diff --git a/bseq.c b/bseq.c
index 0889851..54a25f6 100644
--- a/bseq.c
+++ b/bseq.c
@@ -48,7 +48,7 @@ bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_)
 	}
 	*n_ = n;
 	if (size < chunk_size) { // test if the 2nd file is finished
-		if (kseq_read(ks2) >= 0)
+		if (ks2 && kseq_read(ks2) >= 0)
 			fprintf(stderr, "[W::%s] the 1st file has fewer sequences.\n", __func__);
 	}
 	return seqs;
diff --git a/bwtsw2_aux.c b/bwtsw2_aux.c
index 619930b..a18ffc8 100644
--- a/bwtsw2_aux.c
+++ b/bwtsw2_aux.c
@@ -13,6 +13,7 @@
 #include "bwtsw2.h"
 #include "stdaln.h"
 #include "kstring.h"
+#include "bseq.h"
 
 #include "kseq.h"
 KSEQ_DECLARE(gzFile)
@@ -756,24 +757,14 @@ static void process_seqs(bsw2seq_t *_seq, const bsw2opt_t *opt, const bntseq_t *
 	_seq->n = 0;
 }
 
-static void kseq_to_bsw2seq(const kseq_t *ks, bsw2seq1_t *p)
-{
-	p->tid = -1;
-	p->l = ks->seq.l;
-	p->name = strdup(ks->name.s);
-	p->seq = strdup(ks->seq.s);
-	p->qual = ks->qual.l? strdup(ks->qual.s) : 0;
-	p->comment = ks->comment.l? strdup(ks->comment.s) : 0;
-	p->sam = 0;
-}
-
 void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, const char *fn, const char *fn2)
 {
 	gzFile fp, fp2;
 	kseq_t *ks, *ks2;
-	int l, size = 0, is_pe = 0;
+	int l, is_pe = 0, i, n;
 	uint8_t *pac;
 	bsw2seq_t *_seq;
+	bseq1_t *bseq;
 
 	pac = calloc(bns->l_pac/4+1, 1);
 	if (pac == 0) {
@@ -791,34 +782,25 @@ void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, c
 		ks2 = kseq_init(fp2);
 		is_pe = 1;
 	} else fp2 = 0, ks2 = 0, is_pe = 0;
-	while (kseq_read(ks) >= 0) {
-		if (ks->name.l > 2 && ks->name.s[ks->name.l-2] == '/')
-			ks->name.l -= 2, ks->name.s[ks->name.l] = 0;
-		if (_seq->n == _seq->max) {
-			_seq->max = _seq->max? _seq->max<<1 : 1024;
+	while ((bseq = bseq_read(opt->chunk_size * opt->n_threads, &n, ks, ks2)) != 0) {
+		int size = 0;
+		if (n > _seq->max) {
+			_seq->max = n;
+			kroundup32(_seq->max);
 			_seq->seq = realloc(_seq->seq, _seq->max * sizeof(bsw2seq1_t));
 		}
-		kseq_to_bsw2seq(ks, &_seq->seq[_seq->n++]);
-		size += ks->seq.l;
-		if (ks2) {
-			if (kseq_read(ks2) >= 0) {
-				if (ks2->name.l > 2 && ks2->name.s[ks2->name.l-2] == '/')
-					ks2->name.l -= 2, ks2->name.s[ks2->name.l] = 0;
-				kseq_to_bsw2seq(ks2, &_seq->seq[_seq->n++]); // for PE, _seq->n here must be odd and we do not need to enlarge
-				size += ks->seq.l;
-			} else {
-				fprintf(stderr, "[%s] The second query file has fewer reads. Switched to the single-end mode for the following batches.\n", __func__);
-				is_pe = 0;
-			}
-		}
-		if (size > opt->chunk_size * opt->n_threads) {
-			fprintf(stderr, "[bsw2_aln] read %d sequences/pairs (%d bp)...\n", _seq->n, size);
-			process_seqs(_seq, opt, bns, pac, target, is_pe);
-			size = 0;
+		_seq->n = n;
+		for (i = 0; i < n; ++i) {
+			bseq1_t *b = &bseq[i];
+			bsw2seq1_t *p = &_seq->seq[i];
+			p->tid = -1; p->l = b->l_seq;
+			p->name = b->name; p->seq = b->seq; p->qual = b->qual; p->comment = b->comment; p->sam = 0;
+			size += p->l;
 		}
+		fprintf(stderr, "[bsw2_aln] read %d sequences/pairs (%d bp) ...\n", n, size);
+		free(bseq);
+		process_seqs(_seq, opt, bns, pac, target, is_pe);
 	}
-	fprintf(stderr, "[bsw2_aln] read %d sequences/pairs (%d bp)...\n", _seq->n, size);
-	process_seqs(_seq, opt, bns, pac, target, is_pe);
 	// free
 	free(pac);
 	free(_seq->seq); free(_seq);