Merge pull request #6 from erinyoung/erin-dev

Adjusted check after addition/subtraction

Author: erinyoung

bin/groups.py

@@ -41,14 +41,24 @@
                     match_start = int(end2) + int(end_diff)
                     match_end = int(start2) - int(start_diff)
 
+                if str(match_start) not in divided[chr2].keys():
+                    for potential_start in divided[chr2].keys():
+                        if (int(potential_start) - 20) <= match_start <= (int(potential_start) + 20):
+                            match_start=int(potential_start)
+
+                # sometimes there are small indels
+                if str(match_start) in divided[chr2].keys():
+                    if int(divided[chr2][str(match_start)]) != int(match_end):
+                        match_end=int(divided[chr2][str(match_start)])
+
                 saved_line2= chr2 + ":" + str(match_start) + ":" + str(match_end)
                 new_group = True
 
                 for numbers in group.keys():
                     if saved_line in group[numbers]['list']:
                         new_group = False
                         if (saved_line2 not in group[numbers]['list']) and (start2 in divided[chr2].keys()):
-                            group[numbers]['list'].append(saved_line2)
+                            group[numbers]['list'].append(saved_line2)      
                     elif saved_line2 in group[numbers]['list']:
                         new_group = False
                         if saved_line not in group[numbers]['list']: