验证了fmt-index的正确性，用两种方式进行了实现，第二种记录b1和b2的occ以及大于他们的碱基的occ，更快一些

.vscode/launch.json

@@ -10,7 +10,7 @@
             "request": "launch",
             "program": "${workspaceRoot}/fmtidx",
             "args": [
-                "/home/zzh/data/reference/human_g1k_v37_decoy.fasta.bwt"
+                "/mnt/d/data/reference/human_g1k_v37_decoy.fasta"
             ],
             "cwd": "${workspaceFolder}", // 当前工作路径：当前文件所在的工作空间
         }

Makefile

@@ -1,7 +1,7 @@
 CC=			g++
 NOWARN=     -Wno-unused-result -Wno-unused-function
 CFLAGS=		#-g -Wall $(NOWARN) #-O2
-CPPFLAGS=   -g -Wall $(NOWARN) -O2
+CPPFLAGS=   -g -Wall $(NOWARN) -O3
 WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
 SHOW_PERF=  -DSHOW_PERF
 AR=			ar

bwt.cpp

@@ -150,9 +150,11 @@ void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
     }
     k -= (k >= bwt->primary); // because $ is not in bwt
     p = bwt_occ_intv(bwt, k);
+    // cout << "occ: " << p[0] << ' ' << p[1] << ' ' << p[2] << ' ' << p[3] << endl;
     memcpy(cnt, p, 4 * sizeof(bwtint_t));
     p += sizeof(bwtint_t);                              // sizeof(bwtint_t) = 4*(sizeof(bwtint_t)/sizeof(uint32_t))
     end = p + ((k >> 4) - ((k & ~OCC_INTV_MASK) >> 4)); // this is the end point of the following loop
+    //end = p + 1;
     for (x = 0; p < end; ++p)
         x += __occ_aux4(bwt, *p);
     tmp = *p & ~((1U << ((~k & 15) << 1)) - 1);
@@ -167,6 +169,9 @@ void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
 void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4])
 {
     // double tm_t = realtime();
+    bwt_occ4(bwt, k, cntk);
+    bwt_occ4(bwt, l, cntl);
+    return;
     bwtint_t _k, _l;
     _k = k - (k >= bwt->primary);
     _l = l - (l >= bwt->primary);
@@ -235,13 +240,13 @@ void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_b
 void bwt_search(bwt_t *bwt, const string &q)
 {
     bwtintv_t ik, ok[4];
-    int i, j, c, x = 0;
+    int i, c, x = 0;
 
     bwt_set_intv(bwt, bval(q[x]), ik);
     ik.info = x + 1;
     // cout << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl;
 
-    for (i = x + 1; i < q.size(); ++i)
+    for (i = x + 1; i < (int)q.size(); ++i)
     {
         if (bval(q[i]) < 4)
         {
@@ -255,48 +260,71 @@ void bwt_search(bwt_t *bwt, const string &q)
 }
 
