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Bug fix no score ratio when only one scheme #112

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merged 1 commit into from
Apr 30, 2024
Merged

Bug fix no score ratio when only one scheme #112

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16 changes: 12 additions & 4 deletions viridian/one_sample_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -363,10 +363,16 @@ def detect_amplicon_scheme(self):
return False
best_scheme = id_results["scheme_choice"]["best_scheme"]
best_score = id_results["scheme_choice"]["best_score"]
number_of_schemes = len(id_results["scheme_choice"]["scores"])
score_ratio = id_results["scheme_choice"]["score_ratio"]
logging.info(
f"Amplicon scheme that reads best match to: {best_scheme}, with score {best_score}, and (second best)/best = {score_ratio}"
)
if number_of_schemes > 1:
logging.info(
f"Amplicon scheme that reads best match to: {best_scheme}, with score {best_score}, and (second best)/best = {score_ratio}"
)
else:
logging.info(
f"Amplicon scheme that reads best match to: {best_scheme}, with score {best_score}, not using (second best)/best because only one scheme"
)

if self.force_amp_scheme is None:
score_ok = True
Expand All @@ -376,7 +382,9 @@ def detect_amplicon_scheme(self):
f"Best scheme score is {best_score}, which is less than required minimum score {self.min_scheme_score}"
)
score_ok = False
if score_ratio is None or score_ratio > self.max_scheme_ratio:
if number_of_schemes > 1 and (
score_ratio is None or score_ratio > self.max_scheme_ratio
):
self.log_dict["amplicon_scheme_name"] = None
self.add_errors_to_log(
f"(second best scheme score) / (best score) is {score_ratio}, which is more than the required maximum {self.max_scheme_ratio}"
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