Limit bulk coordinate search to build GRCh37

civicpy/civic.py

@@ -1226,48 +1226,51 @@ def is_sorted(prev_q, current_q):
     def append_match(matches_list, query, ct_row):
         matches_list[query].append(Match(**ct_row.to_dict()))
 
-    while query_pointer < len(sorted_queries) and ct_pointer < len(ct):
-        if last_query_pointer != query_pointer:
-            q = sorted_queries[query_pointer]
-            if match_start is not None:
-                ct_pointer = match_start
-                match_start = None
-            last_query_pointer = query_pointer
-        c = ct.iloc[ct_pointer]
-        q_chr = str(q.chr)
-        c_chr = c.chr
-        if q_chr < c_chr:
-            query_pointer += 1
-            continue
-        if q_chr > c_chr:
-            ct_pointer += 1
-            continue
-        q_start = int(q.start)
-        c_start = c.start
-        q_stop = int(q.stop)
-        c_stop = c.stop
-        if q_start > c_stop:
-            ct_pointer += 1
-            continue
-        if q_stop < c_start:
-            query_pointer += 1
-            continue
-        if search_mode == 'any':
-            append_match(matches, q, c)
-        elif search_mode == 'exact' and q_start == c_start and q_stop == c_stop:
-            q_alt = q.alt
-            c_alt = c.alt
-            q_ref = q.ref
-            c_ref = c.ref
-            if (not (q_alt != '*' and q_alt != c_alt)) and (not (q_ref != '*' and q_ref != c_ref)):
+    if coordinate_query.build == 'GRCh37':
+        while query_pointer < len(sorted_queries) and ct_pointer < len(ct):
+            if last_query_pointer != query_pointer:
+                q = sorted_queries[query_pointer]
+                if match_start is not None:
+                    ct_pointer = match_start
+                    match_start = None
+                last_query_pointer = query_pointer
+            c = ct.iloc[ct_pointer]
+            q_chr = str(q.chr)
+            c_chr = c.chr
+            if q_chr < c_chr:
+                query_pointer += 1
+                continue
+            if q_chr > c_chr:
+                ct_pointer += 1
+                continue
+            q_start = int(q.start)
+            c_start = c.start
+            q_stop = int(q.stop)
+            c_stop = c.stop
+            if q_start > c_stop:
+                ct_pointer += 1
+                continue
+            if q_stop < c_start:
+                query_pointer += 1
+                continue
+            if search_mode == 'any':
+                append_match(matches, q, c)
+            elif search_mode == 'exact' and q_start == c_start and q_stop == c_stop:
+                q_alt = q.alt
+                c_alt = c.alt
+                q_ref = q.ref
+                c_ref = c.ref
+                if (not (q_alt != '*' and q_alt != c_alt)) and (not (q_ref != '*' and q_ref != c_ref)):
+                    append_match(matches, q, c)
+            elif search_mode == 'query_encompassing' and q_start <= c_start and q_stop >= c_stop:
                 append_match(matches, q, c)
-        elif search_mode == 'query_encompassing' and q_start <= c_start and q_stop >= c_stop:
-            append_match(matches, q, c)
-        elif search_mode == 'record_encompassing' and c_start <= q_start and c_stop >= q_stop:
-            append_match(matches, q, c)
-        if match_start is None:
-            match_start = ct_pointer
-        ct_pointer += 1
+            elif search_mode == 'record_encompassing' and c_start <= q_start and c_stop >= q_stop:
+                append_match(matches, q, c)
+            if match_start is None:
+                match_start = ct_pointer
+            ct_pointer += 1
+    else:
+        raise ValueError("Bulk coordinate search only supports build GRCh37")
     return dict(matches)