 // 扩展两次
-void bwt_extend2(const bwt_t *bwt, bwtintv_t *ik, bwtintv_t ok[4], int is_back, int c1)
+void bwt_extend2(const bwt_t *bwt, bwtintv_t *ik, bwtintv_t ok[4], int is_back, int c1, int c2)
 {
     bwtint_t tk[4], tl[4];
+    bwtint_t interval = 0;
     int i;
     bwt_2occ4(bwt, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], tk, tl); // tk表示在k行之前所有各个碱基累积出现次数，tl表示在l行之前的累积
+    //for (i = 3; i > c1; --i)
+    //{
+    //    interval += tl[i] - tk[i];
+    //}
+    //cout << "interval-1: " << interval << endl;
+
     // 这里是反向扩展
     for (i = 0; i != 4; ++i)
     {
         ok[i].x[!is_back] = bwt->L2[i] + 1 + tk[i]; // 起始行位置，互补链
         ok[i].x[2] = tl[i] - tk[i];                 // 间隔
     }
+    // ok[c1].x[!is_back] = bwt->L2[c1] + 1 + tk[c1]; // 起始行位置，互补链
+    // ok[c1].x[2] = tl[c1] - tk[c1];                 // 间隔
+    // 因为计算的是互补碱基，所以3对应着0,2对应1，下边是正向扩展
+    ok[3].x[is_back] = ik->x[is_back] + (ik->x[!is_back] <= bwt->primary && ik->x[!is_back] + ik->x[2] - 1 >= bwt->primary);
+    ok[2].x[is_back] = ok[3].x[is_back] + ok[3].x[2];
+    ok[1].x[is_back] = ok[2].x[is_back] + ok[2].x[2];
+    ok[0].x[is_back] = ok[1].x[is_back] + ok[1].x[2];
+    //cout << (ik->x[!is_back] <= bwt->primary && ik->x[!is_back] + ik->x[2] - 1 >= bwt->primary) << endl;
+    *ik = ok[c1];
+    bwt_2occ4(bwt, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], tk, tl);
+    //cout << (ik->x[!is_back] <= bwt->primary && ik->x[!is_back] + ik->x[2] - 1 >= bwt->primary) << ' ' << ok[c1].x[is_back] << endl;
+    //interval = 0;
+    //for (i = 3; i > c2; --i)
+    //{
+    //    interval += tl[i] - tk[i];
+    //}
+    //cout << "interval-2: " << interval << endl;
+
+    for (i = 0; i != 4; ++i)
+    {
+        ok[i].x[!is_back] = bwt->L2[i] + 1 + tk[i]; // 起始行位置，互补链
+        ok[i].x[2] = tl[i] - tk[i];                 // 间隔
+    }
+
+    // cout << "occ: " << ok[c2].x[2] << endl;
+
+
     // 因为计算的是互补碱基，所以3对应着0,2对应1，下边是正向扩展
     ok[3].x[is_back] = ik->x[is_back] + (ik->x[!is_back] <= bwt->primary && ik->x[!is_back] + ik->x[2] - 1 >= bwt->primary);
     ok[2].x[is_back] = ok[3].x[is_back] + ok[3].x[2];
     ok[1].x[is_back] = ok[2].x[is_back] + ok[2].x[2];
     ok[0].x[is_back] = ok[1].x[is_back] + ok[1].x[2];
 
-    *ik = ok[c1];
+
-    bwt_2occ4(bwt, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], tk, tl);
-    for (i = 0; i != 4; ++i)
-    {
-        ok[i].x[!is_back] = bwt->L2[i] + 1 + tk[i]; // 起始行位置，互补链
-        ok[i].x[2] = tl[i] - tk[i];                 // 间隔
-    }
-    // 因为计算的是互补碱基，所以3对应着0,2对应1，下边是正向扩展
-    ok[3].x[is_back] = ik->x[is_back] + (ik->x[!is_back] <= bwt->primary && ik->x[!is_back] + ik->x[2] - 1 >= bwt->primary);
-    ok[2].x[is_back] = ok[3].x[is_back] + ok[3].x[2];
-    ok[1].x[is_back] = ok[2].x[is_back] + ok[2].x[2];
-    ok[0].x[is_back] = ok[1].x[is_back] + ok[1].x[2];
 }
 
 // 每次扩展两步
 bwtintv_t bwt_search2(bwt_t *bwt, const string &q)
 {
     bwtintv_t ik, ok[4];
-    int i, j, c1, c2, x = 0;
+    int i, c1, c2, x = 0;
 
     bwt_set_intv(bwt, bval(q[x]), ik);
     ik.info = x + 1;
     // cout << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl;
 
-    for (i = x + 1; i + 1 < q.size(); i += 2)
+    for (i = x + 1; i + 1 < (int)q.size(); i += 2)
     {
         if (bval(q[i]) < 4 && bval(q[i + 1]) < 4)
         {
@@ -305,7 +333,7 @@ bwtintv_t bwt_search2(bwt_t *bwt, const string &q)
             c2 = cbval(q[i + 1]);
 
