Revert "feat: credible set quality filtering (#640)"

This reverts commit 0119c44.

src/gentropy/susie_finemapper.py

@@ -23,7 +23,6 @@
 
 from gentropy.common.session import Session
 from gentropy.common.spark_helpers import neglog_pvalue_to_mantissa_and_exponent
-from gentropy.dataset.ld_index import LDIndex
 from gentropy.dataset.study_index import StudyIndex
 from gentropy.dataset.study_locus import StudyLocus
 from gentropy.dataset.summary_statistics import SummaryStatistics
@@ -1169,45 +1168,3 @@ def susie_finemapper_one_studylocus_row_v3_dev_ss_gathered(
         )
 
         return out
-
-    @staticmethod
-    def credible_set_qc(
-        cred_sets: StudyLocus,
-        study_index: StudyIndex,
-        ld_index: LDIndex,
-        p_value_threshold: float = 1e-5,
-        purity_min_r2: float = 0.01,
-    ) -> StudyLocus:
-        """Filter credible sets by lead P-value and min-R2 purity, and performs LD clumping.
-
-        Args:
-            cred_sets (StudyLocus): StudyLocus object with credible sets to filter/clump
-            study_index (StudyIndex): StudyIndex object
-            ld_index (LDIndex): LDIndex object
-            p_value_threshold (float): p-value threshold for filtering credible sets, default is 1e-5
-            purity_min_r2 (float): min-R2 purity threshold for filtering credible sets, default is 0.25
-
-        Returns:
-            StudyLocus: Credible sets which pass filters and LD clumping.
-        """
-        df = (
-            cred_sets.df.withColumn(
-                "pValue", f.col("pValueMantissa") * f.pow(10, f.col("pValueExponent"))
-            )
-            .filter(f.col("pValue") <= p_value_threshold)
-            .filter(f.col("purityMinR2") >= purity_min_r2)
-            .drop("pValue")
-        )
-        cred_sets.df = df
-        cred_sets = (
-            cred_sets.annotate_ld(study_index, ld_index)
-            .clump()
-            .filter(
-                ~f.array_contains(
-                    f.col("qualityControls"),
-                    "Explained by a more significant variant in high LD (clumped)",
-                )
-            )
-        )
-
-        return cred_sets