diff --git a/mate_sw.c b/mate_sw.c
index 285c9e7..6a1891a 100644
--- a/mate_sw.c
+++ b/mate_sw.c
@@ -3,10 +3,15 @@
 
 // 初始化mate sw计算相关的数据
 void init_msw_data(msw_data_t* msw, int n_threads, int msw_batch_size) {
+#define _alloc_msw_num(data, num, data_type) ((data) = calloc(num, sizeof(data_type)))
 #define _alloc_msw(data, data_type) ((data) = calloc(n_threads, sizeof(data_type)))
+    int i = 0, j = 0;
+
+    _alloc_msw(msw->t_msw_tasks, msw_task_v*);
+    for (i = 0; i < n_threads; ++i) {
+        _alloc_msw_num(msw->t_msw_tasks[i], 2, msw_task_v);
+    }
 
-    _alloc_msw(msw->t_msw_tasks_u8, msw_task_v);
-    _alloc_msw(msw->t_msw_tasks_i16, msw_task_v);
     _alloc_msw(msw->t_msw_buf, msw_buf_t);
     _alloc_msw(msw->t_msw_stats, msw_stats_t);
     _alloc_msw(msw->t_msw_ref_buf, byte_vv);
@@ -23,7 +28,6 @@ void init_msw_data(msw_data_t* msw, int n_threads, int msw_batch_size) {
     _alloc_msw(msw->t_msw_2_kswrs, msw_kswr_v);
 
     // 初始化缓存空间
-    int i = 0, j = 0;
     msw_ref_t init_ref = {0};
     msw_seq_t init_seq = {0};
     kswr_avx_t init_kswr = {0};
diff --git a/mate_sw.h b/mate_sw.h
index 30a4a42..47932c5 100644
--- a/mate_sw.h
+++ b/mate_sw.h
@@ -34,8 +34,8 @@ typedef kvec_t(msw_task_t*) msw_task_ptr_v;
 
 // 每个seq保留task所在的线程，和数组idx
 typedef struct {
-    int arr_idx; // 是u8还是i16
     int thread_idx; // 在哪个线程
+    int arr_idx;    // 是u8还是i16
     int task_idx; // 数组内的索引
 } msw_seq_task_t;
 
@@ -73,9 +73,8 @@ typedef kvec_t(kswr_avx_t) msw_kswr_v;
 
 // mate sw相关的所有数据
 typedef struct {
-    msw_task_v* t_msw_tasks_u8;  // 线程内收集需要做mate sw的任务的数据
-    msw_task_v* t_msw_tasks_i16;
-    msw_task_ptr_v p_msw_tasks_u8; // 线程共享的mate sw task指针
+    msw_task_v** t_msw_tasks;       // 0是u8, 1是i16，线程内收集需要做mate sw的任务的数据
+    msw_task_ptr_v p_msw_tasks_u8;  // 线程共享的mate sw task指针
     msw_task_ptr_v p_msw_tasks_i16;
     msw_buf_t* t_msw_buf; // 每个线程一个，mate sw 缓存
     msw_stats_t* t_msw_stats; // 每个线程一个，统计信息
diff --git a/paired_sam.c b/paired_sam.c
index 9464733..60ac32d 100644
--- a/paired_sam.c
+++ b/paired_sam.c
@@ -77,7 +77,7 @@ static inline void revseq(int l, uint8_t* s) {
 
