diff --git a/bwamem.c b/bwamem.c
index 38ab6e6b..f7809492 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -607,113 +607,6 @@ static inline int infer_bw(int l1, int l2, int score, int a, int q, int r)
 	return w;
 }
 
-void bwa_hit2sam(kstring_t *str, const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, const bwahit_t *p_, int is_hard, const bwahit_t *m)
-{
-#define is_mapped(x) ((x)->rb >= 0 && (x)->rb < (x)->re && (x)->re <= bns->l_pac<<1)
-	int score, n_cigar, is_rev = 0, rid, mid, copy_mate = 0, NM = -1;
-	uint32_t *cigar = 0;
-	int64_t pos = -1;
-	bwahit_t ptmp, *p = &ptmp;
-
-	if (!p_) { // in this case, generate an unmapped alignment
-		memset(&ptmp, 0, sizeof(bwahit_t));
-		ptmp.rb = ptmp.re = -1;
-	} else ptmp = *p_;
-	p->flag |= m? 1 : 0; // is paired in sequencing
-	p->flag |= !is_mapped(p)? 4 : 0; // is mapped
-	p->flag |= m && !is_mapped(m)? 8 : 0; // is mate mapped
-	if (m && !is_mapped(p) && is_mapped(m)) {
-		p->rb = m->rb; p->re = m->re; p->qb = 0; p->qe = s->l_seq;
-		copy_mate = 1;
-	}
-	p->flag |= p->rb >= bns->l_pac? 0x10 : 0; // is reverse strand
-	p->flag |= m && m->rb >= bns->l_pac? 0x20 : 0; // is mate on reverse strand
-	if (is_mapped(p) && m && !is_mapped(m) && (p->flag&0x10)) p->flag |= 0x20; // if mate is unmapped, it takes the strand of the current read
-	kputs(s->name, str); kputc('\t', str);
-	if (is_mapped(p)) { // has a coordinate, no matter whether it is mapped or copied from the mate
-		int sam_flag = p->flag&0xff; // the flag that will be outputed to SAM; it is not always the same as p->flag
-		if (p->flag&0x10000) sam_flag |= 0x100;
-		if (!copy_mate) {
-			int w2;
-			w2 = infer_bw(p->qe - p->qb, p->re - p->rb, p->score, mat[0], q, r);
-			w2 = w2 < w? w2 : w;
-			cigar = bwa_gen_cigar(mat, q, r, w2, bns->l_pac, pac, p->qe - p->qb, (uint8_t*)&s->seq[p->qb], p->rb, p->re, &score, &n_cigar, &NM);
-			p->flag |= n_cigar == 0? 4 : 0; // FIXME: check why this may happen (this has already happened)
-		} else n_cigar = 0, cigar = 0;
-		pos = bns_depos(bns, p->rb < bns->l_pac? p->rb : p->re - 1, &is_rev);
-		bns_cnt_ambi(bns, pos, p->re - p->rb, &rid);
-		kputw(sam_flag, str); kputc('\t', str);
-		kputs(bns->anns[rid].name, str); kputc('\t', str); kputuw(pos - bns->anns[rid].offset + 1, str); kputc('\t', str);
-		kputw(p->qual, str); kputc('\t', str);
-		if (n_cigar) {
-			int i, clip5, clip3;
-			clip5 = is_rev? s->l_seq - p->qe : p->qb;
-			clip3 = is_rev? p->qb : s->l_seq - p->qe;
-			if (clip5) { kputw(clip5, str); kputc("SH"[(is_hard!=0)], str); }
-			for (i = 0; i < n_cigar; ++i) {
-				kputw(cigar[i]>>4, str); kputc("MIDSH"[cigar[i]&0xf], str);
-			}
-			if (clip3) { kputw(clip3, str); kputc("SH"[(is_hard!=0)], str); }
-		} else kputc('*', str);
-	} else { // no coordinate
-		kputw(p->flag, str);
-		kputs("\t*\t0\t0\t*", str);
-		rid = -1;
-	}
-	if (m && is_mapped(m)) { // then print mate pos and isize
-		pos = bns_depos(bns, m->rb < bns->l_pac? m->rb : m->re - 1, &is_rev);
-		bns_cnt_ambi(bns, pos, m->re - m->rb, &mid);
-		kputc('\t', str);
-		if (mid == rid) kputc('=', str);
-		else kputs(bns->anns[mid].name, str);
-		kputc('\t', str); kputuw(pos - bns->anns[mid].offset + 1, str);
-		kputc('\t', str);
-		if (mid == rid) {
-			int64_t p0 = p->rb < bns->l_pac? p->rb : (bns->l_pac<<1) - 1 - p->rb;
-			int64_t p1 = m->rb < bns->l_pac? m->rb : (bns->l_pac<<1) - 1 - m->rb;
-			kputw(-(p0 - p1 + (p0 > p1? 1 : p0 < p1? -1 : 0)), str);
-		} else kputw(0, str);
-		kputc('\t', str);
-	} else if (m && is_mapped(p)) { // then copy the position
-		kputsn("\t=\t", 3, str);
-		kputuw(pos - bns->anns[rid].offset + 1, str);
-		kputsn("\t0\t", 3, str);
-	} else kputsn("\t*\t0\t0\t", 7, str);
-	if (p->flag&0x100) { // for secondary alignments, don't write SEQ and QUAL
-		kputsn("*\t*", 3, str);
-	} else if (!(p->flag&0x10)) { // print SEQ and QUAL, the forward strand
-		int i, qb = 0, qe = s->l_seq;
-		if (!(p->flag&4) && is_hard) qb = p->qb, qe = p->qe;
-		ks_resize(str, str->l + (qe - qb) + 1);
-		for (i = qb; i < qe; ++i) str->s[str->l++] = "ACGTN"[(int)s->seq[i]];
-		kputc('\t', str);
-		if (s->qual) { // printf qual
-			ks_resize(str, str->l + (qe - qb) + 1);
-			for (i = qb; i < qe; ++i) str->s[str->l++] = s->qual[i];
-			str->s[str->l] = 0;
-		} else kputc('*', str);
-	} else { // the reverse strand
-		int i, qb = 0, qe = s->l_seq;
-		if (!(p->flag&4) && is_hard) qb = p->qb, qe = p->qe;
-		ks_resize(str, str->l + (qe - qb) + 1);
-		for (i = qe-1; i >= qb; --i) str->s[str->l++] = "TGCAN"[(int)s->seq[i]];
-		kputc('\t', str);
-		if (s->qual) { // printf qual
-			ks_resize(str, str->l + (qe - qb) + 1);
-			for (i = qe-1; i >= qb; --i) str->s[str->l++] = s->qual[i];
-			str->s[str->l] = 0;
-		} else kputc('*', str);
-	}
-	if (NM >= 0) { kputsn("\tNM:i:", 6, str); kputw(NM, 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); }
-	if (s->comment) { kputc('\t', str); kputs(s->comment, str); }
-	kputc('\n', str);
-	free(cigar);
-#undef is_mapped
-}
-
 static inline int get_rlen(int n_cigar, const uint32_t *cigar)
 {
 	int k, l;
@@ -834,46 +727,6 @@ int mem_approx_mapq_se(const mem_opt_t *opt, const mem_alnreg_t *a)
 	return mapq;
 }
 
