Mem should set the mate cigar tag.

nh13 · nh13 · commit 3b96dcee7fbc · 2017-07-03T08:51:00.000-07:00
diff --git a/bwamem.c b/bwamem.c
@@ -809,6 +809,19 @@ static inline int get_rlen(int n_cigar, const uint32_t *cigar)
 	return l;
 }
 
+static inline void add_cigar(const mem_opt_t *opt, mem_aln_t *p, kstring_t *str, int which)
+{
+	int i;
+	if (p->n_cigar) { // aligned
+		for (i = 0; i < p->n_cigar; ++i) {
+			int c = p->cigar[i]&0xf;
+			if (!(opt->flag&MEM_F_SOFTCLIP) && !p->is_alt && (c == 3 || c == 4))
+				c = which? 4 : 3; // use hard clipping for supplementary alignments
+			kputw(p->cigar[i]>>4, str); kputc("MIDSH"[c], str);
+		}
+	} else kputc('*', str); // having a coordinate but unaligned (e.g. when copy_mate is true)
+}
+
 void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq1_t *s, int n, const mem_aln_t *list, int which, const mem_aln_t *m_)
 {
 	int i, l_name;
@@ -835,14 +848,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 		kputs(bns->anns[p->rid].name, str); kputc('\t', str); // RNAME
 		kputl(p->pos + 1, str); kputc('\t', str); // POS
 		kputw(p->mapq, str); kputc('\t', str); // MAPQ
-		if (p->n_cigar) { // aligned
-			for (i = 0; i < p->n_cigar; ++i) {
-				int c = p->cigar[i]&0xf;
-				if (!(opt->flag&MEM_F_SOFTCLIP) && !p->is_alt && (c == 3 || c == 4))
-					c = which? 4 : 3; // use hard clipping for supplementary alignments
-				kputw(p->cigar[i]>>4, str); kputc("MIDSH"[c], str);
-			}
-		} else kputc('*', str); // having a coordinate but unaligned (e.g. when copy_mate is true)
+		add_cigar(opt, p, str, which);
 	} else kputsn("*\t0\t0\t*", 7, str); // without coordinte
 	kputc('\t', str);
 
@@ -899,6 +905,7 @@ void mem_aln2sam(const mem_opt_t *opt, const bntseq_t *bns, kstring_t *str, bseq
 		kputsn("\tNM:i:", 6, str); kputw(p->NM, str);
 		kputsn("\tMD:Z:", 6, str); kputs((char*)(p->cigar + p->n_cigar), str);
 	}
+	if (m->n_cigar) { kputsn("\tMC:Z:", 6, str); add_cigar(opt, m, str, which); }
 	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); }
