Dev

src/_version.py

@@ -1,4 +1,4 @@
 """version.py
 Version of the software
 """
-__version__ = "0.6.5"
+__version__ = "0.7.0"

src/plot.py

@@ -1321,7 +1321,7 @@ def argparser():
     parser.add_argument('--no_samples', required=False, action='store_false', help="hide sample points")
     parser.add_argument('--save_svg', required=False, action='store_true', help="save as svg. tweak --region and --xrange to capture the necessary part of the plot")
     parser.add_argument('--xrange', required=False, type=int, default=PLOT_X_RANGE, help="initial x range")
-    parser.add_argument('-o', '--output_dir', required=True, type=str, default="", help="output dir")
+    parser.add_argument('-o', '--output_dir', required=False, type=str, default="", help="output dir")
     return parser
 
 if __name__ == "__main__":

src/plot_signal.py

@@ -46,7 +46,7 @@ def plot_function(args, p, read_id, signal_tuple, draw_data):
     p.line('x', 'y', name="sig_plot_line", line_width=2, source=source)
     # add a circle renderer with a size, color, and alpha
     sample_labels = p.circle(x, y, radius=draw_data["point_size"], color="red", alpha=0.5, visible=draw_data['no_samples'])
-    toggle_samples = Toggle(label="samples", button_type="danger", active=True, height=30, width=60)
+    toggle_samples = Toggle(label="samples", button_type="default", active=draw_data['no_samples'], height=30, width=60)
     toggle_samples.js_link('active', sample_labels, 'visible')
 
     # show the tooltip
@@ -101,7 +101,7 @@ def run(args):
     indt = "\t\t\t\t\t\t\t\t"
     draw_data = {}
     draw_data["point_size"] = args.point_size
-    draw_data["no_samples"] = args.no_samples
+    draw_data["no_samples"] = args.show_samples
     draw_data["xrange"] = args.xrange
     draw_data["sig_dir"] = "->"
     if args.reverse_signal:
@@ -112,6 +112,12 @@ def run(args):
     end_index = int(end_index)  # keep it 1-based for slicing
     x, x_real, y = plot_utils.load_signal(args, args.read_id, s5, start_index, end_index, scale_params)
 
+    # resolve -1 sentinel to actual signal length
+    if end_index == -1:
+        end_index = x_real[-1] if len(x_real) > 0 else start_index + 1
+    if draw_data["xrange"] == -1:
+        draw_data["xrange"] = len(x)
+
     if args.reverse_signal:
         # reverse the signal
         y = np.flip(y)
@@ -163,10 +169,10 @@ def argparser():
     parser.add_argument('--no_pa', required=False, action='store_false', help="skip converting the signal to pA values")
     parser.add_argument('--remove_signal_outliers', required=False, action='store_true', help="remove signal outliers that are outside the raw value range [0, 2000]")
     parser.add_argument('--point_size', required=False, type=int, default=0.5, help="signal point radius [0.5]")
-    parser.add_argument('--sig_plot_limit', required=False, type=int, default=SIG_PLOT_LENGTH, help="maximum number of signal samples to plot")
-    parser.add_argument('--no_samples', required=False, action='store_false', help="hide sample points")
+    parser.add_argument('--sig_plot_limit', required=False, type=int, default=-1, help="maximum number of signal samples to plot (-1 for full signal)")
+    parser.add_argument('--show_samples', required=False, action='store_true', help="show sample points (default: hidden)")
     parser.add_argument('--save_svg', required=False, action='store_true', help="save as svg. tweak --region and --xrange to capture the necessary part of the plot")
-    parser.add_argument('--xrange', required=False, type=int, default=PLOT_X_RANGE, help="initial x range")
+    parser.add_argument('--xrange', required=False, type=int, default=-1, help="initial x range to display (-1 for full signal)")
     parser.add_argument('-o', '--output_dir', required=True, type=str, default="", help="output dir")
     return parser
 

src/plot_utils.py

@@ -14,6 +14,7 @@
 
 from bokeh.io.export import export_svgs
 import os
+import sys
 
 PLOT_X_RANGE = 300
 PLOT_HEIGHT = 600
@@ -91,20 +92,17 @@ def read_readid_color_file(filepath, default_color='#1f77b4'):
 
 def svg_export_works(output_dir):
     try:
-        # Create dummy Bokeh plot
         p = figure(title="SVG test")
         p.line([0, 1], [0, 1])
         p.output_backend = "svg"
-
-        # Fixed test file name
         temp_svg_path = output_dir + "/__svg_test.svg"
-
         export_svgs(p, filename=temp_svg_path)
-
-        # Optionally clean up
         os.remove(temp_svg_path)
-    except Exception as e:
-        raise RuntimeError(f"SVG export requires a headless browser. None (Firefox+geckodriver or Chromium+chromedriver) found in the PATH : {e}")
+    except Exception:
+        print("Error: --save_svg requires a headless browser which was not found on PATH.")
+        print("  Install Firefox + geckodriver:  conda install -c conda-forge firefox geckodriver")
+        print("  Install Chromium + chromedriver: apt install chromium-browser chromium-driver")
+        sys.exit(1)
 
 def get_base_color_map():
     base_color_map = {'A': '#d6f5d6', 'C': '#ccccff', 'T': '#ffcccc', 'G': '#ffedcc', 'U': '#ffcccc', 'N': '#fafafe', 'M': '#000000', 'R': '#000000', 'W': '#000000', 'S': '#000000', 'Y': '#000000', 'K': '#000000', 'V': '#000000', 'H': '#000000', 'D': '#000000', 'B': '#000000'}