Commit fbfb9bf7 authored by Theo Serralta's avatar Theo Serralta

Modify filter

parent 35e59a9c
......@@ -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:
......
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