From af4d120a593c673911a156043f864b358b6656fe Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Mon, 18 Nov 2024 18:02:20 -0500
Subject: [PATCH] fix(call): errors from offsetting the entire flank seq
---
strkit/call/repeats.py | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/strkit/call/repeats.py b/strkit/call/repeats.py
index dec855c..381c353 100644
--- a/strkit/call/repeats.py
+++ b/strkit/call/repeats.py
@@ -154,6 +154,13 @@ 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):
+ # 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
+ if r_offset >= len(flank_right_seq):
+ r_offset = 0 # same here
+
if l_offset > 0:
tr_seq = flank_left_seq[-1*l_offset:] + tr_seq # first, move a chunk of the left flank to the TR seq
flank_left_seq = flank_left_seq[:-1*l_offset] # then, remove that chunk from the left flank