Modify filter

cnv_sv_caller_gpu.py

@@ -1422,7 +1422,7 @@ def segmentation(events, segment, chr):
     elapsed_time = end_time - start_time
     logging.info(f"Leaving segmentation for {chr} (Time taken: {elapsed_time:.4f} seconds)") 
 
-def display_results_vcf(sample, segment, signal, lengthFilter, output_file, chr, normalize_depth_results):
+def display_results_vcf(sample, segment, signal, lengthFilter, output_file, chr, depth_results):
     """
     Generate a VCF file containing structural variant calls based on segmented regions and signal data.
 
@@ -1488,7 +1488,7 @@ def display_results_vcf(sample, segment, signal, lengthFilter, output_file, chr,
                 if (segment[k][elt]["end"] - segment[k][elt]["start"]) < lengthFilter:
                     continue
                 #sys.stderr.write("\t [segment[k][elt] %s\n" % [segment[k][elt]])
-                if np.mean(normalize_depth_results[segment[k][elt]["start"]:segment[k][elt]["end"]]) >= 10:
+                if np.mean(depth_results[segment[k][elt]["start"]:segment[k][elt]["end"]]) >= 10:
                     if int(signal[k][segment[k][elt]["start"]]) < 0:
                         f.write(
                             "%s\t%s\t.\tN\t<DEL>\t.\t.\tSVTYPE=DEL;END=%s;VALUE=%s\tGT:GQ\t./.:0\n"
@@ -2318,7 +2318,7 @@ def main_calcul(
     segmentation(events, segment, chr)
 
     # Appel fonction display_results_vcf
-    display_results_vcf(sample, segment, signal, lengthFilter, output_file, chr, normalize_depth_results)
+    display_results_vcf(sample, segment, signal, lengthFilter, output_file, chr, depth_results)
 
     # #Ecrire les résultats dans le fichier de sortie
     # with open(output_file, 'a') as f: