "NA") {
             is_ref = 0;
@@ -244,7 +246,16 @@ GraphTuple Graph::update (const std::string& graphfile,
             opt.verbose = true;
             opt.prefixFilenameOut = outpref;
 
-            cout << "Simplfying merged coloured compacted DBGs..." << endl;
+            // add filenames to graph
+            for (const auto& entry : _ref_paths)
+            {
+                opt.filename_ref_in.push_back(entry);
+            }
+            for (const auto& entry : _read_paths)
+            {
+                opt.filename_seq_in.push_back(entry);
+            }
+
             ccdbg_a.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose);
             cout << "Building colours for merged compacted DBGs..." << endl;
             ccdbg_a.buildColors(opt);

diff --git a/src/indexing.cpp b/src/indexing.cpp
@@ -1,16 +1,16 @@
 // ggCaller header
 #include "indexing.h"
 
-ColoredCDBG<MyUnitigMap> buildGraphvoid (const std::string& infile_1,
+ColoredCDBG<MyUnitigMap> buildGraph (const std::string& infile_1,
                         const std::string& infile_2,
                         const bool is_ref,
                         const int kmer,
                         const int threads,
                         const bool verb,
                         const bool write_graph,
                         const std::string& output_prefix,
-                        std::vector<std::string> _ref_paths,
-                        std::vector<std::string> _read_paths)
+                        std::vector<std::string>& _ref_paths,
+                        std::vector<std::string>& _read_paths)
 {
     std::ifstream infile1(infile_1);
     std::ifstream infile2(infile_2);
@@ -70,8 +70,8 @@ ColoredCDBG<> buildGraphvoid (const std::string& infile_1,
                         const bool verb,
                         const bool write_graph,
                         const std::string& output_prefix,
-                        std::vector<std::string> _ref_paths,
-                        std::vector<std::string> _read_paths)
+                        std::vector<std::string>& _ref_paths,
+                        std::vector<std::string>& _read_paths)
 {
     std::ifstream infile1(infile_1);
     std::ifstream infile2(infile_2);

diff --git a/src/indexing.h b/src/indexing.h
@@ -6,13 +6,15 @@
 #include "translation.h"
 
 ColoredCDBG<MyUnitigMap> buildGraph (const std::string& infile_1,
-                                     const std::string& infile_2,
-                                     const bool is_ref,
-                                     const int kmer,
-                                     const int threads,
-                                     const bool verb,
-                                     const bool write_graph,
-                                     const std::string& output_prefix);
+                                        const std::string& infile_2,
+                                        const bool is_ref,
+                                        const int kmer,
+                                        const int threads,
+                                        const bool verb,
+                                        const bool write_graph,
+                                        const std::string& output_prefix,
+                                        std::vector<std::string>& _ref_paths,
+                                        std::vector<std::string>& _read_paths);
 
 ColoredCDBG<> buildGraphvoid (const std::string& infile_1,
                         const std::string& infile_2,
@@ -21,7 +23,9 @@ ColoredCDBG<> buildGraphvoid (const std::string& infile_1,
                         const int threads,
                         const bool verb,
                         const bool write_graph,
-                        const std::string& output_prefix);
+                        const std::string& output_prefix,
+                        std::vector<std::string>& _ref_paths,
+                        std::vector<std::string>& _read_paths);
 
 std::vector<std::size_t> findIndex(const std::string& seq,
                                    const std::string& subseq,