From b525117be9ed75f3bde2b7934145654b4d018f2c Mon Sep 17 00:00:00 2001 From: David Ochoa Date: Wed, 25 Sep 2024 11:41:43 +0100 Subject: [PATCH] fix: clean unused study_locus step parameter (#786) --- src/gentropy/config.py | 1 - src/gentropy/study_locus_validation.py | 2 -- 2 files changed, 3 deletions(-) diff --git a/src/gentropy/config.py b/src/gentropy/config.py index 3293a882a..c56a9dfb3 100644 --- a/src/gentropy/config.py +++ b/src/gentropy/config.py @@ -503,7 +503,6 @@ class StudyLocusValidationStepConfig(StepConfig): valid_study_locus_path: str = MISSING invalid_study_locus_path: str = MISSING invalid_qc_reasons: list[str] = MISSING - gwas_significance: float = WindowBasedClumpingStepConfig.gwas_significance _target_: str = "gentropy.study_locus_validation.StudyLocusValidationStep" diff --git a/src/gentropy/study_locus_validation.py b/src/gentropy/study_locus_validation.py index 287cd5645..fc69f6855 100644 --- a/src/gentropy/study_locus_validation.py +++ b/src/gentropy/study_locus_validation.py @@ -19,7 +19,6 @@ def __init__( session: Session, study_index_path: str, study_locus_path: list[str], - gwas_significance: float, valid_study_locus_path: str, invalid_study_locus_path: str, invalid_qc_reasons: list[str] = [], @@ -30,7 +29,6 @@ def __init__( session (Session): Session object. study_index_path (str): Path to study index file. study_locus_path (list[str]): Path to study locus dataset. - gwas_significance (float): GWAS significance threshold. valid_study_locus_path (str): Path to write the valid records. invalid_study_locus_path (str): Path to write the output file. invalid_qc_reasons (list[str]): List of invalid quality check reason names from `StudyLocusQualityCheck` (e.g. ['SUBSIGNIFICANT_FLAG']).