Added end2 tag for cnvs without depth supported converted into bnds

Author: kjaisingh

src/sv-pipeline/scripts/single_sample/convert_cnvs_without_depth_support_to_bnds.py

@@ -100,11 +100,17 @@ def main():
                 if not has_depth_support_autosome(record, case_sample) and pesr_support:
                     record.info['SVTYPE'] = 'BND'
                     record.alts = ['<BND>']
+                    record.stop = record.pos
+                    record.info['CHR2'] = record.contig
+                    record.info['END2'] = record.stop
             else:
                 if not has_depth_support_allosome(record, case_sample, samples_by_sex[case_sample_sex]) \
                         and pesr_support:
                     record.info['SVTYPE'] = 'BND'
                     record.alts = ['<BND>']
+                    record.stop = record.pos
+                    record.info['CHR2'] = record.contig
+                    record.info['END2'] = record.stop
         fout.write(record)