            // double tm_t = realtime();
-            bwt_extend2(bwt, &ik, ok, 0, c1);
+            bwt_extend2(bwt, &ik, ok, 0, c1, c2);
             // t7 += realtime() - tm_t;
 
             ik = ok[c2];
@@ -317,7 +345,7 @@ bwtintv_t bwt_search2(bwt_t *bwt, const string &q)
             break;
         }
     }
-    if (i < q.size() && bval(q[i]) < 4)
+    if (i < (int)q.size() && bval(q[i]) < 4)
     { // 最后一次扩展
         c1 = cbval(q[i]);
         // double tm_t = realtime();

fmt_index.cpp

@@ -7,6 +7,7 @@
 #include <stdio.h>
 #include <algorithm>
 #include <string.h>
+#include <immintrin.h>
 
 #include "util.h"
 #include "fmt_index.h"
@@ -112,6 +113,33 @@ void fmt_gen_cnt_table(FMTIndex *fmt)
 	}
 }
 
+// 生成occ，每个字节对应一个pattern
+void fmt_gen_cnt_occ(FMTIndex *fmt)
+{
+	// 0-8：大于a的occ，8-16：大于b的occ，16-24：b的occ
+	int i, a, b, ti;
+	uint32_t oa, ooa, ob, oob;
+	for (i = 0; i != 256; ++i) // 遍历单个字节的各种情况
+	{
+		for (a = 0; a < 4; ++a) // ba格式
+		{
+			oa = 0;
+			ooa = 0;
+			oa += ((i >> 4 & 3) == a) + ((i & 3) == a);
+			ooa += ((i >> 4 & 3) > a) + ((i & 3) > a);
+			for (b = 0; b < 4; ++b)
+			{
+				oob = ob = 0;
+				oob += ((i >> 6 & 3) > b && (i >> 4 & 3) == a) + ((i >> 2 & 3) > b && (i & 3) == a);
+				ob += ((i >> 6 & 3) == b && (i >> 4 & 3) == a) + ((i >> 2 & 3) == b && (i & 3) == a);
+
+				ti = a << 2 | b;
+				fmt->cnt_occ[ti][i]= ob << 24 | oob << 16 | oa << 8 | ooa ;
+			}
+		}
+	}
+}
+
 void dump_fmt(const char *fn, const FMTIndex *fmt)
 {
 	FILE *fp;
@@ -147,6 +175,7 @@ FMTIndex *restore_fmt(const char *fn)
 	fmt->seq_len = fmt->L2[4];
 	fclose(fp);
 	fmt_gen_cnt_table(fmt); // 字节所能表示的各种碱基组合中，各个碱基的累积数量
+	fmt_gen_cnt_occ(fmt);
 	return fmt;
 }
 
@@ -336,9 +365,9 @@ void fmt_e2_occ4(const FMTIndex *fmt, bwtint_t k, int b, uint32_t cnt1[4], uint3
 void fmt_e2_2occ4(const FMTIndex *fmt, bwtint_t k, bwtint_t l, int b,
 			   uint32_t cntk1[4], uint32_t cntk2[4], uint32_t cntl1[4], uint32_t cntl2[4])
 {
-	// fmt_e2_occ4(fmt, k, b, cntk1, cntk2);
+	fmt_e2_occ4(fmt, k, b, cntk1, cntk2);
-	// fmt_e2_occ4(fmt, l, b, cntl1, cntl2);
+	fmt_e2_occ4(fmt, l, b, cntl1, cntl2);
-	// return;
+	return;
 	// double tm_t = realtime();
 	bwtint_t _k, _l;
 	_k = k - (k >= fmt->primary); // 换算成了seq的行
@@ -453,7 +482,7 @@ void fmt_e1_occ4(const FMTIndex *fmt, bwtint_t k, uint32_t cnt[4])
 // 对k行和l行同时计算bwt str的occ，如果k和l落在同一个interval区间，可以减少一些计算量和访存
 void fmt_e1_2occ4(const FMTIndex *fmt, bwtint_t k, bwtint_t l, uint32_t cntk[4], uint32_t cntl[4])
 {
-	//double tm_t = realtime();
+	double tm_t = realtime();
 	bwtint_t _k, _l;
 	_k = k - (k >= fmt->primary); // 换算成了seq的行
 	_l = l - (l >= fmt->primary);
@@ -500,11 +529,11 @@ void fmt_e1_2occ4(const FMTIndex *fmt, bwtint_t k, bwtint_t l, uint32_t cntk[4],
 		cntl[2] += y1 >> 16 & 0xff;
 		cntl[3] += y1 >> 24;
 	}
-	//t11 += realtime() - tm_t;
+	t11 += realtime() - tm_t;
 }
 
