fix(call): impose max iters on ref cn getter + fix ref cn logic

Was accidentally passing db_seq instead of tr_seq to get_repeat_count
and mis-calculating start_count, resulting in too many iterations and possibly
bad ref copy numbers.

strkit/call/call_locus.py

@@ -815,18 +815,22 @@ def call_locus(
 
     # Get reference repeat count by our method, so we can calculate offsets from reference
     ref_cn: Union[int, float]
-    (ref_cn, _), l_offset, r_offset = get_ref_repeat_count(
+    ref_max_iters: int = 100
+    (ref_cn, _), l_offset, r_offset, r_n_is = get_ref_repeat_count(
         round(len(ref_seq) / motif_size),  # Initial estimate of copy number based on coordinates + motif size
         ref_seq,
         ref_left_flank_seq,
         ref_right_flank_seq,
         motif,
         ref_size=right_coord-left_coord,  # reference size, in terms of coordinates (not TRF-recorded size)
+        max_iters=ref_max_iters,
         respect_coords=respect_ref,
     )
     call_dict_base["ref_cn"] = ref_cn  # tag call dictionary with ref_cn
 
-    logger_.debug(f"{locus_log_str} - got ref. copy number: {ref_cn} ({l_offset=}; {r_offset=})")
+    logger_.debug(
+        f"{locus_log_str} - got ref. copy number: {ref_cn} ({l_offset=}; {r_offset=}; iters={r_n_is}; "
+        f"slow_ref_count={any(x > 50 for x in r_n_is)})")
 
     # If our reference repeat count getter has altered the TR boundaries a bit (which is done to allow for
     # more spaces in which an indel could end up), adjust our coordinates to match.

strkit/call/repeats.py

@@ -126,15 +126,18 @@ def get_ref_repeat_count(
     flank_right_seq: str,
     motif: str,
     ref_size: int,
+    max_iters: int,
     respect_coords: bool = False,
     local_search_range: int = DEFAULT_LOCAL_SEARCH_RANGE,  # TODO: Parametrize for user
-) -> tuple[tuple[Union[int, float], int], int, int]:
+) -> tuple[tuple[Union[int, float], int], int, int, tuple[int, int]]:
     l_offset: int = 0
     r_offset: int = 0
 
     db_seq: str = f"{flank_left_seq}{tr_seq}{flank_right_seq}"
     motif_size = len(motif)
 
+    n_offset_scores: int = 0
+
     if not respect_coords:  # Extend out coordinates from initial definition
         to_explore: list[tuple[int, Literal[-1, 0, 1]]] = [
             (start_count - 1, -1), (start_count + 1, 1), (start_count, 0)]
@@ -165,6 +168,8 @@ def get_ref_repeat_count(
                     fwd_sizes_scores_adj[i] = fwd_rs = res[0]
                     rev_sizes_scores_adj[i] = rev_rs = res[1]
 
+                    n_offset_scores += 1
+
                 fwd_scores.append((i, fwd_rs, i))
                 rev_scores.append((i, rev_rs, i))
 
@@ -196,12 +201,13 @@ def get_ref_repeat_count(
 
     # ------------------------------------------------------------------------------------------------------------------
 
-    final_res, _ = get_repeat_count(
-        round(start_count + (max(0, l_offset) + max(0, r_offset)) / motif_size),  # always start with int here
-        db_seq,
+    final_res, n_iters_final_count = get_repeat_count(
+        # always start with int here:
+        round(((start_count * motif_size) + (max(0, l_offset) + max(0, r_offset))) / motif_size),
+        tr_seq,
         flank_left_seq,
         flank_right_seq,
         motif,
-        max_iters=100)
+        max_iters=max_iters)
 
-    return final_res, l_offset, r_offset
+    return final_res, l_offset, r_offset, (n_offset_scores, n_iters_final_count)