实现了kmer index，有效果，但是随着序列扩展到后边，扩展的耗时越来越长

bwt.cpp

@@ -251,9 +251,25 @@ bwtintv_t bwt_search(bwt_t *bwt, const string &q)
     bwtintv_t ik, ok[4];
     int i, c, x = 0;
 
+    //double tt = realtime();
+
     bwt_set_intv(bwt, bval(q[x]), ik);
     ik.info = x + 1;
 
+    for (i = x + 1; i < 12; ++i)
+    {
+        if (bval(q[i]) < 4)
+        {
+            c = cbval(q[i]);
+            bwt_extend(bwt, &ik, ok, 0);
+            ik = ok[c];
+            ik.info = i + 1;
+        }
+    }
+    //t5 += realtime() - tt;
+    x = 11;
+
+    //tt = realtime();
     for (i = x + 1; i < (int)q.size(); ++i)
     {
         if (bval(q[i]) < 4)
@@ -264,6 +280,7 @@ bwtintv_t bwt_search(bwt_t *bwt, const string &q)
             ik.info = i + 1;
         }
     }
+    //t6 += realtime() - tt;
     return ik;
 }
 

fmt_index.cpp

@@ -514,9 +514,28 @@ bwtintv_t fmt_search(FMTIndex *fmt, const string &q)
 	int i, c1, c2, x = 0;
 	int qlen = (int)q.size();
 
+	//double tt = realtime();
 	fmt_set_intv(fmt, bval(q[x]), ik);
 	ik.info = x + 1;
+	for (i = x + 1; i + 1 < 12; i += 2)
+	{
+		if (bval(q[i]) < 4 && bval(q[i + 1]) < 4)
+		{
+			c1 = cbval(q[i]);
+			c2 = cbval(q[i + 1]);
+			fmt_extend2(fmt, &ik, &ok, 0, c1, c2);
+			ik = ok;
+			ik.info = i + 1;
+		}
+		else
+		{
+			break;
+		}
+	}
+	x = 11;
+	//t3 += realtime() - tt;
 
+	//tt = realtime();
 	// 每次扩展两个碱基
 	for (i = x + 1; i + 1 < qlen; i += 2)
 	{
@@ -540,6 +559,7 @@ bwtintv_t fmt_search(FMTIndex *fmt, const string &q)
 		ik = ok;
 		ik.info = i + 1;
 	}
+	//t4 += realtime() - tt;
 	return ik;
 }
 
@@ -638,15 +658,15 @@ bwtintv_t fmt_search_use_kmer(FMTIndex *fmt, const string &q)
 	// 先利用kmer进行索引查询
 	uint32_t qbit = 0;
 	x = min(KMER_LEN, qlen);
-	double tt = realtime();
+	//double tt = realtime();
 	for (i = 0; i < x; ++i)
 	{
 		qbit |= bval(q[i]) << ((KMER_LEN - 1 - i) << 1);
 	}
 	kmer_getval_at(&fmt->kmer_entry[qbit], &ik, x - 1);
-	t1 += realtime() - tt;
+	//t1 += realtime() - tt;
 
-	tt = realtime();
+	//tt = realtime();
 	// 每次扩展两个碱基
 	for (i = x; i + 1 < qlen; i += 2)
 	{
@@ -670,7 +690,7 @@ bwtintv_t fmt_search_use_kmer(FMTIndex *fmt, const string &q)
 		ik = ok;
 		ik.info = i + 1;
 	}
-	t2 += realtime() - tt;
+	//t2 += realtime() - tt;
 	return ik;
 }
 
@@ -778,7 +798,7 @@ int main_fmtidx(int argc, char **argv)
 	// 生成随机序列进行测试
 	int seq_size = 10000000;
 	// int seq_size = 1;
-	int seq_len = 19;
+	int seq_len = 23;
 	vector<string> seq_arr(seq_size);
 	// seq_arr[0] = "GCGATACTAAGA";
 	// seq_arr[0] = "GAGAGCTGTTCCCGTGTTTTCCATGGTTT";
@@ -812,6 +832,8 @@ int main_fmtidx(int argc, char **argv)
 	cout << "[time fmt kmer search:] " << time_fmt_kmer_search << "s" << endl;
 
 	cout << "t1: " << t1 << "s; t2: " << t2 << "s" << endl;
+	cout << "t3: " << t3 << "s; t4: " << t4 << "s" << endl;
+	cout << "t5: " << t5 << "s; t4: " << t6 << "s" << endl;
 
 #endif
 

fmt_index.h

@@ -5,7 +5,7 @@
 #define FMT_OCC_INTERVAL (1LL << FMT_OCC_INTV_SHIFT)
 #define FMT_OCC_INTV_MASK (FMT_OCC_INTERVAL - 1)
 
-#define FMT_MID_INTV_SHIFT 4
+#define FMT_MID_INTV_SHIFT 5
 #define FMT_MID_INTERVAL (1LL << FMT_MID_INTV_SHIFT)
 #define FMT_MID_INTV_MASK (FMT_MID_INTERVAL - 1)
 
@@ -38,7 +38,7 @@
 #define __fmt_mid_sum(x) \
     ((x) >> 24 & 0xff) + ((x) >> 16 & 0xff) + ((x) >> 8 & 0xff) + ((x) & 0xff)
 
-#define KMER_LEN 10
+#define KMER_LEN 12
 #define KMER_ARR_SIZE ((1 << (KMER_LEN << 1)))
 // 用来保存kmer对应的fmt的位置信息
 struct KmerEntry