make node length hack optional

.gitignore

@@ -10,4 +10,7 @@ docs/sphinx_build
 docs/sphinx_build_man
 docs/_build
 Testing/
-.idea/
+.idea/
+.vscode/
+.cmake/
+cmake-build-debug/

src/algorithms/draw.cpp

@@ -166,7 +166,7 @@ Coordinates adjustNodeLength(double x1, double y1, double x2, double y2, double
     // Return the new coordinates
     return Coordinates{new_x1, new_y1, new_x2, new_y2};
 }
-Coordinates adjustNodeEndpoints(const handle_t& handle, const std::vector<double>& X, const std::vector<double>& Y, double scale, double x_off, double y_off, double sparsification_factor) {
+Coordinates adjustNodeEndpoints(const handle_t& handle, const std::vector<double>& X, const std::vector<double>& Y, double scale, double x_off, double y_off, double sparsification_factor, bool lengthen_left_nodes) {
     // Original coordinates
     uint64_t a = 2 * number_bool_packing::unpack_number(handle);
     double x1 = (X[a] * scale) - x_off;
@@ -178,7 +178,7 @@ Coordinates adjustNodeEndpoints(const handle_t& handle, const std::vector<double
     double length = std::sqrt(std::pow(x2 - x1, 2) + std::pow(y2 - y1, 2));
 
     // Adjust length based on 1.0 / sparsification_factor
-    double new_length = sparsification_factor == 0 ? length : length * (1.0 / sparsification_factor);
+    double new_length = !lengthen_left_nodes || sparsification_factor == 0 ? length : length * (1.0 / sparsification_factor);
 
     // Calculate the midpoint
     double mid_x = (x1 + x2) / 2.0;
@@ -207,7 +207,8 @@ void draw_svg(std::ostream &out,
 			  const double& line_width,
 			  std::vector<algorithms::color_t>& node_id_to_color,
               ska::flat_hash_map<handlegraph::nid_t, std::set<std::string>>& node_id_to_label_map,
-              const float& sparsification_factor) {
+              const float& sparsification_factor,
+              const bool& lengthen_left_nodes) {
 
     std::vector<std::vector<handle_t>> weak_components;
     coord_range_2d_t rendered_range;
@@ -251,7 +252,7 @@ void draw_svg(std::ostream &out,
                 continue; // Skip this node to output a lighter SVG (do not nodes with labels, if any)
             }
 
-            Coordinates newEndpoints = adjustNodeEndpoints(handle, X, Y, scale, x_off, y_off, sparsification_factor);
+            Coordinates newEndpoints = adjustNodeEndpoints(handle, X, Y, scale, x_off, y_off, sparsification_factor, lengthen_left_nodes);
 
             if (color == COLOR_BLACK || color == COLOR_LIGHTGRAY) {
                 out << "<line x1=\""
@@ -294,7 +295,7 @@ void draw_svg(std::ostream &out,
 
         // color highlights
         for (auto& handle : highlights) {
-            Coordinates newEndpoints = adjustNodeEndpoints(handle, X, Y, scale, x_off, y_off, sparsification_factor);
+            Coordinates newEndpoints = adjustNodeEndpoints(handle, X, Y, scale, x_off, y_off, sparsification_factor, lengthen_left_nodes);
             algorithms::color_t color = node_id_to_color.empty() ? COLOR_BLACK : node_id_to_color[graph.get_id(handle)];
             out << "<line x1=\""
                 << newEndpoints.x1

src/algorithms/draw.hpp

@@ -73,7 +73,8 @@ void draw_svg(std::ostream &out,
 			  const double& line_width,
 			  std::vector<algorithms::color_t>& node_id_to_color,
               ska::flat_hash_map<handlegraph::nid_t, std::set<std::string>>& node_id_to_label_map,
-              const float& sparsification_factor);
+              const float& sparsification_factor,
+              const bool& lengthen_left_nodes);
 
 std::vector<uint8_t> rasterize(const std::vector<double> &X,
                                const std::vector<double> &Y,

src/subcommand/draw_main.cpp

@@ -51,7 +51,8 @@ int main_draw(int argc, char **argv) {
                                                 "Colors are derived from the 4th column, if present, else from the path name."
                                                 "If the 4th column value is in the format 'string#RRGGBB', the RRGGBB color (in hex notation) will be used.",
                                                 {'b', "bed-file"});
-    args::ValueFlag<float> node_sparsification(parser, "N", "Remove this fraction of nodes from the SVG output (to output smaller files) (default: 0.0, keep all nodes).", {'f', "svg-sparse-factor"});
+    args::ValueFlag<float> node_sparsification(visualizations_opts, "N", "Remove this fraction of nodes from the SVG output (to output smaller files) (default: 0.0, keep all nodes).", {'f', "svg-sparse-factor"});
+    args::Flag lengthen_left_nodes(visualizations_opts, "lengthen", "When node sparsitication is active, lengthen the remaining nodes proportionally with the sparsification factor", {'l', "svg-lengthen-nodes"});
     args::Group threading(parser, "[ Threading ]");
 	args::ValueFlag<uint64_t> nthreads(threading, "N", "Number of threads to use for parallel operations.", {'t', "threads"});
 	args::Group processing_info_opts(parser, "[ Processing Information ]");
@@ -111,7 +112,7 @@ int main_draw(int argc, char **argv) {
             if (infile == "-") {
                 graph.deserialize(std::cin);
             } else {
-                utils::handle_gfa_odgi_input(infile, "draw", args::get(progress), num_threads, graph);
+                utils::handle_gfa_odgi_input(infile, "draw", lengthen_left_nodes, num_threads, graph);
             }
         }
     }
@@ -231,7 +232,7 @@ int main_draw(int argc, char **argv) {
         // todo could be done with callbacks
         std::vector<double> X = layout.get_X();
         std::vector<double> Y = layout.get_Y();
-        algorithms::draw_svg(f, X, Y, graph, svg_scale, border_bp, _png_line_width, node_id_to_color, node_id_to_label_map, sparse_nodes);
+        algorithms::draw_svg(f, X, Y, graph, svg_scale, border_bp, _png_line_width, node_id_to_color, node_id_to_label_map, sparse_nodes, args::get(lengthen_left_nodes));
         f.close();    
     }