添加了直接扩展两个碱基的函数

.vscode/launch.json

@@ -18,8 +18,8 @@
                 "-R",
                 "'@RG\\tID:normal\\tSM:normal\\tPL:illumina\\tLB:normal\\tPG:bwa'",
                 "~/reference/human_g1k_v37_decoy.fasta",
-                "~/fastq/ssn_r1.fq",
+                "~/data/fastq/ds/d1_1.fq",
-                "~/fastq/ssn_r2.fq",
+                "~/data/fastq/ds/d1_2.fq",
                 "-o",
                 "/dev/null"
             ],

bwamem.c

@@ -1407,6 +1407,10 @@ static void mem_collect_intv_batch(const mem_opt_t *opt, const FMTIndex *fmt, in
 	tmp_time = realtime_msec();
 #endif
 
+	s2n += 1;
+	if (max_seed_len == len - start_N_num)
+		s1n += 1;
+		
 #ifdef FILTER_FULL_MATCH
 	if (max_seed_len == len - start_N_num) goto collect_intv_end;
 #endif

fastmap.c

@@ -458,6 +458,7 @@ int main_mem(int argc, char *argv[])
 	fprintf(stderr, "time_seed_3: %f s\n", avg_seed_3 / 1000.0 / opt->n_threads);
 	fprintf(stderr, "time_bwt_sa: %f s\n", avg_sa / 1000.0 / opt->n_threads);
 	fprintf(stderr, "time_bsw: %f s\n", avg_bsw / 1000.0 / opt->n_threads);
+	fprintf(stderr, "full_match: %ld, all: %ld\n", s1n, s2n);
 	fprintf(stderr, "\n");
 
 	fclose(gfp1);

fmt_idx.c

@@ -669,18 +669,117 @@ static inline void fmt_reverse_intvs(bwtintv_v *p)
     }
 }
 