 // 扩展一个碱基
-void fmt_extend1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_back, int b1)
+void fmt_extend1_1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_back, int b1)
 {
 	uint32_t tk[4], tl[4];
 	int i;
@@ -525,7 +554,7 @@ void fmt_extend1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_bac
 }
 
 // 扩展两个碱基
-void fmt_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_back, int b1, int b2)
+void fmt_extend2_1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_back, int b1, int b2)
 {
 	uint32_t tk1[4], tl1[4], tk2[4], tl2[4];
 	int i;
@@ -539,8 +568,8 @@ void fmt_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_bac
 		ok[i].x[!is_back] = fmt->L2[i] + 1 + tk2[i]; // 起始行位置，互补链
 		ok[i].x[2] = tl2[i] - tk2[i];  				// 间隔
 	}
-	ok[b2].x[!is_back] = fmt->L2[b2] + 1 + tk2[b2];
+	// ok[b2].x[!is_back] = fmt->L2[b2] + 1 + tk2[b2];
-	ok[b2].x[2] = tl2[b2] - tk2[b2];
+	// ok[b2].x[2] = tl2[b2] - tk2[b2];
 
 	// 因为计算的是互补碱基，所以3对应着0,2对应1，下边是正向扩展
 
@@ -558,10 +587,130 @@ void fmt_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_bac
 