 // 计算当前seq是否需要做matesw，需要的话保存必要的数据
 static void get_matesw_tasks(const mem_opt_t* opt, const bntseq_t* bns, const uint8_t* pac, const mem_pestat_t pes[4], const mem_alnreg_t* a, int a_j,
-                            bseq1_t* seq, mem_alnreg_v* ma, int64_t sid, msw_stats_t* stats, msw_task_v* msw8, msw_task_v* msw16, int64_t n_processed, int tid) {
+                            bseq1_t* seq, mem_alnreg_v* ma, int64_t sid, msw_stats_t* stats, msw_task_v* msw_tasks, int64_t n_processed, int tid) {
     int64_t l_pac = bns->l_pac;
     int l_ms = seq->l_seq;
     int i, r, skip[4], rid;
@@ -119,10 +119,11 @@ static void get_matesw_tasks(const mem_opt_t* opt, const bntseq_t* bns, const ui
             // fprintf(stderr, "zzh here\n");
             int xtra = KSW_XSUBO | KSW_XSTART | (l_ms * opt->a < 250 ? KSW_XBYTE : 0) | (opt->min_seed_len * opt->a);
             msw_task_t* p;
-            if ((xtra & KSW_XBYTE))
-                p = kv_pushp(msw_task_t, *msw8);
-            else
-                p = kv_pushp(msw_task_t, *msw16);
+            int msw_idx = 0; // u8
+            if (!(xtra & KSW_XBYTE))
+                msw_idx = 1; // i16
+            msw_task_v* task_arr = &msw_tasks[msw_idx];
+            p = kv_pushp(msw_task_t, *task_arr);
             p->is_rev = is_rev;
             p->skip = skip[0] | skip[1] << 1 | skip[2] << 2 | skip[3] << 3;
             p->xtra = xtra;
@@ -132,10 +133,9 @@ static void get_matesw_tasks(const mem_opt_t* opt, const bntseq_t* bns, const ui
             p->aj = a_j;
             p->to = task_order++; // 有啥用？ 应该是用来合并u8和i16的时候排序用
 
-            msw_seq_task_t seq_task = {0, tid, msw8->n - 1};
+            msw_seq_task_t seq_task = {tid, msw_idx, task_arr->n - 1};
             kv_push(msw_seq_task_t, seq->msw_task, seq_task);
-            // kv_push(msw_task_t*, seq->msw, p);  // 将matesw任务和对应的seq关联起来，这里放指针是不行的，因为指针位置会变，要保存offset才行
-            // kv_push(int, seq->msw, msw8->n - 1); // 这里需要考虑i16, 本线程的msw的offset
+            // 将matesw任务和对应的seq关联起来，这里放指针是不行的，因为指针位置会变，要保存offset才行
         }
     }
 }
@@ -155,6 +155,7 @@ static void worker_matesw_tasks(void* data, int idx, int tid) {
     kv_init(aj[1]);
     kv_init(b[0]);
     kv_init(b[1]);
+    
     for (id = startIdx; id < endIdx; id += 2) {
         int64_t i_s = id;
         bseq1_t* s = &w->seqs[i_s];
@@ -176,7 +177,7 @@ static void worker_matesw_tasks(void* data, int idx, int tid) {
         for (i = 0; i < 2; ++i)
             for (j = 0; j < b[i].n && j < opt->max_matesw; ++j)
                 get_matesw_tasks(opt, w->bns, w->pac, w->pes, &b[i].a[j], aj[i].a[j], &s[!i], &a[!i], i_s + !i, &w->msw->t_msw_stats[tid],
-                                &w->msw->t_msw_tasks_u8[tid], &w->msw->t_msw_tasks_i16[tid], w->n_processed, tid);
+                                 w->msw->t_msw_tasks[tid], w->n_processed, tid);
     }
     free(b[0].a);
     free(b[1].a);
@@ -559,9 +560,8 @@ no_pairing:
     free(h[1].cigar);
 
 end_clear:
-    //_destory_clear_vec(s[0].msw);
-    //_destory_clear_vec(s[1].msw);
 
+// 清理seq相关的内存空间
     _destory_clear_vec(s[0].msw_task);
     _destory_clear_vec(s[1].msw_task);
 
