From f5e83701abfd9a9452623add7b39060d4ee2af6d Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Wed, 21 Jul 2021 11:12:27 -0700 Subject: [PATCH] Add the mate mapping quality tag --- bwamem.c | 1 + 1 file changed, 1 insertion(+) diff --git a/bwamem.c b/bwamem.c index 966e8d0..03e2a05 100644 --- a/bwamem.c +++ b/bwamem.c @@ -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); }