+int fmt_smem_forward(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv, int min_seed_len, bwtintv_v *mem)
+{
+    int i, ret, kmer_len;
+    bwtintv_t ik = {0}, ok1 = {0}, ok2 = {0};
+    bwtintv_t mt = {0};
+    uint32_t qbit = 0;
+    mem->n = 0;
+    if (q[x] > 3) return x + 1;
+
+    if (min_intv < 1) min_intv = 1; // the interval size should be at least 1
+
+    qbit = build_forward_kmer(&q[x], len - x, HASH_KMER_LEN, &kmer_len);
+    bwt_kmer_get(&fmt->kmer_hash, &ik, qbit, kmer_len-1); // 初始碱基位置
+    ik.info = x + kmer_len;
+
+// check change of the interval size and whether the interval size is too small to be extended further
+#define PUSH_VAL_AND_SKIP_FORWARD(iv)         \
+    do                                \
+    {                                 \
+        kv_push(bwtintv_t, *mem, iv); \
+        goto fmt_smem_forward_end;    \
+    } while (0)
+
+    if (kmer_len != HASH_KMER_LEN) // 遇到了N或者到了序列最后
+        PUSH_VAL_AND_SKIP_FORWARD(ik);
+
+    // 扩展kmer之后的碱基
+    //    __builtin_prefetch(fmt_occ_intv(fmt, ik.x[1] - 1), 0, 2);
+    //    __builtin_prefetch(fmt_occ_intv(fmt, ik.x[1] - 1 + ik.x[2]), 0, 2);
+    for (i = (int)ik.info; i + 1 < len; i += 2)
+    { // forward search
+        if (q[i] < 4 && q[i + 1] < 4)
+        {
+            fmt_extend2(fmt, &ik, &ok1, &ok2, 0, 3 - q[i], 3 - q[i + 1]);
+            __builtin_prefetch(fmt_occ_intv(fmt, ok2.x[1] - 1), 0, 2);
+            __builtin_prefetch(fmt_occ_intv(fmt, ok2.x[1] - 1 + ok2.x[2]), 0, 2);
+#if 1
+            if (min_intv == 1 && ok2.x[2] == min_intv)
+            {
+                direct_extend(fmt, len, q, x, i + 2, ok2.x[0], &mt);
+                kv_push(bwtintv_t, *mem, mt);
+                ret = (uint32_t)mt.info;
+                goto fmt_smem_forward_end;
+            }
+#endif
+            if (ok2.x[2] < min_intv) {
+                if (ok1.x[2] < min_intv) {
+                    PUSH_VAL_AND_SKIP_FORWARD(ik);
+                } else {
+                    ok1.info = i + 1;
+                    PUSH_VAL_AND_SKIP_FORWARD(ok1);
+                }
+            } else {
+                ik = ok2;
+                ik.info = i + 2;
+            }
+        }
+        else if (q[i] < 4) // q[i+1] >= 4
+        {
+            fmt_extend1(fmt, &ik, &ok1, 0, 3 - q[i]);
+            if (ok1.x[2] < min_intv) {
+                PUSH_VAL_AND_SKIP_FORWARD(ik);
+            } else {
+                ok1.info = i + 1;
+                PUSH_VAL_AND_SKIP_FORWARD(ok1);
+            }
+        }
+        else // q[i] >= 4
+        {
+            PUSH_VAL_AND_SKIP_FORWARD(ik);
+        }
+    }
+    for (; i == len - 1; ++i) // 扩展到了最后一个碱基
+    {
+        if (q[i] < 4)
+        {
+            fmt_extend1(fmt, &ik, &ok1, 0, 3 - q[i]);
+            if (ok1.x[2] < min_intv) {
+                PUSH_VAL_AND_SKIP_FORWARD(ik);
+            } else {
+                ok1.info = i + 1;
+                PUSH_VAL_AND_SKIP_FORWARD(ok1);
+            }
+        }
+        else
+            PUSH_VAL_AND_SKIP_FORWARD(ik);
+    }
+
+fmt_smem_forward_end:
+    if (mem->n == 0)
+        kv_push(bwtintv_t, *mem, ik);
+    ret = mem->a[0].info;
+    mem->a[0].info |= (uint64_t)(x) << 32;
+    if (mt.num_match == 0)
+        ret = (uint32_t)mem->a[0].info; // this will be the returned value，扩展到的最远的位置
+    return ret;
+}
+
 // 找smem（seed）
 int fmt_smem(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv, int min_seed_len, bwtintv_v *mem, bwtintv_v *tmpvec)
 {
+    if (x == 0 || q[x - 1] > 3)
+        return fmt_smem_forward(fmt, len, q, x, min_intv, min_seed_len, mem);
+
     int i, j, ret, kmer_len;
     bwtintv_t ik = {0}, ok1 = {0}, ok2 = {0};
     bwtintv_t mt = {0};
     bwtintv_v *curr;
     uint32_t qbit = 0;
     mem->n = 0;
-    int only_forward = x == 0 || q[x - 1] > 3;
+    if (q[x] > 3) return x + 1;
-    if (q[x] > 3)
-        return x + 1;
 
     if (min_intv < 1)
         min_intv = 1; // the interval size should be at least 1
@@ -708,11 +807,7 @@ int fmt_smem(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv
     } while (0)
 
