new get_relative_coords function

CRISPResso2/CRISPRessoShared.py

@@ -1679,8 +1679,36 @@ def set_guide_array(vals, guides, property_name):
             ret_array[idx] = int(val)
     return ret_array
 
-
 def get_relative_coordinates(to_sequence, from_sequence):
+
+    s1inds_gap_left = []
+    s1inds_gap_right = []
+    left_val = -1
+    gap_length = 0
+
+    for i in range(len(to_sequence)):
+        if to_sequence[i] == '-':
+            s1inds_gap_left.append(left_val)
+            gap_length += 1
+
+        elif from_sequence[i] == '-':
+            continue
+
+        else:
+            s1inds_gap_right.extend([i]*(gap_length+1))
+            gap_length = 0
+
+            left_val = i
+            s1inds_gap_left.append(left_val)
+
+    return s1inds_gap_left, s1inds_gap_right
+
+
+
+
+
+
+def old_get_relative_coordinates(to_sequence, from_sequence):
     """Given an alignment, get the relative coordinates of the second sequence to the first.
 
     For example, from_sequence[i] matches to to_sequence[inds[i]]. A `-1`