@@ -612,14 +612,13 @@ static void workder_gen_sam(void* data, int idx, int tid) {
 #ifdef SAM_EXACT
         _clear_vec(bb[0]);
         _clear_vec(bb[1]);
-        for (i = 0; i < 2; ++i)
-            //for (j = 0; j < s[!i].msw.n; ++j) {
-            //    msw_task_t* t = s[!i].msw.a[j];
+        for (i = 0; i < 2; ++i) {
             for (k = 0; k < s[!i].msw_task.n; ++k) {
                 msw_seq_task_t st = s[!i].msw_task.a[k];
-                msw_task_t* t = &w->msw->t_msw_tasks_u8[st.thread_idx].a[st.task_idx];
+                msw_task_t* t = &w->msw->t_msw_tasks[st.thread_idx][st.arr_idx].a[st.task_idx];
                 kv_push(mem_alnreg_t, bb[i], a[i].a[t->aj]);
             }
+        }
 #endif
 
         for (i = 0; i < 2; ++i) {
@@ -627,12 +626,10 @@ static void workder_gen_sam(void* data, int idx, int tid) {
 #ifndef SAM_EXACT
             int origin_n = a[si].n;
 #endif
-            // 这里应该先给task排序，因为u8和i16是分开排序的，需要合在一起
-            //for (k = 0; k < s[si].msw.n; ++k) {
-            //    msw_task_t* t = s[si].msw.a[k];
+            // 这里应该先给task排序，因为u8和i16是分开排序的，需要合在一起，不用了，添加task的时候已经排序过了
             for (k = 0; k < s[si].msw_task.n; ++k) {
                 msw_seq_task_t st = s[si].msw_task.a[k];
-                msw_task_t* t = &w->msw->t_msw_tasks_u8[st.thread_idx].a[st.task_idx];
+                msw_task_t* t = &w->msw->t_msw_tasks[st.thread_idx][st.arr_idx].a[st.task_idx];
 #ifdef SAM_EXACT
                 mem_alnreg_t* b = &bb[i].a[k];
 #else
@@ -691,14 +688,18 @@ static void workder_gen_sam(void* data, int idx, int tid) {
 }
 
 // 划分matesw任务
-static void gather_matesw_task(mem_worker_t* w, msw_task_v* thread_tasks, msw_task_ptr_v* tasks) {
-    _clear_vec(*tasks);
+static void gather_matesw_task(mem_worker_t* w, msw_task_v** thread_tasks) {
+    _clear_vec(w->msw->p_msw_tasks_u8);
+    _clear_vec(w->msw->p_msw_tasks_i16);
     int i = 0, j = 0;
     for (i = 0; i < w->opt->n_threads; ++i) {
-        for (j = 0; j < thread_tasks[i].n; ++j) {
-            msw_task_t* tp = &thread_tasks[i].a[j];
-            kv_push(msw_task_t*, *tasks, tp);
-            // kv_push(msw_task_t*, w->seqs[tp->seq_id].msw, tp);
+        for (j = 0; j < thread_tasks[i][0].n; ++j) {
+            msw_task_t* tp = &thread_tasks[i][0].a[j];
+            kv_push(msw_task_t*, w->msw->p_msw_tasks_u8, tp);
+        }
+        for (j = 0; j < thread_tasks[i][1].n; ++j) {
+            msw_task_t* tp = &thread_tasks[i][1].a[j];
+            kv_push(msw_task_t*, w->msw->p_msw_tasks_i16, tp);
         }
     }
 }
@@ -749,14 +750,15 @@ static void alloc_update_cache_avx512(mem_worker_t* w) {
 
 // 针对pair end数据，生成sam的过程
 void gen_paired_sam(mem_worker_t* w) {
-    int i = 0;
-    for (i = 0; i < w->opt->n_threads; ++i) {
-        w->msw->t_msw_tasks_u8[i].n = 0; // 清空之前的数据
-        w->msw->t_msw_tasks_i16[i].n = 0;
-    }
     if (w->opt->flag & MEM_F_NO_RESCUE) {
         kt_for(w->opt->n_threads, worker_sam, w, w->n_reads >> 1);  // generate alignment
     } else {
+        // 清空一下任务数组，不能放到线程里去做
+        int i = 0;
+        for (i = 0; i < w->opt->n_threads; ++i) {
+            _clear_vec(w->msw->t_msw_tasks[i][0]);
+            _clear_vec(w->msw->t_msw_tasks[i][1]);
+        }
         int batch_n = (w->n_reads + w->opt->batch_size - 1) / w->opt->batch_size;
 
