zzh
/
fast-bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Add the mate mapping quality tag

This commit is contained in:
Nils Homer 2021-07-21 11:12:27 -07:00 committed by GitHub
parent d587a9561b
commit f5e83701ab
1 changed files with 1 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
bwamem.c
View File

@ -932,6 +932,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
kputsn("\tMD:Z:", 6, str); kputs((char*)(p->cigar + p->n_cigar), str);
}
if (m && m->n_cigar) { kputsn("\tMC:Z:", 6, str); add_cigar(opt, m, str, which); }
if (m) { kputsn("\tMQ:i:", 6, str); kputw(m->mapq, str);}
if (p->score >= 0) { kputsn("\tAS:i:", 6, str); kputw(p->score, str); }
if (p->sub >= 0) { kputsn("\tXS:i:", 6, str); kputw(p->sub, str); }
if (bwa_rg_id[0]) { kputsn("\tRG:Z:", 6, str); kputs(bwa_rg_id, str); }