修正了几个bug，但是目前结果还是不一致，还得继续调试

Makefile

@@ -1,5 +1,5 @@
 CC=			gcc
-CFLAGS=		-g -Wall -Wno-unused-function -mavx2 -mavx512bw #-O3
+CFLAGS=		-g -Wall -Wno-unused-function -mavx2 -mavx512bw -O3
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
 
 SHOW_PERF= -DSHOW_PERF

mate_sw.h

@@ -16,7 +16,8 @@
 
 // 需要做mate sw的read
 typedef struct {
-    int is_rev;  // seq是否在反向互补链上
+    uint8_t is_rev;  // seq是否在反向互补链上
+    uint8_t skip; // 记录任务创建时候的skip状态
     int xtra;
     int64_t rb, re;  // ref的起始截止位置，左闭右开
     int64_t seq_id;  // 对应的当前数据块的seq id

paired_sam.c

@@ -93,7 +93,7 @@ static void get_matesw_tasks(const mem_opt_t* opt, const bntseq_t* bns, const ui
         return;  // consistent pair exist; no need to perform SW
     int task_order = 0;
     for (r = 0; r < 4; ++r) {
-        int is_rev, is_larger;
+        uint8_t is_rev, is_larger;
         int64_t rb, re;  // 左闭右开
         if (skip[r])
             continue;
@@ -124,6 +124,7 @@ static void get_matesw_tasks(const mem_opt_t* opt, const bntseq_t* bns, const ui
             else
                 p = kv_pushp(msw_task_t, *msw16);
             p->is_rev = is_rev;
+            p->skip = skip[0] | skip[1] << 1 | skip[2] << 2 | skip[3] << 3;
             p->xtra = xtra;
             p->rb = rb;
             p->re = re;
@@ -396,64 +397,21 @@ static int check_add_align(kswr_avx_t aln, int min_seed_len, int is_rev, int64_t
 
 #define raw_mapq(diff, a) ((int)(6.02 * (diff) / (a) + .499))
 
-// 最后再计算并生成sam数据
+// 根据比对结果生成sam
-static void workder_gen_sam(void* data, int idx, int tid) {
+void generate_sam(const mem_opt_t* opt, const bntseq_t* bns, const uint8_t* pac, const mem_pestat_t pes[4], uint64_t id, bseq1_t s[2], mem_alnreg_v a[2],
-    mem_worker_t* w = (mem_worker_t*)data;
+             seq_sam_t ss[2], int64_t n_processed, int tid) {
-    const mem_opt_t* opt = w->opt;
-    const bntseq_t* bns = w->bns;
-    const uint8_t* pac = w->pac;
-    const mem_pestat_t *pes = w->pes;
     
-    int startIdx = idx * opt->batch_size;
+    int i, j, z[2], o, subo, n_sub, extra_flag = 1, n_pri[2], n_aa[2];
-    int endIdx = (idx + 1) * opt->batch_size;
+    kstring_t str;
-    if (endIdx > w->n_reads)
-        endIdx = w->n_reads;
-
-    int id = 0, i = 0, j = 0, k = 0;
-
-    for (id = startIdx; id < endIdx; id += 2) {
-        // 初始化变量
-        bseq1_t* s = &w->seqs[id];
-        mem_alnreg_v* a = &w->regs[id];
-        seq_sam_t* ss = &w->sams[id];
-        int z[2], o, subo, n_sub, extra_flag = 1, n_pri[2], n_aa[2];
     mem_aln_t h[2], g[2], aa[2][2];
+
+    // int cmp = strcmp("ERR194147.17699", s[0].name);
+
+    str.l = str.m = 0;
+    str.s = 0;
     memset(h, 0, sizeof(mem_aln_t) * 2);
     memset(g, 0, sizeof(mem_aln_t) * 2);
     n_aa[0] = n_aa[1] = 0;
-
-        int n[2] = {0};
-        for (i = 0; i < 2; ++i) {
-            int si = !i;
-            // 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];
-                // kswr_avx_t aln = t->aln; fprintf(gf[0], "id-%ld score-%d te-%d qe-%d score2-%d te2-%d tb-%d qb-%d\n", s[si].id + w->n_processed, aln.score, aln.te, aln.qe, aln.score2, aln.te2, aln.tb, aln.qb);
-
-                n[i] += check_add_align(t->aln, opt->min_seed_len, t->is_rev, bns->l_pac, &a[!si].a[t->aj], s[si].l_seq, (uint8_t*)s[si].seq, &a[si], t->rb);
-            }
-        }
-        // 处理完2个pair read之后再排序，因为上面操作有插入，排序后之前记录的索引就无效了，所以上面不能排序，要两个pair read处理完之后再排序
-        for (i = 0; i < 2; ++i) {
-            int tmp;
-            if (n[i] > 0) {
-                for (j = 0; j < n[i]; ++j) { // 在这里排序
-                    // move b s.t. ma is sorted
-                    int nidx = a[i].n - n[i] + j;
-                    mem_alnreg_t* b = &a[i].a[nidx];
-                    for (k = 0; k < nidx; ++k)  // find the insertion point
-                        if (a[i].a[k].score < b->score)
-                            break;
-                    tmp = k;
-                    for (k = nidx; k > tmp; --k) a[i].a[k] = a[i].a[k - 1];
-                    a[i].a[k] = *b;
-                }
-
-                a[i].n = mem_sort_dedup_patch(opt, 0, 0, 0, a[i].n, a[i].a);
-            }
-        }
-
-        ////////////////////////////////////////////////////////////
     n_pri[0] = mem_mark_primary_se(opt, a[0].n, a[0].a, id << 1 | 0);
     n_pri[1] = mem_mark_primary_se(opt, a[1].n, a[1].a, id << 1 | 1);
     if (opt->flag & MEM_F_PRIMARY5) {
@@ -543,7 +501,7 @@ static void workder_gen_sam(void* data, int idx, int tid) {
             }
         }
         ss[0].sam.l = 0;
-            //PROF_START(aln2sam);
+        // PROF_START(aln2sam);
         for (i = 0; i < n_aa[0]; ++i) mem_aln2sam(opt, bns, &ss[0].sam, &s[0], n_aa[0], aa[0], i, &h[1]);  // write read1 hits
         ss[1].sam.l = 0;
         for (i = 0; i < n_aa[1]; ++i) mem_aln2sam(opt, bns, &ss[1].sam, &s[1], n_aa[1], aa[1], i, &h[0]);  // write read2 hits
@@ -561,7 +519,9 @@ static void workder_gen_sam(void* data, int idx, int tid) {
     } else
         goto no_pairing;
 
