diff --git a/bwa.c b/bwa.c
index 0e9e606..08881c0 100644
--- a/bwa.c
+++ b/bwa.c
@@ -178,9 +178,10 @@ uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pa
 
 int bwa_fix_xref2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_ins, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re)
 {
-	int is_rev;
-	int64_t cb, ce, fm;
+	int is_rev, ori_ql = *qe - *qb;
+	int64_t cb, ce, fm, ori_rl = *re - *rb;
 	bntann1_t *ra;
+	assert(ori_ql > 0 && ori_rl > 0);
 	if (*rb < bns->l_pac && *re > bns->l_pac) { // cross the for-rev boundary; actually with BWA-MEM, we should never come to here
 		*qb = *qe = *rb = *re = -1;
 		return -1; // unable to fix
@@ -218,7 +219,7 @@ int bwa_fix_xref2(const int8_t mat[25], int o_del, int e_del, int o_ins, int e_i
 		}
 		free(cigar);
 	}
-	return (*qb == *qe || *rb == *re)? -2 : 0;
+	return (*qe - *qb < .33 * ori_ql || *re - *rb < .33 * ori_rl)? -2 : 0;
 }
 
 int bwa_fix_xref(const int8_t mat[25], int q, int r, int w, const bntseq_t *bns, const uint8_t *pac, uint8_t *query, int *qb, int *qe, int64_t *rb, int64_t *re)
diff --git a/bwamem.c b/bwamem.c
index bfb45d9..9a58968 100644
--- a/bwamem.c
+++ b/bwamem.c
@@ -905,7 +905,11 @@ void mem_reg2sam_se(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pa
 		if (p->secondary >= 0 && !(opt->flag&MEM_F_ALL)) continue;
 		if (p->secondary >= 0 && p->score < a->a[p->secondary].score * opt->drop_ratio) continue;
 		q = kv_pushp(mem_aln_t, aa);
-		*q = mem_reg2aln(opt, bns, pac, s->l_seq, s->seq, p);
+		*q = mem_reg2aln2(opt, bns, pac, s->l_seq, s->seq, p, s->name);
+		if (q->rid < 0) {
+			--aa.n;
+			continue;
+		}
 		q->flag |= extra_flag; // flag secondary
 		if (p->secondary >= 0) q->sub = -1; // don't output sub-optimal score
 		if (k && p->secondary < 0) // if supplementary
@@ -982,11 +986,10 @@ mem_aln_t mem_reg2aln2(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t
 		query[i] = query_[i] < 5? query_[i] : nst_nt4_table[(int)query_[i]];
 	a.mapq = ar->secondary < 0? mem_approx_mapq_se(opt, ar) : 0;
 	if (ar->secondary >= 0) a.flag |= 0x100; // secondary alignment
-	if (bwa_fix_xref2(opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re) < 0) {
-		if (name) fprintf(stderr, "[E::%s] Internal code inconsistency for read '%s'. Please contact the developer. Sorry.\n", __func__, name);
-		else fprintf(stderr, "[E::%s] Internal code inconsistency. Please contact the developer. Sorry.\n", __func__);
-		a.rid = -1; a.pos = -1; a.flag |= 0x4;
-		return a;
+	if ((ret = bwa_fix_xref2(opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, opt->w, bns, pac, (uint8_t*)query, &qb, &qe, &rb, &re)) < 0) {
+		if (bwa_verbose >= 2 && name)
+			fprintf(stderr, "[W::%s] A cross-chr hit of read '%s' has been dropped.\n", __func__, name);
+		goto err_reg2aln;
 	}
 	tmp = infer_bw(qe - qb, re - rb, ar->truesc, opt->a, opt->o_del, opt->e_del);
 	w2  = infer_bw(qe - qb, re - rb, ar->truesc, opt->a, opt->o_ins, opt->e_ins);
@@ -1002,6 +1005,11 @@ mem_aln_t mem_reg2aln2(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t
 		last_sc = score;
 		w2 <<= 1;
 	} while (++i < 3 && score < ar->truesc - opt->a);
+	if (score < 0) {
+		if (bwa_verbose >= 2 && name)
+			fprintf(stderr, "[W::%s] A hit to read '%s' has been dropped.\n", __func__, name);
+		goto err_reg2aln;
+	}
 	l_MD = strlen((char*)(a.cigar + a.n_cigar)) + 1;
 	a.NM = NM;
 	pos = bns_depos(bns, rb < bns->l_pac? rb : re - 1, &is_rev);
@@ -1036,6 +1044,13 @@ mem_aln_t mem_reg2aln2(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t
 	a.score = ar->score; a.sub = ar->sub > ar->csub? ar->sub : ar->csub;
 	free(query);
 	return a;
+
+err_reg2aln:
+	free(a.cigar);
+	memset(&a, 0, sizeof(mem_aln_t));
+	a.rid = -1; a.pos = -1; a.flag |= 0x4;
+	free(query);
+	return a;
 }
 
 mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_query, const char *query_, const mem_alnreg_t *ar)
diff --git a/bwamem.h b/bwamem.h
index a6d6aa9..7cfe8b8 100644
--- a/bwamem.h
+++ b/bwamem.h
@@ -148,6 +148,7 @@ extern "C" {
 	 * @return       CIGAR, strand, mapping quality and forward-strand position
 	 */
 	mem_aln_t mem_reg2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_seq, const char *seq, const mem_alnreg_t *ar);
+	mem_aln_t mem_reg2aln2(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac, int l_seq, const char *seq, const mem_alnreg_t *ar, const char *name);
 
 	/**
 	 * Infer the insert size distribution from interleaved alignment regions
diff --git a/bwamem_extra.c b/bwamem_extra.c
index 58e9f67..157026c 100644
--- a/bwamem_extra.c
+++ b/bwamem_extra.c
@@ -89,8 +89,9 @@ void mem_reg2ovlp(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac,
 		int is_rev, rid, qb = p->qb, qe = p->qe;
 		int64_t pos, rb = p->rb, re = p->re;
 		if (bwa_fix_xref2(opt->mat, opt->o_del, opt->e_del, opt->o_ins, opt->e_ins, opt->w, bns, pac, (uint8_t*)s->seq, &qb, &qe, &rb, &re) < 0) {
-			fprintf(stderr, "[E::%s] Internal errors when processing read '%s'. Please let the developer know. Abort. Sorry.\n", __func__, s->name);
-			exit(1);
+			if (bwa_verbose >= 2)
+				fprintf(stderr, "[W::%s] A cross-chr hit of read '%s' has been dropped.\n", __func__, s->name);
+			continue;
 		}
 		pos = bns_depos(bns, rb < bns->l_pac? rb : re - 1, &is_rev);
 		rid = bns_pos2rid(bns, pos);
diff --git a/main.c b/main.c
index 91f28bc..dec0b04 100644
--- a/main.c
+++ b/main.c
@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.7.8+dev-r469"
+#define PACKAGE_VERSION "0.7.8+dev-r470"
 #endif
 
 int bwa_fa2pac(int argc, char *argv[]);