diff --git a/cb_sniffer.py b/cb_sniffer.py index 09d9d88..38e0172 100644 --- a/cb_sniffer.py +++ b/cb_sniffer.py @@ -117,7 +117,7 @@ def count_barcodes(self, bam_fil, bar, indel, mapq=0, baseq=0): barUcodes['{}'.format(q_name)].append(qstring) # barcode without mutations - if indel > 0 and self.alt == '-': + if indel > 0: # print('{}:{}:{}:{}:{}:{}'.format(read.indel, read.alignment.get_tag('CB'),read.alignment.cigarstring, # read.query_position,self.alt,pileupcolumn.pos)) @@ -167,7 +167,7 @@ def count_barcodes(self, bam_fil, bar, indel, mapq=0, baseq=0): # print(ustring) # print('{}\t{}\t{}'.format(ref_tag, refU_tag, 'ref')) else: - + #print(indel,read.query_position,read.alignment.query_sequence[read.query_position]) if read.alignment.query_sequence[read.query_position] != self.alt: ref_tag = read.alignment.get_tag('CB') # UB