diff --git a/CommandLines.h b/CommandLines.h
index f240a6c..a1c7424 100644
--- a/CommandLines.h
+++ b/CommandLines.h
@@ -3,7 +3,7 @@
 
 #include <pthread.h>
 
-#define HA_VERSION "0.3.0-dirty-r178"
+#define HA_VERSION "0.3.0-dirty-r179"
 
 #define VERBOSE 0
 #define VERBOSE_GFA 0
diff --git a/Correct.h b/Correct.h
index 791106a..01f3c1c 100644
--- a/Correct.h
+++ b/Correct.h
@@ -1173,4 +1173,4 @@ long long* max_t_pos, long long* max_q_pos, long long* score, long long* droped)
 #define GAP_EXT_KSW 2
 #define Z_DROP_KSW 400
 #define BAND_KSW 50
-#endif
\ No newline at end of file
+#endif
diff --git a/Hash_Table.cpp b/Hash_Table.cpp
index f209741..b54f868 100644
--- a/Hash_Table.cpp
+++ b/Hash_Table.cpp
@@ -12,6 +12,9 @@ pthread_mutex_t output_mutex;
 #define overlap_region_key(a) ((a).y_id)
 KRADIX_SORT_INIT(overlap_region_sort, overlap_region, overlap_region_key, member_size(overlap_region, y_id))
 
+#define oreg_xs_lt(a, b) (((uint64_t)(a).x_pos_s<<32|(a).x_pos_e) < ((uint64_t)(b).x_pos_s<<32|(b).x_pos_e))
+KSORT_INIT(or_xs, overlap_region, oreg_xs_lt)
+
 void overlap_region_sort_y_id(overlap_region *a, long long n)
 {
 	radix_sort_overlap_region_sort(a, a + n);
@@ -30,6 +33,7 @@ void init_overlap_region_alloc(overlap_region_alloc* list)
         init_window_list_alloc(&(list->list[i].boundary_cigars));
     }
 }
+
 void clear_overlap_region_alloc(overlap_region_alloc* list)
 {
     list->length = 0;
@@ -58,7 +62,6 @@ void destory_overlap_region_alloc(overlap_region_alloc* list)
     free(list->list);
 }
 
-
 int get_fake_gap_pos(Fake_Cigar* x, int index)
 {
     return (x->buffer[index]>>32);
@@ -269,64 +272,6 @@ void append_overlap_region_alloc_debug(overlap_region_alloc* list, overlap_regio
     list->length++;
 }
 
-int cmp_by_x_pos_s(const void * a, const void * b)
-{
-    if ((*(overlap_region*)a).x_pos_s > (*(overlap_region*)b).x_pos_s)
-    {
-        return 1;
-    }
-    else if ((*(overlap_region*)a).x_pos_s < (*(overlap_region*)b).x_pos_s)
-    {
-        return -1;
-    }
-    else
-    {
-
-        if ((*(overlap_region*)a).x_pos_e > (*(overlap_region*)b).x_pos_e)
-        {
-            return 1;
-        }
-        else if ((*(overlap_region*)a).x_pos_e < (*(overlap_region*)b).x_pos_e)
-        {
-            return -1;
-        }
-        else
-        {
-            return 0;
-        }
-        
-    }
-}
-
-int cmp_by_x_pos_e(const void * a, const void * b)
-{
-    if ((*(overlap_region*)a).x_pos_e > (*(overlap_region*)b).x_pos_e)
-    {
-        return 1;
-    }
-    else if ((*(overlap_region*)a).x_pos_e < (*(overlap_region*)b).x_pos_e)
-    {
-        return -1;
-    }
-    else
-    {
-
-        if ((*(overlap_region*)a).x_pos_s > (*(overlap_region*)b).x_pos_s)
-        {
-            return 1;
-        }
-        else if ((*(overlap_region*)a).x_pos_s < (*(overlap_region*)b).x_pos_s)
-        {
-            return -1;
-        }
-        else
-        {
-            return 0;
-        }
-        
-    }
-}
-
 void debug_chain(k_mer_hit* a, long long a_n, Chain_Data* dp)
 {
     long long i, j, current_j;
@@ -709,7 +654,7 @@ void calculate_overlap_region_by_chaining(Candidates_list* candidates, overlap_r
 
     destory_fake_cigar(&(tmp_region.f_cigar));
 
