diff --git a/nanovar/nv_alt_seq.py b/nanovar/nv_alt_seq.py index 5d91851..c82f275 100644 --- a/nanovar/nv_alt_seq.py +++ b/nanovar/nv_alt_seq.py @@ -62,9 +62,13 @@ def make_bed(line, sv_type, sv_id): elif sv_type == 'Del': start = int(data[6].split('~')[1].split(':')[1].split('-')[0]) - 1 end = int(data[6].split('~')[1].split(':')[1].split('-')[1]) - else: # ['Nov_Ins', 'E-Nov_Ins_bp', 'S-Nov_Ins_bp', 'Inv', 'Inv(1)', 'Inv(2)', 'TDupl', 'Intra-Ins', 'Intra-Ins(1)', 'Intra-Ins(2)'] + elif sv_type in ['Nov_Ins', 'E-Nov_Ins_bp', 'S-Nov_Ins_bp']: end = int(data[6].split('~')[1].split(':')[1].split('-')[0]) start = end - 1 + else: # ['Inv', 'Inv(1)', 'Inv(2)', 'TDupl', 'Intra-Ins', 'Intra-Ins(1)', 'Intra-Ins(2)'] + # end = int(data[6].split('~')[1].split(':')[1].split('-')[0]) + # start = end - 1 # Might be causing issue #89 + return '' start = max(start, 0) end = max(end, 1) bed_line = '\t'.join([chrm, str(start), str(end), sv_id]) + '\n'