fix(call): don't allow eating into VCF anchor with ref offset

strkit/call/call_locus.py

@@ -878,6 +878,7 @@ def call_locus(
         ref_right_flank_seq,
         motif,
         ref_size=right_coord-left_coord,  # reference size, in terms of coordinates (not TRF-recorded size)
+        vcf_anchor_size=vcf_anchor_size,  # guarantee we still have some flanking stuff left to anchor with
         max_iters=ref_max_iters,
         respect_coords=respect_ref,
         local_search_range=ref_local_search_range,

strkit/call/repeats.py

@@ -81,6 +81,7 @@ def get_ref_repeat_count(
     flank_right_seq: str,
     motif: str,
     ref_size: int,
+    vcf_anchor_size: int,
     max_iters: int,
     respect_coords: bool = False,
     local_search_range: int = DEFAULT_LOCAL_SEARCH_RANGE,  # TODO: Parametrize for user
@@ -154,7 +155,7 @@ def get_ref_repeat_count(
         l_offset = rev_top_res[1][1]
         r_offset = fwd_top_res[1][1]
 
-        if l_offset >= len(flank_left_seq):
+        if l_offset >= len(flank_left_seq) - vcf_anchor_size:
             # don't do anything weird if we're removing the entire flank sequence
             # TODO: this can be caused by NNNNNNN - see chr5:139453668-139454525 in GRCh38
             l_offset = 0