-    qsort(overlap_list->list, overlap_list->length, sizeof(overlap_region), cmp_by_x_pos_s);
+	ks_introsort_or_xs(overlap_list->length, overlap_list->list);
 }
 
 void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
diff --git a/Hash_Table.h b/Hash_Table.h
index bf535c9..fff5945 100644
--- a/Hash_Table.h
+++ b/Hash_Table.h
@@ -80,24 +80,23 @@ typedef struct
 
 typedef struct
 {
-    uint64_t x_id;
+    uint32_t x_id;
     ///the begining and end of the whole overlap
-    uint64_t x_pos_s;
-    uint64_t x_pos_e;
-    uint64_t x_pos_strand;
+    uint32_t x_pos_s;
+    uint32_t x_pos_e;
+    uint32_t x_pos_strand;
 
-    uint64_t y_id;
-    uint64_t y_pos_s;
-    uint64_t y_pos_e;
-    uint64_t y_pos_strand;
+    uint32_t y_id;
+    uint32_t y_pos_s;
+    uint32_t y_pos_e;
+    uint32_t y_pos_strand;
 
-    uint64_t overlapLen;
-    uint64_t shared_seed;
-    uint64_t align_length;
-    ///uint64_t total_errors;
+    uint32_t overlapLen;
+    uint32_t shared_seed;
+    uint32_t align_length;
     uint8_t is_match;
     uint8_t without_large_indel;
-    uint64_t non_homopolymer_errors;
+    uint32_t non_homopolymer_errors;
 
     window_list* w_list;
     uint64_t w_list_size;
@@ -163,7 +162,7 @@ void resize_fake_cigar(Fake_Cigar* x, uint64_t size);
 int get_fake_gap_pos(Fake_Cigar* x, int index);
 int get_fake_gap_shift(Fake_Cigar* x, int index);
 
-inline long long y_start_offset(long long x_start, Fake_Cigar* o)
+static inline long long y_start_offset(long long x_start, Fake_Cigar* o)
 {
     if(x_start == get_fake_gap_pos(o, o->length - 1))
     {
@@ -189,18 +188,6 @@ inline long long y_start_offset(long long x_start, Fake_Cigar* o)
     return get_fake_gap_shift(o, i - 1);
 }
 
-inline void print_fake_gap(Fake_Cigar* o)
-{
-    long long i;
-    for (i = 0; i < (long long)o->length; i++)
-    {
-        fprintf(stderr, "**i: %lld, gap_pos_in_x: %d, gap_shift: %d\n", 
-           i, get_fake_gap_pos(o, i),
-           get_fake_gap_shift(o, i));
-    }
-
-}
-
 void resize_Chain_Data(Chain_Data* x, long long size);
 void init_window_list_alloc(window_list_alloc* x);
 void clear_window_list_alloc(window_list_alloc* x);
diff --git a/Process_Read.h b/Process_Read.h
index aa06c55..e4baf86 100644
--- a/Process_Read.h
+++ b/Process_Read.h
@@ -24,8 +24,6 @@
 #define Get_NAME(R_INF, ID) ((R_INF).name + (R_INF).name_index[(ID)])
 
 
-
-
 extern uint8_t seq_nt6_table[256];
 extern char bit_t_seq_table[256][4];
 extern char bit_t_seq_table_rc[256][4];
@@ -33,7 +31,6 @@ extern char s_H[5];
 extern char rc_Table[5];
 
 
-
 #define RC_CHAR(x) rc_Table[seq_nt6_table[(uint8_t)x]]
 
 void init_aux_table();