Remove debug outputs

vgteam · Oct 26, 2021 · f281c30 · f281c30
1 parent 45d0e9a
commit f281c30
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Showing 4 changed files with 30 additions and 143 deletions.
diff --git a/src/Bluntifier.cpp b/src/Bluntifier.cpp
@@ -5,6 +5,19 @@ using std::to_string;
 namespace bluntifier{
 
 
+void print_paths(handlegraph::PathHandleGraph& gfa_graph){
+    cerr << "\nPaths in graph: " << '\n';
+    gfa_graph.for_each_path_handle([&](const handlegraph::path_handle_t& p){
+        auto name = gfa_graph.get_path_name(p);
+        cerr << name << ":" << '\n';
+        gfa_graph.for_each_step_in_path(p, [&](const handlegraph::step_handle_t& s){
+            auto h = gfa_graph.get_handle_of_step(s);
+            cerr << '\t' << gfa_graph.get_id(h) << '\t' << gfa_graph.get_sequence(h) << '\n';
+        });
+    });
+}
+
+
 ProvenanceInfo::ProvenanceInfo(size_t start, size_t stop, bool reversal):
     start(start),
     stop(stop),
@@ -207,22 +220,6 @@ void Bluntifier::splice_subgraphs(){
     size_t i = 0;
     for (auto& subgraph: subgraphs) {
 
-        {
-            string test_path_prefix = "test_bluntify_subgraph_" + to_string(i);
-            ofstream test_output(test_path_prefix + ".gfa");
-            handle_graph_to_gfa(gfa_graph, test_output);
-            test_output.close();
-
-            if (gfa_graph.get_node_count() < 200) {
-                string command = "vg convert -g " + test_path_prefix + ".gfa -p | vg view -d - | dot -Tpng -o "
-                                 + test_path_prefix + ".png";
-
-                cerr << "Running: " << command << '\n';
-
-                run_command(command);
-            }
-        }
-
         // First, copy the subgraph into the GFA graph
         subgraph.graph.increment_node_ids(gfa_graph.max_node_id());
         copy_path_handle_graph(&subgraph.graph, &gfa_graph);
@@ -240,8 +237,6 @@ void Bluntifier::splice_subgraphs(){
                 bool is_oo_child;
                 tie(is_oo_parent, is_oo_child) = is_oo_node(node_id);
 
-                cerr << node_id << (is_oo_child ? " is_oo_child " : "") << (is_oo_parent ? " is_oo_parent " : "") << '\n';
-
                 if (not is_oo_child) {
 
                     // Find the path handle for the path that was copied into the GFA graph
@@ -255,6 +250,7 @@ void Bluntifier::splice_subgraphs(){
                         }
                     });
 
+                    // This can be ignored in the case where there is a full-node overlap
 //                    if (parent_handles.empty() and not is_oo_parent) {
 //                        throw runtime_error("ERROR: biclique terminus does not have any parent: " + to_string(node_id));
 //                    }
@@ -276,13 +272,12 @@ void Bluntifier::splice_subgraphs(){
                     }
                 }
                 else{
-                    cerr << "Skipping oo child: " << node_id << '\n';
+                    // Do nothing
                 }
 
                 if (subgraph.paths_per_handle[1-side].count(handle) == 0
                     and subgraph.paths_per_handle[1-side].count(gfa_graph.flip(handle)) == 0) {
                     to_be_destroyed.emplace(gfa_graph.get_id(handle));
-                    cerr << "To be destroyed: " << gfa_graph.get_id(handle) << '\n';
                 }
             }
         }
@@ -291,7 +286,6 @@ void Bluntifier::splice_subgraphs(){
 
 
 void Bluntifier::write_provenance(){
-
 
     ofstream file(provenance_path);
 
@@ -535,22 +529,6 @@ void Bluntifier::bluntify(){
 
     gfa_to_handle_graph(gfa_path, gfa_graph, id_map, overlaps);
 