         // 1. 计算哪些read需要matesw
@@ -773,17 +775,20 @@ void gen_paired_sam(mem_worker_t* w) {
 
         // 2. 收集每个线程中的msw任务
         PROF_START(gather_matesw_task);
-        gather_matesw_task(w, w->msw->t_msw_tasks_u8, &w->msw->p_msw_tasks_u8);
-        gather_matesw_task(w, w->msw->t_msw_tasks_i16, &w->msw->p_msw_tasks_i16);
+        gather_matesw_task(w, w->msw->t_msw_tasks);
         PROF_END(gprof[G_gather_matesw_task], gather_matesw_task);
         
         PROF_START(calc_matesw);
-        int msw_batch_n = (w->msw->p_msw_tasks_u8.n + w->opt->msw_batch_size - 1) / w->opt->msw_batch_size;
+        int msw_batch_n = 0;
         // 3. 处理msw任务
-        if (w->msw->p_msw_tasks_u8.n > 0)
+        if (w->msw->p_msw_tasks_u8.n > 0) {
+            msw_batch_n = (w->msw->p_msw_tasks_u8.n + w->opt->msw_batch_size - 1) / w->opt->msw_batch_size;
             kt_for(w->opt->n_threads, worker_calc_matesw_avx512_u8, w, msw_batch_n);
-        if (w->msw->p_msw_tasks_i16.n > 0)
+        }
+        if (w->msw->p_msw_tasks_i16.n > 0) {
+            msw_batch_n = (w->msw->p_msw_tasks_i16.n + w->opt->msw_batch_size - 1) / w->opt->msw_batch_size;
             kt_for(w->opt->n_threads, worker_calc_matesw_avx512_i16, w, msw_batch_n);
+        }
         PROF_END(gprof[G_calc_matesw], calc_matesw);
         
         // 4. 生成sam
@@ -791,5 +796,5 @@ void gen_paired_sam(mem_worker_t* w) {
         kt_for(w->opt->n_threads, workder_gen_sam, w, batch_n);
         PROF_END(gprof[G_gen_sam], gen_sam);
     }
-    fprintf(stderr, "zzh %d : 8: %ld 16: %ld\n", i, w->msw->p_msw_tasks_u8.n, w->msw->p_msw_tasks_i16.n);
+    fprintf(stderr, "zzh : u8: %ld i16: %ld\n",  w->msw->p_msw_tasks_u8.n, w->msw->p_msw_tasks_i16.n);
 }
\ No newline at end of file
diff --git a/run.sh b/run.sh
index fd7d398..eba86de 100755
--- a/run.sh
+++ b/run.sh
@@ -1,11 +1,11 @@
-thread=64
+thread=1
 
 make clean; make -j 32
 
-n1=~/data/dataset/D2/n1.fq.gz
-n2=~/data/dataset/D2/n2.fq.gz
-#n1=~/data/dataset/D2/d1.fq
-#n2=~/data/dataset/D2/d2.fq
+#n1=~/data/dataset/D2/n1.fq.gz
+#n2=~/data/dataset/D2/n2.fq.gz
+n1=~/data/dataset/D2/d1.fq
+n2=~/data/dataset/D2/d2.fq
 
 #n1=~/data/SRR25735656_1.fastq.gz
 #n2=~/data/SRR25735656_2.fastq.gz
@@ -17,8 +17,8 @@ reference=~/data/reference/fmt/human_g1k_v37_decoy.fasta
 
 #out=/dev/null
 #out=./oldsam-D2-out.sam
-out=./D2-1.sam
-#out=./d.sam
+#out=./D2-1.sam
+out=./d.sam
 prog=./fastalign
 #prog=/home/zzh/fastbwa