-    no_pairing:
+    goto end_clear;
+
+no_pairing:
     for (i = 0; i < 2; ++i) {
         int which = -1;
         if (a[i].n) {
@@ -590,11 +550,87 @@ static void workder_gen_sam(void* data, int idx, int tid) {
     free(h[0].cigar);
     free(h[1].cigar);
 
+end_clear:
     _destory_clear_vec(s[0].msw);
     _destory_clear_vec(s[1].msw);
 
     free(a[0].a);
     free(a[1].a);
+}
+
+// 最后再计算并生成sam数据
+static void workder_gen_sam(void* data, int idx, int tid) {
+    mem_worker_t* w = (mem_worker_t*)data;
+    const mem_opt_t* opt = w->opt;
+    const bntseq_t* bns = w->bns;
+    const uint8_t* pac = w->pac;
+    const mem_pestat_t *pes = w->pes;
+
+    int startIdx = idx * opt->batch_size;
+    int endIdx = (idx + 1) * opt->batch_size;
+    if (endIdx > w->n_reads)
+        endIdx = w->n_reads;
+
+    int id = 0, i = 0, j = 0, k = 0;
+
+    for (id = startIdx; id < endIdx; id += 2) {
+        // 初始化变量
+        bseq1_t* s = &w->seqs[id];
+        mem_alnreg_v* a = &w->regs[id];
+        seq_sam_t* ss = &w->sams[id];
+
+        // int cmp = strcmp("ERR194147.1548", s[0].name);
+
+        int n[2] = {0}, nn[2] = {0};
+        for (i = 0; i < 2; ++i) {
+            int si = !i;
+            int origin_n = a[si].n;
+            // 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];
+                mem_alnreg_t* b = &a[i].a[t->aj];
+                mem_alnreg_v* ma = &a[si];
+                uint8_t skip = 0;
+                if (n[si]) {  // 添加了新的aln，需要检测skip
+                    for (j = origin_n; j < ma->n; ++j) {  // check which orinentation has been found
+                        int64_t dist;
+                        int r;
+                        r = mem_infer_dir(bns->l_pac, b->rb, ma->a[j].rb, &dist);
+                        if (dist >= pes[r].low && dist <= pes[r].high)
+                            skip |= 1 << r;
+                    }
+                }
+                if ((t->skip | skip) != 15)  { // 检查新添加的aln是不是把当前的任务skip掉了
+                    kswr_avx_t aln = t->aln; fprintf(gf[0], "id-%ld score-%d te-%d qe-%d score2-%d te2-%d tb-%d qb-%d\n", s[si].id +
+                    w->n_processed, aln.score, aln.te, aln.qe, aln.score2, aln.te2, aln.tb, aln.qb);
+                    nn[si] += 1;
+                    n[si] += check_add_align(t->aln, opt->min_seed_len, t->is_rev, bns->l_pac, b, s[si].l_seq, (uint8_t*)s[si].seq, ma, t->rb);
+                }
+            }
+        }
+        // 处理完2个pair read之后再排序，因为上面操作有插入，排序后之前记录的索引就无效了，所以上面不能排序，要两个pair read处理完之后再排序
+        for (i = 0; i < 2; ++i) {
+            int tmp;
+            if (nn[i] > 0) {
+                for (j = 0; j < n[i]; ++j) { // 在这里排序
+                    // move b s.t. ma is sorted
+                    int nidx = a[i].n - n[i] + j;
+                    mem_alnreg_t b = a[i].a[nidx]; // 用指针一定要慎重，注意指向的地址内容会变
+                    for (k = 0; k < nidx; ++k)  // find the insertion point
+                        if (a[i].a[k].score < b.score)
+                            break;
+                    tmp = k;
+                    for (k = nidx; k > tmp; --k) a[i].a[k] = a[i].a[k - 1];
+                    a[i].a[k] = b;
+                }
+
+                a[i].n = mem_sort_dedup_patch(opt, 0, 0, 0, a[i].n, a[i].a);
+            }
+        }
+
+        ////////////////////////////////////////////////////////////
+
+        generate_sam(opt, bns, pac, pes, id >> 1, s, a, ss, w->n_processed, tid);
     }
 }
 

run.sh

@@ -1,6 +1,6 @@
-thread=64
+thread=1
 
-make -j 16
+make clean; make -j 32
 
 n1=~/data/dataset/D2/n1.fq.gz
 n2=~/data/dataset/D2/n2.fq.gz
@@ -11,7 +11,7 @@ n2=~/data/dataset/D2/n2.fq.gz
 reference=~/data/reference/fmt/human_g1k_v37_decoy.fasta
 
 out=/dev/null
-#out=~/data/D2-out.sam
+#out=./oldsam-D2-out.sam
 prog=./fastalign
 #prog=/home/zzh/fastbwa