judge channels implemented

src/poretitioner/utils/segment.py

@@ -393,6 +393,14 @@ def segment(
     local_logger.debug(
         f"Segmenting configuration '{bulk_f5_filepath}' and saving results at location '{save_location}' "
     )
+    good_channels = judge_channels(
+        bulk_f5_filepath,
+        segment_config.open_channel_prior_mean,
+        segment_config.open_channel_prior_stdv,
+    )
+
+    object.__setattr__(segment_config, "good_channels", good_channels)
+
     return parallel_find_captures(
         config,
         segment_config,

src/tests/test_segment.py

@@ -611,7 +611,6 @@ def prep_capture_windows_test():
         assert count_by_channel[channel_number] == 4
 
 
-@pytest.mark.xfail(reason="Need to implement config (filters currently in progress).")
 class TestParallelFindCaptures:
     def parallel_find_captures_test(self):
         bulk_f5_fname = "src/tests/data/bulk_fast5_dummy.fast5"
@@ -735,7 +734,11 @@ def segment_test(self):
             "translocation_delay": 20,
             "open_channel_prior_mean": 220,
             "open_channel_prior_stdv": 50,
-            "good_channels": [1, 3],
+            "good_channels": [
+                1,
+                2,
+                3,
+            ],  # this will be internally overwritten by the good channels calculation, which should not include channel 2
             "end_tolerance": 50,
             "terminal_capture_only": False,
             "n_captures_per_file": 1000,