 	*ik = ok[b2];
 }
+
+static inline int __occ_aux(uint64_t y, int c)
+{
+	// reduce nucleotide counting to bits counting
+	y = ((c & 2) ? y : ~y) >> 1 & ((c & 1) ? y : ~y) & 0x5555555555555555ull;
+	// count the number of 1s in y
+	y = (y & 0x3333333333333333ull) + (y >> 2 & 0x3333333333333333ull);
+	return ((y + (y >> 4)) & 0xf0f0f0f0f0f0f0full) * 0x101010101010101ull >> 56;
+}
+
+// 扩展两个个碱基，计算bwt base为b的pre-bwt str中各个碱基的occ
+void fmt_e2_occ(const FMTIndex *fmt, bwtint_t k, int b1, int b2, bwtint_t cnt[4])
+{
+	uint32_t x;
+	uint32_t *p, *q, tmp, *end;
+	bwtint_t bwt_k_line = k, bwt_k_base_line = k >> OCC_INTV_SHIFT << OCC_INTV_SHIFT;
+	int i, ti;
+	cnt[0] = 0;
+	cnt[1] = 0;
+	cnt[2] = 0;
+	if (k == (bwtint_t)(-1))
+	{
+		p = fmt->bwt + 4 + b1 * 4;
+		for (i = 3; i > b2; --i)
+			cnt[2] += p[i];
+		cnt[3] = p[b2];
+		return;
+	}
+	ti = b1 << 2 | b2;
+	_mm_prefetch((const char *)(&fmt->cnt_occ[ti]), _MM_HINT_T0);
+	k -= (k >= fmt->primary); // k由bwt矩阵对应的行转换成bwt字符串对应的行（去掉了$，所以大于$的行，都减掉1）
+	p = fmt_occ_intv(fmt, k);
+	// cout << "occ: " << p[0] << ' ' << p[1] << ' ' << p[2] << ' ' << p[3] << endl;
+	for (i = 3; i > b1; --i) cnt[0] += p[i];
+	cnt[1] = p[b1];
+	q = p + 4 + b1 * 4;
+	for (i = 3; i > b2; --i) cnt[2] += q[i];
+	cnt[3] = q[b2];
+	p += 20;											// 该地址是bwt和pre_bwt字符串数据的首地址
+	end = p + ((k >> 3) - ((k & ~OCC_INTV_MASK) >> 3)); // this is the end point of the following loop
+	//if ((int)(end - p) > 8)
+	//	cout << "interval: " << (int)(end - p) << endl;
+
+	// end = p + 2 + (end - p) / 6;
+	// end = p + 2;
+	for (x = 0; p < end; ++p)
+	{
+		x += __fmt_occ_e2_aux2(fmt, ti, *p);
+	}
+	tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
+	// print_base_uint32(tmp);
+	x += __fmt_occ_e2_aux2(fmt, ti, tmp);
+	if (b1 == 0)
+	{
+		x -= (~k & 7) << 8;
+		if (b2 == 0)
+			x -= (~k & 7) << 24;
+	}
+
+	// 如果跨过了second_primary,那么可能需要减掉一次累积值
+	if (b1 == fmt->first_base && bwt_k_base_line < fmt->sec_primary && bwt_k_line >= fmt->sec_primary)
+	{
+		if (b2 == fmt->last_base)
+			x -= 1 << 24;
+		else if (b2 < fmt->last_base)
+			x -= 1 << 16;
+	}
+
+	cnt[0] += x & 0xff;
+	cnt[1] += x >> 8 & 0xff;
+	cnt[2] += x >> 16 & 0xff;
+	cnt[3] += x >> 24 & 0xff;
+}
+
+void fmt_e2_2occ(const FMTIndex *fmt, bwtint_t k, bwtint_t l, 
+				int b1, int b2, bwtint_t cntk[4], bwtint_t cntl[4])
+{
+	// double tm_t = realtime();
+	fmt_e2_occ(fmt, k, b1, b2, cntk);
+	fmt_e2_occ(fmt, l, b1, b2, cntl);
+	return;
+	bwtint_t _k, _l;
+	_k = k - (k >= fmt->primary); // 换算成了seq的行
+	_l = l - (l >= fmt->primary);
+	if (_l >> OCC_INTV_SHIFT != _k >> OCC_INTV_SHIFT || k == (bwtint_t)(-1) || l == (bwtint_t)(-1))
+	{
+		fmt_e2_occ(fmt, k, b1, b2, cntk);
+		fmt_e2_occ(fmt, l, b1, b2, cntl);
+	}
+	else
+	{
+	}
+}
+
+// 扩展两个碱基
+void fmt_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok, int is_back, int b1, int b2)
+{
+	bwtint_t tk[4], tl[4], first_pos;
+	// tk表示在k行之前所有各个碱基累积出现次数，tl表示在l行之前的累积
+	fmt_e2_2occ(fmt, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], b1, b2, tk, tl);
+
+	// 这里是反向扩展
+	ok->x[!is_back] = fmt->L2[b2] + 1 + tk[3];
+	ok->x[2] = tl[3] - tk[3];
+
+	// 第一次正向扩展
+	ok->x[is_back] = ik->x[is_back] + (ik->x[!is_back] <= fmt->primary && ik->x[!is_back] + ik->x[2] - 1 >= fmt->primary) + tl[0] - tk[0];
+	// 第二次正向扩展
+	// cout << "inteval-1: " << tl[0] - tk[0] << endl;
+	// cout << (ik->x[!is_back] <= fmt->primary && ik->x[!is_back] + ik->x[2] - 1 >= fmt->primary) << endl;
+	// cout << (ok->x[!is_back] <= fmt->primary && ok->x[!is_back] + ok->x[2] - 1 >= fmt->primary) << ' ' << ok->x[is_back] << endl;
+	// cout << "inteval-2: " << tl[2] - tk[2] << endl;
+	// cout << "occ: " << tl[3] - tk[3] << endl;
+
+	first_pos = fmt->L2[b1] + 1 + tk[1];
+	ok->x[is_back] = ok->x[is_back] + (first_pos <= fmt->primary && first_pos + tl[1] - tk[1] - 1 >= fmt->primary) + tl[2] - tk[2];
+}
+
 // 利用fmt搜索seed，完整搜索，只需要单向搜索
 bwtintv_t fmt_search(FMTIndex *fmt, const string &q)
 {
-	bwtintv_t ik, ok[4];
+	bwtintv_t ik;
+	// bwtintv_t ok[4];
+	bwtintv_t ok;
 	int i, c1, c2, x = 0;
 	int qlen = (int)q.size();
 