     // 处理kmer对应的匹配信息
-    if (only_forward)
+    for (curr->n = 0, j = 1; j < kmer_len; ++j)
-        j = kmer_len - 1;
-    else
-        j = 1;
-    for (curr->n = 0; j < kmer_len; ++j)
     {
         bwt_kmer_get(&fmt->kmer_hash, &ok1, qbit, j);
         CHECK_INTV_CHANGE(ik, ok1, x + j + 1);
@@ -739,7 +834,7 @@ int fmt_smem(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv
                 direct_extend(fmt, len, q, x, i + 2, ok2.x[0], &mt);
                 kv_push(bwtintv_t, *mem, mt);
                 ret = (uint32_t)mt.info;
-                if (only_forward || mt.rm[0].qs == 0 || q[mt.rm[0].qs - 1] > 3)
+                if (mt.rm[0].qs == 0 || q[mt.rm[0].qs - 1] > 3)
                     goto fmt_smem_end;
                 goto backward_search;
             }
@@ -793,9 +888,9 @@ backward_search:
     for (j = 0; j < curr->n; ++j)
     {
         bwtintv_t *p = &curr->a[j]; // 前向扩展的种子
-                                    //        __builtin_prefetch(fmt_occ_intv(fmt, p->x[0] - 1), 0, 2);
+        // __builtin_prefetch(fmt_occ_intv(fmt, p->x[0] - 1), 0, 2);
-                                    //        __builtin_prefetch(fmt_occ_intv(fmt, p->x[0] - 1 + p->x[2]), 0, 2);
+        // __builtin_prefetch(fmt_occ_intv(fmt, p->x[0] - 1 + p->x[2]), 0, 2);
-        if (!only_forward && p->info - x < HASH_KMER_LEN)
+        if (p->info - x < HASH_KMER_LEN)
         {
             if (last_kmer_start && kmer_len == HASH_KMER_LEN && p->info == last_kmer_start && p->info - kmer_len > 0 && q[p->info - kmer_len] < 4)
                 qbit = ((qbit << 2) | (3 - q[p->info - kmer_len])) & ((1L << (kmer_len << 1)) - 1); // 创建反向kmer

run.sh

@@ -1,10 +1,24 @@
-thread=32
+thread=1
+#n_r1=~/data/fastq/zy/wgs/n1.fq
+#n_r2=~/data/fastq/zy/wgs/n2.fq
+#n_r1=~/data/fastq/ds/n1.fq
+#n_r2=~/data/fastq/ds/n2.fq
+#n_r1=~/data/fastq/platinum/n1.fq
+#n_r2=~/data/fastq/platinum/n2.fq
+#n_r1=~/data/fastq/zy/t1.fq
+#n_r2=~/data/fastq/zy/t2.fq
+n_r1=~/data/fastq/zy/n1.fq
+n_r2=~/data/fastq/zy/n2.fq
+#n_r1=~/data/fastq/ds/d1_1.fq
+#n_r2=~/data/fastq/ds/d1_2.fq
+#n_r1=~/data/fastq/ds/wes/n1.fq
+#n_r2=~/data/fastq/ds/wes/n2.fq
 #n_r1=~/fastq/ZY2105177532213010_L4_1.fq
 #n_r2=~/fastq/ZY2105177532213010_L4_2.fq
-#n_r1=~/fastq/na12878/nas_1.fq
+#n_r1=~/data/fastq/na12878/nas_1.fq
-#n_r2=~/fastq/na12878/nas_2.fq
+#n_r2=~/data/fastq/na12878/nas_2.fq
-n_r1=~/data/fastq/na12878/na_1.fq
+#n_r1=~/data/fastq/na12878/na_1.fq
-n_r2=~/data/fastq/na12878/na_2.fq
+#n_r2=~/data/fastq/na12878/na_2.fq
 #n_r1=~/fastq/na12878/na12878_r1.fq
 #n_r2=~/fastq/na12878/na12878_r2.fq
 #n_r1=~/fastq/n_r1.fq
@@ -14,10 +28,10 @@ n_r2=~/data/fastq/na12878/na_2.fq
 #n_r1=~/data/fastq/ZY2105177532213000/sn_r1.fq
 #n_r2=~/data/fastq/ZY2105177532213000/sn_r2.fq
 #reference=~/data/reference/human_g1k_v37_decoy.fasta
-#n_r1=~/fastq/sn_r1.fq
+#n_r1=~/data/fastq/sn_r1.fq
-#n_r2=~/fastq/sn_r2.fq
+#n_r2=~/data/fastq/sn_r2.fq
-#n_r1=~/fastq/ssn_r1.fq
+#n_r1=~/data/fastq/ssn_r1.fq
-#n_r2=~/fastq/ssn_r2.fq
+#n_r2=~/data/fastq/ssn_r2.fq
 #n_r1=~/fastq/ERR194147_1_120w.fastq
 #n_r2=~/fastq/ERR194147_2_120w.fastq
 #n_r1=~/fastq/tiny_n_r1.fq