lint(call): rename candidate_snvs_dict to candidate_snvs + reflow

strkit/call/call_locus.py

@@ -463,7 +463,7 @@ def call_alleles_with_incorporated_snvs(
     read_dict_extra: dict[str, dict],
     n_reads_in_dict: int,  # We could derive this again, but we already have before...
     useful_snvs: list[tuple[int, int]],
-    candidate_snvs_dict: CandidateSNVs,
+    candidate_snvs: CandidateSNVs,
     # ---
     snv_quality_threshold: int,
     # ---
@@ -656,7 +656,7 @@ def call_alleles_with_incorporated_snvs(
         n_alleles,
         read_dict,
         useful_snvs,
-        candidate_snvs_dict,
+        candidate_snvs,
         # ---
         snv_quality_threshold,
         # ---
@@ -909,10 +909,10 @@ def call_locus(
 
     # Find candidate SNVs, if we're using SNV data
 
-    candidate_snvs_dict: Optional[CandidateSNVs] = None  # Lookup dictionary for candidate SNVs by position
+    candidate_snvs: Optional[CandidateSNVs] = None  # Lookup dictionary for candidate SNVs by position
     if n_overlapping_reads and should_incorporate_snvs and snv_vcf_file:
         # ^^ n_overlapping_reads check since otherwise we will have invalid left/right_most_coord
-        candidate_snvs_dict = snv_vcf_file.get_candidate_snvs(
+        candidate_snvs = snv_vcf_file.get_candidate_snvs(
             snv_vcf_contigs, snv_vcf_file_format, contig, left_most_coord, right_most_coord
         )
 
@@ -1309,7 +1309,7 @@ def call_locus(
                 read_dict_extra,
                 read_q_coords,
                 read_r_coords,
-                candidate_snvs_dict,
+                candidate_snvs,
                 params.min_allele_reads,
                 significant_clip_snv_take_in,
                 only_known_snvs,
@@ -1329,7 +1329,7 @@ def call_locus(
                     read_dict_extra=read_dict_extra,
                     n_reads_in_dict=n_reads_in_dict,
                     useful_snvs=useful_snvs,
-                    candidate_snvs_dict=candidate_snvs_dict,
+                    candidate_snvs=candidate_snvs,
                     # ---
                     snv_quality_threshold=snv_min_base_qual,
                     # ---

strkit/call/repeats.py

@@ -40,15 +40,13 @@ def score_ref_boundaries(db_seq: str, tr_candidate: str, flank_left_seq: str, fl
 
     # Always assign parasail results to variables due to funky memory allocation behaviour
     ext_r_seq = f"{flank_left_seq}{tr_candidate}"
-    r_fwd = parasail.sg_de_scan_sat(
-        ext_r_seq, db_seq, indel_penalty, indel_penalty, dna_matrix)
+    r_fwd = parasail.sg_de_scan_sat(ext_r_seq, db_seq, indel_penalty, indel_penalty, dna_matrix)
     r_adj = r_fwd.end_ref + 1 - len(flank_left_seq) - ref_size  # Amount to tweak boundary on the right side by
 
     db_seq_rev = db_seq[::-1]
     ext_l_seq = f"{tr_candidate}{flank_right_seq[max(r_adj, 0):]}"[::-1]  # reverse
 
-    r_rev = parasail.sg_de_scan_sat(
-        ext_l_seq, db_seq_rev, indel_penalty, indel_penalty, dna_matrix)
+    r_rev = parasail.sg_de_scan_sat(ext_l_seq, db_seq_rev, indel_penalty, indel_penalty, dna_matrix)
     l_adj = r_rev.end_ref + 1 - len(flank_right_seq) - ref_size  # Amount to tweak boundary on the left side by
 
     return (r_fwd.score, r_adj), (r_rev.score, l_adj)

strkit/call/snvs.py

@@ -27,7 +27,7 @@ def call_and_filter_useful_snvs(
     n_alleles: int,
     read_dict: dict[str, ReadDict],
     useful_snvs: list[tuple[int, int]],
-    candidate_snvs_dict: CandidateSNVs,
+    candidate_snvs: CandidateSNVs,
     # ---
     snv_quality_threshold: int,
     # ---
@@ -42,7 +42,7 @@ def call_and_filter_useful_snvs(
     :param n_alleles: The number of alleles called for this locus.
     :param read_dict: Dictionary of read data. Must already have peaks assigned.
     :param useful_snvs: List of tuples representing useful SNVs: (SNV index, reference position)
-    :param candidate_snvs_dict: A dictionary of useful SNVs, indexed by reference position. Used to look up IDs.
+    :param candidate_snvs: A dictionary of useful SNVs, indexed by reference position. Used to look up IDs.
     :param snv_quality_threshold: Minimum PHRED score needed to incorporate a read base into the genotype.
     :param snv_genotype_cache: Cache for SNV genotype/phase set information.
     :param locus_log_str: Locus string representation for logging purposes.
@@ -134,7 +134,7 @@ def call_and_filter_useful_snvs(
             logger_.warning(f"{locus_log_str} - for SNV position {u_ref}: got degenerate call {call} from {peak_counts=}")
             skipped = True
 
-        snv_rec = candidate_snvs_dict.get(u_ref)
+        snv_rec = candidate_snvs.get(u_ref)
         if snv_rec is not None:
             snv_id = snv_rec["id"]
             if snv_id == ".":