Optimize function calcul_mappability

CNV/test_gpu_mean_depth.py

@@ -8,7 +8,6 @@ import pycuda.autoinit
 from pycuda.compiler import SourceModule
 import pycuda.gpuarray as gpuarray
 from pycuda.autoinit import context
-from bisect import bisect_right
 
 # Options
 try:
@@ -157,16 +156,24 @@ def dico_mappabilite(mappability_file):
     return mappability_dico #Dictionnaire avec les bornes de mappabilité en fonction des positions pour chaque chromosome.
     
 def calcul_mappability(seq_length, mappability, chr):
-    map_data = np.zeros(seq_length, dtype = np.float32)
+    map_data = np.zeros(seq_length, dtype=np.float32)
     sys.stderr.write("\t map_data =\n")
     sorted_keys = sorted(mappability[chr].keys())
     sys.stderr.write("\t sorted_keys =\n")
     
-    for i in range(seq_length):
-        bound_index = bisect_right(sorted_keys, i) - 1
-        nearest_bound = sorted_keys[bound_index] if bound_index >= 0 else 0
-        map_data[i] = mappability[chr][nearest_bound]
-        #print(f" i : {i}\t sorted_keys[i] : {sorted_keys[i]}\tbound_index : {bound_index}\t nearest_bound : {nearest_bound}\t map_data[i] : {map_data[i]}\t sorted_keys[bound_index] : {sorted_keys[bound_index]}")
+    prev_bound = 0
+    prev_mappability = 0
+    
+    for bound in sorted_keys:
+        for i in range(prev_bound, min(seq_length, bound)):
+            map_data[i] = prev_mappability
+        prev_bound = bound
+        prev_mappability = mappability[chr][bound]
+    
+    # Fill remaining positions if sequence length exceeds last bound
+    for i in range(prev_bound, seq_length):
+        map_data[i] = prev_mappability
+    
     return map_data
 
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