diff --git a/bseq.c b/bseq.c
index 94b7fca..95f063d 100644
--- a/bseq.c
+++ b/bseq.c
@@ -4,12 +4,16 @@
 #include <string.h>
 #include <assert.h>
 #include "bseq.h"
+#include "kvec.h"
 #include "kseq.h"
 KSEQ_INIT2(, gzFile, gzread)
 
+#define CHECK_PAIR_THRES 1000000
+
 struct mm_bseq_file_s {
 	gzFile fp;
 	kseq_t *ks;
+	mm_bseq1_t s;
 };
 
 mm_bseq_file_t *mm_bseq_open(const char *fn)
@@ -31,32 +35,61 @@ void mm_bseq_close(mm_bseq_file_t *fp)
 	free(fp);
 }
 
+static inline int mm_qname_same(const char *s1, const char *s2)
+{
+	int l1, l2;
+	l1 = strlen(s1);
+	l2 = strlen(s2);
+	if (l1 != l2 || l1 < 3) return 0;
+	if (!(s1[l1-1] >= '1' && s1[l1-1] <= '2' && s1[l1-2] == '/')) return 0;
+	if (!(s2[l2-1] >= '1' && s2[l2-1] <= '2' && s2[l2-2] == '/')) return 0;
+	return (strncmp(s1, s2, l1 - 2) == 0);
+}
+
+static inline void kseq2bseq(kseq_t *ks, mm_bseq1_t *s, int with_qual)
+{
+	s->name = strdup(ks->name.s);
+	s->seq = strdup(ks->seq.s);
+	s->qual = with_qual && ks->qual.l? strdup(ks->qual.s) : 0;
+	s->l_seq = ks->seq.l;
+}
+
 mm_bseq1_t *mm_bseq_read(mm_bseq_file_t *fp, int chunk_size, int with_qual, int *n_)
 {
-	int size = 0, m, n;
-	mm_bseq1_t *seqs;
+	int64_t size = 0;
+	kvec_t(mm_bseq1_t) a = {0,0,0};
 	kseq_t *ks = fp->ks;
-	m = n = 0; seqs = 0;
+	if (fp->s.seq) {
+		kv_resize(mm_bseq1_t, 0, a, 256);
+		kv_push(mm_bseq1_t, 0, a, fp->s);
+		size = fp->s.l_seq;
+		memset(&fp->s, 0, sizeof(mm_bseq1_t));
+	}
 	while (kseq_read(ks) >= 0) {
 		mm_bseq1_t *s;
 		assert(ks->seq.l <= INT32_MAX);
-		if (n >= m) {
-			m = m? m<<1 : 256;
-			seqs = (mm_bseq1_t*)realloc(seqs, m * sizeof(mm_bseq1_t));
+		if (a.m == 0) kv_resize(mm_bseq1_t, 0, a, 256);
+		kv_pushp(mm_bseq1_t, 0, a, &s);
+		kseq2bseq(ks, s, with_qual);
+		size += s->l_seq;
+		if (size >= chunk_size) {
+			if (a.a[a.n-1].l_seq < CHECK_PAIR_THRES) {
+				while (kseq_read(ks) >= 0) {
+					kseq2bseq(ks, &fp->s, with_qual);
+					if (mm_qname_same(fp->s.name, a.a[a.n-1].name)) {
+						kv_push(mm_bseq1_t, 0, a, fp->s);
+						memset(&fp->s, 0, sizeof(mm_bseq1_t));
+					} else break;
+				}
+			}
+			break;
 		}
-		s = &seqs[n];
-		s->name = strdup(ks->name.s);
-		s->seq = strdup(ks->seq.s);
-		s->qual = with_qual && ks->qual.l? strdup(ks->qual.s) : 0;
-		s->l_seq = ks->seq.l;
-		size += seqs[n++].l_seq;
-		if (size >= chunk_size) break;
 	}
-	*n_ = n;
-	return seqs;
+	*n_ = a.n;
+	return a.a;
 }
 
 int mm_bseq_eof(mm_bseq_file_t *fp)
 {
-	return ks_eof(fp->ks->f);
+	return (ks_eof(fp->ks->f) && fp->s.seq == 0);
 }