-void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h)
-{
-	h->rb = a->rb; h->re = a->re; h->qb = a->qb; h->qe = a->qe;
-	h->score = a->score;
-	h->sub = a->secondary >= 0? -1 : a->sub > a->csub? a->sub : a->csub;
-	h->qual = 0; // quality unset
-	h->flag = a->secondary >= 0? 0x100 : 0; // only the "secondary" bit is set
-}
-
-void mem_sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const bwahit_t *m)
-{
-	int k;
-	kstring_t str;
-	str.l = str.m = 0; str.s = 0;
-	if (a->n > 0 && a->a[0].score >= opt->T) {
-		int mapq0 = -1;
-		for (k = 0; k < a->n; ++k) {
-			bwahit_t h;
-			mem_alnreg_t *p = &a->a[k];
-			if (p->score < opt->T) continue;
-			if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
-			if (p->secondary >= 0 && p->score < a->a[p->secondary].score * .5) continue;
-			mem_alnreg2hit(p, &h);
-			bwa_fix_xref(opt->mat, opt->q, opt->r, opt->w, bns, pac, (uint8_t*)s->seq, &h.qb, &h.qe, &h.rb, &h.re);
-			h.flag |= extra_flag;
-			if ((opt->flag&MEM_F_NO_MULTI) && k && p->secondary < 0) h.flag |= 0x10000; // print the sequence, but flag as secondary (for Picard)
-			h.qual = p->secondary >= 0? 0 : mem_approx_mapq_se(opt, p);
-			if (k == 0) mapq0 = h.qual;
-			else if (h.qual > mapq0) h.qual = mapq0;
-			bwa_hit2sam(&str, opt->mat, opt->q, opt->r, p->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP, m);
-		}
-	} else {
-		bwahit_t h;
-		memset(&h, 0, sizeof(bwahit_t));
-		h.rb = h.re = -1; h.flag = extra_flag;
-		bwa_hit2sam(&str, opt->mat, opt->q, opt->r, opt->w, bns, pac, s, &h, opt->flag&MEM_F_HARDCLIP, m);
-	}
-	s->sam = str.s;
-}
-
 void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, bseq1_t *s, mem_alnreg_v *a, int extra_flag, const mem_aln_t *m)
 {
 	kstring_t str;
@@ -1024,7 +877,6 @@ static void *worker2(void *data)
 	if (!(w->opt->flag&MEM_F_PE)) {
 		for (i = w->start; i < w->n; i += w->step) {
 			mem_mark_primary_se(w->opt, w->regs[i].n, w->regs[i].a);
-			//mem_sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
 			mem_reg2sam_se(w->opt, w->bns, w->pac, &w->seqs[i], &w->regs[i], 0, 0);
 			free(w->regs[i].a);
 		}
diff --git a/bwamem.h b/bwamem.h
index 55cff76f..ae201e6a 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -59,13 +59,6 @@ typedef struct {
 	double avg, std;
 } mem_pestat_t;
 
-typedef struct { // TODO: This is an intermediate struct only. Better get rid of it.
-	int64_t rb, re;
-	int qb, qe, flag, qual;
-	// optional info
-	int score, sub;
-} bwahit_t;
-
 typedef struct { // This struct is only used for the convenience of API.
 	int64_t pos;     // forward strand 5'-end mapping position
 	int rid;         // reference sequence index in bntseq_t; <0 for unmapped
diff --git a/bwamem_pair.c b/bwamem_pair.c
index 7cbf5e03..5f2c7bb9 100644
--- a/bwamem_pair.c
+++ b/bwamem_pair.c
@@ -169,7 +169,6 @@ int mem_matesw(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const me
 
 int mem_pair(const mem_opt_t *opt, int64_t l_pac, const uint8_t *pac, const mem_pestat_t pes[4], bseq1_t s[2], mem_alnreg_v a[2], int id, int *sub, int *n_sub, int z[2])
 {
-	extern void mem_alnreg2hit(const mem_alnreg_t *a, bwahit_t *h);
 	pair64_v v, u;
 	int r, i, k, y[4], ret; // y[] keeps the last hit
 	kv_init(v); kv_init(u);