diff --git a/bwase.c b/bwase.c
index afe8154..84430fe 100644
--- a/bwase.c
+++ b/bwase.c
@@ -404,6 +404,26 @@ static int64_t pos_5(const bwa_seq_t *p)
 	return -1;
 }
 
+void bwa_print_seq(FILE *stream, bwa_seq_t *seq) {
+	char buffer[4096];
+	const int bsz = sizeof(buffer);
+	int i, j, l;
+	
+	if (seq->strand == 0) {
+		for (i = 0; i < seq->full_len; i += bsz) {
+			l = seq->full_len - i > bsz ? bsz : seq->full_len - i;
+			for (j = 0; j < l; j++) buffer[j] = "ACGTN"[seq->seq[i + j]];
+			err_fwrite(buffer, 1, l, stream);
+		}
+	} else {
+		for (i = seq->full_len - 1; i >= 0; i -= bsz) {
+			l = i + 1 > bsz ? bsz : i + 1;
+			for (j = 0; j < l; j++) buffer[j] = "TGCAN"[seq->seq[i - j]];
+			err_fwrite(buffer, 1, l, stream);
+		}
+	}
+}
+
 void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, int mode, int max_top2)
 {
 	int j;
@@ -455,10 +475,8 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 		else err_printf("\t*\t0\t0\t");
 
 		// print sequence and quality
-		if (p->strand == 0)
-			for (j = 0; j != p->full_len; ++j) putchar("ACGTN"[(int)p->seq[j]]);
-		else for (j = 0; j != p->full_len; ++j) putchar("TGCAN"[p->seq[p->full_len - 1 - j]]);
-		putchar('\t');
+		bwa_print_seq(stdout, p);
+		err_putchar('\t');
 		if (p->qual) {
 			if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
 			err_printf("%s", p->qual);
@@ -500,14 +518,16 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 				}
 			}
 		}
-		putchar('\n');
+		err_putchar('\n');
 	} else { // this read has no match
-		ubyte_t *s = p->strand? p->rseq : p->seq;
+		//ubyte_t *s = p->strand? p->rseq : p->seq;
 		int flag = p->extra_flag | SAM_FSU;
 		if (mate && mate->type == BWA_TYPE_NO_MATCH) flag |= SAM_FMU;
 		err_printf("%s\t%d\t*\t0\t0\t*\t*\t0\t0\t", p->name, flag);
-		for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
-		putchar('\t');
+		//Why did this work differently to the version above??
+		//for (j = 0; j != p->len; ++j) putchar("ACGTN"[(int)s[j]]);
+		bwa_print_seq(stdout, p);
+		err_putchar('\t');
 		if (p->qual) {
 			if (p->strand) seq_reverse(p->len, p->qual, 0); // reverse quality
 			err_printf("%s", p->qual);
@@ -515,7 +535,7 @@ void bwa_print_sam1(const bntseq_t *bns, bwa_seq_t *p, const bwa_seq_t *mate, in
 		if (bwa_rg_id) err_printf("\tRG:Z:%s", bwa_rg_id);
 		if (p->bc[0]) err_printf("\tBC:Z:%s", p->bc);
 		if (p->clip_len < p->full_len) err_printf("\tXC:i:%d", p->clip_len);
-		putchar('\n');
+		err_putchar('\n');
 	}
 }
 
diff --git a/fastmap.c b/fastmap.c
index 504e22e..5cb83fc 100644
--- a/fastmap.c
+++ b/fastmap.c
@@ -91,9 +91,9 @@ int main_fastmap(int argc, char *argv[])
 	while (kseq_read(seq) >= 0) {
 		printf("SQ\t%s\t%ld", seq->name.s, seq->seq.l);
 		if (print_seq) {
-			putchar('\t');
-			puts(seq->seq.s);
-		} else putchar('\n');
+			err_putchar('\t');
+			err_puts(seq->seq.s);
+		} else err_putchar('\n');
 		for (i = 0; i < seq->seq.l; ++i)
 			seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
 		smem_set_query(iter, seq->seq.l, (uint8_t*)seq->seq.s);
@@ -112,11 +112,11 @@ int main_fastmap(int argc, char *argv[])
 						bns_cnt_ambi(bns, pos, len, &ref_id);
 						printf("\t%s:%c%ld", bns->anns[ref_id].name, "+-"[is_rev], (long)(pos - bns->anns[ref_id].offset) + 1);
 					}
-				} else fputs("\t*", stdout);
-				putchar('\n');
+				} else err_puts("\t*");
+				err_putchar('\n');
 			}
 		}
-		puts("//");
+		err_puts("//");
 	}
 
 	smem_iter_destroy(iter);
diff --git a/utils.c b/utils.c
index dc16308..93c17c9 100644
--- a/utils.c
+++ b/utils.c
@@ -195,6 +195,28 @@ int err_fprintf(FILE *stream, const char *format, ...)
     return done;
 }
 
+int err_fputc(int c, FILE *stream)
+{
+	int ret = putc(c, stream);
+	if (EOF == ret)
+	{
+		_err_fatal_simple("fputc", strerror(errno));
+	}
+
+	return ret;
+}
+
+int err_fputs(const char *s, FILE *stream)
+{
+	int ret = fputs(s, stream);
+	if (EOF == ret)
+	{
+		_err_fatal_simple("fputs", strerror(errno));
+	}
+
+	return ret;
+}
+
 int err_fflush(FILE *stream) 
 {
     int ret = fflush(stream);
diff --git a/utils.h b/utils.h
index f824245..b904701 100644
--- a/utils.h
+++ b/utils.h
@@ -76,6 +76,10 @@ extern "C" {
         ATTRIBUTE((format(printf, 2, 3)));
 	int err_printf(const char *format, ...)
         ATTRIBUTE((format(printf, 1, 2)));
+	int err_fputc(int c, FILE *stream);
+#define err_putchar(C) err_fputc((C), stdout)
+	int err_fputs(const char *s, FILE *stream);
+#define err_puts(S) err_fputs((S), stdout)
 	int err_fflush(FILE *stream);
 	int err_fclose(FILE *stream);
 	int err_gzclose(gzFile file);