Merge branch 'max-trim-percent' into 'master'

set a max trim percent threshold

See merge request machine-learning/bonito!103

bonito/reader.py

@@ -108,9 +108,9 @@ def read_chunks(read, chunksize=4000, overlap=400):
         yield ReadChunk(read, block.numpy(), i+1, blocks.shape[0])
 
 
-def trim(signal, window_size=40, threshold=2.4, min_trim=10, min_elements=3, max_samples=8000):
-    seen_peak = False
+def trim(signal, window_size=40, threshold=2.4, min_trim=10, min_elements=3, max_samples=8000, max_trim=0.3):
 
+    seen_peak = False
     num_windows = min(max_samples, len(signal)) // window_size
 
     for pos in range(num_windows):
@@ -121,7 +121,7 @@ def trim(signal, window_size=40, threshold=2.4, min_trim=10, min_elements=3, max
             seen_peak = True
             if window[-1] > threshold:
                 continue
-            if end >= min(max_samples, len(signal)):
+            if end >= min(max_samples, len(signal)) or end / len(signal) > max_trim:
                 return min_trim
             return end