diff --git a/granite/lib/shared_functions.py b/granite/lib/shared_functions.py index 48cd4a1..6650904 100644 --- a/granite/lib/shared_functions.py +++ b/granite/lib/shared_functions.py @@ -238,9 +238,9 @@ def variant_type(REF, ALT): ''' return variant type as snv, ins, del ''' if len(ALT.split(',')) > 1: return 'snv' # TO DECIDE WHAT TO DO, as snv for now - elif len(REF) > len(ALT) or ALT == '*': + elif len(REF) > len(ALT) or ALT in ['*', '-']: return 'del' - elif len(REF) < len(ALT) or REF == '*': + elif len(REF) < len(ALT) or REF in ['*', '-']: return 'ins' #end if return 'snv' @@ -254,9 +254,9 @@ def variant_type_ext(REF, ALT): return 'mav' #end if # normal variant - if len(REF) < len(ALT) or REF == '*': + if len(REF) < len(ALT) or REF in ['*', '-']: return 'ins' - elif len(REF) > len(ALT) or ALT == '*': + elif len(REF) > len(ALT) or ALT in ['*', '-']: return 'del' elif len(REF) == len(ALT) and len(REF) != 1: return 'mnv'