-    {
-        string test_path_prefix = "test_bluntify_start";
-        ofstream test_output(test_path_prefix + ".gfa");
-        handle_graph_to_gfa(gfa_graph, test_output);
-        test_output.close();
-
-        if (gfa_graph.get_node_count() < 200) {
-            string command = "vg convert -g " + test_path_prefix + ".gfa -p | vg view -d - | dot -Tpng -o "
-                             + test_path_prefix + ".png";
-
-            cerr << "Running: " << command << '\n';
-
-            run_command(command);
-        }
-    }
-
     log_progress("Computing adjacency components...");
 
     // Compute Adjacency Components and store in vector
@@ -590,67 +568,18 @@ void Bluntifier::bluntify(){
             child_to_parent,
             overlapping_overlap_nodes);
 
-
-    for (size_t i=0; i<bicliques.size(); i++) {
-        cout << "Biclique " << i << '\n';
-        for (auto& edge: bicliques[i]) {
-            cout << "\t(" << gfa_graph.get_id(edge.first);
-            cout << (gfa_graph.get_is_reverse(edge.first) ? "-" : "+");
-            cout << ") -> (" << gfa_graph.get_id(edge.second);
-            cout << (gfa_graph.get_is_reverse(edge.second) ? "-" : "+") << ") ";
-            cout << gfa_graph.get_sequence(edge.first) << " " << gfa_graph.get_sequence(edge.second) << '\n';
-        }
-    }
-
     log_progress("Duplicating node termini...");
 
     super_duper.duplicate_all_node_termini(gfa_graph);
 
-    {
-        string test_path_prefix = "test_bluntify_duped";
-        ofstream test_output(test_path_prefix + ".gfa");
-        handle_graph_to_gfa(gfa_graph, test_output);
-        test_output.close();
-
-        if (gfa_graph.get_node_count() < 200) {
-            string command = "vg convert -g " + test_path_prefix + ".gfa -p | vg view -d - | dot -Tpng -o "
-                             + test_path_prefix + ".png";
-
-            cerr << "Running: " << command << '\n';
-
-            run_command(command);
-        }
-    }
-
     log_progress("Harmonizing biclique edge orientations...");
 
-    for (size_t i=0; i<bicliques.size(); i++) {
-        cout << "Biclique " << i << '\n';
-        for (auto& edge: bicliques[i]) {
-            cout << "\t(" << gfa_graph.get_id(edge.first);
-            cout << (gfa_graph.get_is_reverse(edge.first) ? "-" : "+");
-            cout << ") -> (" << gfa_graph.get_id(edge.second);
-            cout << (gfa_graph.get_is_reverse(edge.second) ? "-" : "+") << ") ";
-            cout << gfa_graph.get_sequence(edge.first) << " " << gfa_graph.get_sequence(edge.second) << '\n';
-        }
-    }
-
     harmonize_biclique_orientations();
 
     log_progress("Aligning overlaps...");
 
     subgraphs.resize(bicliques.size());
 
-    cerr << "\nPaths in graph: " << '\n';
-    gfa_graph.for_each_path_handle([&](const handlegraph::path_handle_t& p){
-        auto name = gfa_graph.get_path_name(p);
-        cerr << name << ":" << '\n';
-        gfa_graph.for_each_step_in_path(p, [&](const handlegraph::step_handle_t& s){
-            auto h = gfa_graph.get_handle_of_step(s);
-            cerr << '\t' << gfa_graph.get_id(h) << '\t' << gfa_graph.get_sequence(h) << '\n';
-        });
-    });
-
     for (size_t i=0; i<bicliques.size(); i++){
         align_biclique_overlaps(i);
     }
@@ -688,21 +617,21 @@ void Bluntifier::bluntify(){
     handle_graph_to_gfa(gfa_graph, cout);
 
     // Output an image of the graph, can be uncommented for debugging
-    {
-        string test_path_prefix = "test_bluntify_final";
-        ofstream test_output(test_path_prefix + ".gfa");
-        handle_graph_to_gfa(gfa_graph, test_output);
-        test_output.close();
-
-        if (gfa_graph.get_node_count() < 200) {
-            string command = "vg convert -g " + test_path_prefix + ".gfa -p | vg view -d - | dot -Tpng -o "
-                             + test_path_prefix + ".png";
-
-            cerr << "Running: " << command << '\n';
-
-            run_command(command);
-        }
-    }
+//    {
+//        string test_path_prefix = "test_bluntify_final";
+//        ofstream test_output(test_path_prefix + ".gfa");
+//        handle_graph_to_gfa(gfa_graph, test_output);
+//        test_output.close();
+//
+//        if (gfa_graph.get_node_count() < 200) {
+//            string command = "vg convert -g " + test_path_prefix + ".gfa -p | vg view -d - | dot -Tpng -o "
+//                             + test_path_prefix + ".png";
+//
+//            cerr << "Running: " << command << '\n';
+//
+//            run_command(command);
+//        }
+//    }
 }
 
 

diff --git a/src/BluntifierAlign.cpp b/src/BluntifierAlign.cpp
@@ -171,11 +171,6 @@ bool Bluntifier::biclique_overlaps_are_exact(size_t i){
             auto query_start = gfa_graph.get_length(edge.first) - alignment.operations[0].length;
             auto ref_start = 0;
 
-//            cerr << "explicitizing: " << gfa_graph.get_id(edge.first);
-//            cerr << "->" << gfa_graph.get_id(edge.second);
-//            cerr << " length=" << gfa_graph.get_length(edge.first) << ',';
-//            cerr << gfa_graph.get_length(edge.second) << '\n';
-
             auto explicit_cigar_operations = alignment.explicitize_mismatches(gfa_graph, edge, ref_start, query_start);
 
             sizes.emplace(explicit_cigar_operations[0].length);

diff --git a/src/Cigar.cpp b/src/Cigar.cpp
@@ -257,8 +257,6 @@ vector<Cigar> Alignment::explicitize_mismatches(
             char query_base = graph.get_base(edge.second, iterator.query_index);
             char ref_base = graph.get_base(edge.first, iterator.ref_index);
 
-//            std::cerr << iterator.query_index << " " << query_base << '-' << ref_base << " " << iterator.ref_index << '\n';
-
             if (ref_base == query_base){
                 // If the last operation was already a Match (=), then extend its length
                 if (not explicit_operations.empty() and explicit_operations.back().type() == '='){

diff --git a/src/OverlappingOverlapSplicer.cpp b/src/OverlappingOverlapSplicer.cpp
@@ -71,8 +71,6 @@ tuple<handle_t, size_t, size_t, bool> OverlappingOverlapSplicer::seek_to_path_ba
         string& path_name,
         size_t target_base_index){
 
-    cerr << "seeking path: " << path_name << '\n';
-
     auto path_handle = gfa_graph.get_path_handle(path_name);
     auto step = gfa_graph.path_begin(path_handle);
 
@@ -86,8 +84,6 @@ tuple<handle_t, size_t, size_t, bool> OverlappingOverlapSplicer::seek_to_path_ba
         step_handle = gfa_graph.get_handle_of_step(step);
         auto step_length = gfa_graph.get_length(step_handle);
 
-        cerr << target_base_index << " " << cumulative_index << " " << intra_handle_index << " " << gfa_graph.get_sequence(step_handle) << '\n';
-
         if (cumulative_index + step_length > target_base_index){
             intra_handle_index = target_base_index - cumulative_index;
             fail = false;
@@ -102,8 +98,6 @@ tuple<handle_t, size_t, size_t, bool> OverlappingOverlapSplicer::seek_to_path_ba
 
     remainder = target_base_index - cumulative_index;
 
-    cerr << (fail ? "FAIL with remainder " + to_string(remainder) : "PASS with remainder " + to_string(remainder)) << '\n';
-
     return {step_handle, intra_handle_index, remainder, fail};
 }
 
@@ -115,8 +109,6 @@ tuple<handle_t, size_t, size_t, bool> OverlappingOverlapSplicer::seek_to_reverse
         string& path_name,
         size_t target_base_index){
 
-    cerr << "seeking REVERSE path: " << path_name << '\n';
-
     auto path_handle = gfa_graph.get_path_handle(path_name);
     auto step = gfa_graph.path_back(path_handle);
 
@@ -130,8 +122,6 @@ tuple<handle_t, size_t, size_t, bool> OverlappingOverlapSplicer::seek_to_reverse
         step_handle = gfa_graph.flip(gfa_graph.get_handle_of_step(step));
         auto step_length = gfa_graph.get_length(step_handle);
 
-        cerr << target_base_index << " " << cumulative_index << " " << intra_handle_index << " " << gfa_graph.get_sequence(step_handle) << '\n';
-
         if (cumulative_index + step_length > target_base_index){
             intra_handle_index = target_base_index - cumulative_index;
             fail = false;
@@ -146,8 +136,6 @@ tuple<handle_t, size_t, size_t, bool> OverlappingOverlapSplicer::seek_to_reverse
 
     remainder = target_base_index - cumulative_index;
 
-    cerr << (fail ? "FAIL with remainder " + to_string(remainder) : "PASS with remainder " + to_string(remainder)) << '\n';
-
     return {step_handle, intra_handle_index, remainder, fail};
 }
 
@@ -160,8 +148,6 @@ void OverlappingOverlapSplicer::find_splice_pairs(
 
     array <vector <overlapping_child_iter>, 2> other_children;
 
-    overlap_info.print(gfa_graph);
-
     for (auto side: {0,1}) {
         for (auto oo: overlap_info.overlapping_children[side]){
 
@@ -414,23 +400,6 @@ void OverlappingOverlapSplicer::find_splice_pairs(
 void OverlappingOverlapSplicer::splice_overlapping_overlaps(MutablePathDeletableHandleGraph& gfa_graph) {
 
     for (auto& oo_item: overlapping_overlap_nodes) {
-        // Output an image of the graph, can be uncommented for debugging
-        {
-            string test_path_prefix = "test_bluntify_splice_" + to_string(oo_item.first);
-            std::ofstream test_output(test_path_prefix + ".gfa");
-            handle_graph_to_gfa(gfa_graph, test_output);
-            test_output.close();
-
-            if (gfa_graph.get_node_count() < 200) {
-                string command = "vg convert -g " + test_path_prefix + ".gfa -p | vg view -d - | dot -Tpng -o "
-                                 + test_path_prefix + ".png";
-
-                cerr << "Running: " << command << '\n';
-
-                run_command(command);
-            }
-        }
-
         auto node_id = oo_item.first;
         auto& overlap_info = oo_item.second;
 
@@ -479,17 +448,13 @@ void OverlappingOverlapSplicer::splice_overlapping_overlaps(MutablePathDeletable
 
             if (left_index + 1 < gfa_graph.get_length(left_handle) and not left_fail) {
                 division_sites[left_handle].emplace(left_index + 1);
-                cerr << "Splice site for parent node " << node_id << " with children " << gfa_graph.get_id(left_handle) << " (" << gfa_graph.get_id(right_handle) << ") = " << left_index + 1 << '\n';
             }
 
             if (right_index < gfa_graph.get_length(right_handle) and right_index > 0 and not right_fail) {
                 division_sites[right_handle].emplace(right_index);
-                cerr << "Splice site for parent node " << node_id << " with children " << gfa_graph.get_id(right_handle) << " (" << gfa_graph.get_id(left_handle) << ") = " << right_index << '\n';
             }
         }
 
-        cerr << "Dividing nodes at oo splice sites... " << '\n';
-
         // Do the divisions in bulk
         for (auto& item: division_sites) {
             vector<size_t> sites;