@@ -577,7 +726,9 @@ bwtintv_t fmt_search(FMTIndex *fmt, const string &q)
 			c1 = cbval(q[i]);
 			c2 = cbval(q[i + 1]);
 			//double tm_t = realtime();
-			fmt_extend2(fmt, &ik, ok, 0, c1, c2);
+			fmt_extend2(fmt, &ik, &ok, 0, c1, c2);
+			//fmt_extend2_1(fmt, &ik, ok, 0, c1, c2);
+			ik = ok;
 			// t8 += realtime() - tm_t;
 			ik.info = i + 1;
 			// cout << "fmt  : " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl;
@@ -591,7 +742,7 @@ bwtintv_t fmt_search(FMTIndex *fmt, const string &q)
 	{ // 最后一次扩展
 		c1 = cbval(q[i]);
 		//double tm_t = realtime();
-		fmt_extend1(fmt, &ik, ok, 0, c1);
+		// fmt_extend1(fmt, &ik, ok, 0, c1);
 		//t9 += realtime() - tm_t;
 		ik.info = i + 1;
 		// cout << "fmt  : " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl;
@@ -616,6 +767,7 @@ int main_fmtidx(int argc, char **argv)
 	FMTIndex *fmt = restore_fmt(fmt_idx.c_str());
 
 	vector<string> seed_arr(10000000);
+	seed_arr[0] = "CCGTCATCATCCG";
 	srand(time(NULL));
 
 	t1 = realtime();
@@ -633,25 +785,24 @@ int main_fmtidx(int argc, char **argv)
 	t4 = realtime();
 	for (int i = 0; i < (int)seed_arr.size(); ++i)
 	{
-		// bwtintv_t p1 = 
+		bwtintv_t p1 = 
 		bwt_search2(bwt, seed_arr[i]);
-		// bwtintv_t p2 = fmt_search(fmt, seed_arr[i]);
+		bwtintv_t p2 = fmt_search(fmt, seed_arr[i]);
-		// if (p1.x[1] != p2.x[1] || p1.x[2] != p2.x[2] || p1.x[3] != p2.x[3])
+		if (p1.x[0] != p2.x[0] || p1.x[1] != p2.x[1] || p1.x[2] != p2.x[2])
-		// 	cout << seed_arr[i] << endl
+			cout << seed_arr[i] << endl
-		// 		 << p1.x[1] << ' ' << p1.x[2] << ' ' << p1.x[3] << endl
+				 << p1.x[0] << ' ' << p1.x[1] << ' ' << p1.x[2] << endl
-		// 		 << p2.x[1] << ' ' << p2.x[2] << ' ' << p2.x[3] << endl;
+		 		 << p2.x[0] << ' ' << p2.x[1] << ' ' << p2.x[2] << endl;
 	}
 	t4 = realtime() - t4;
 	cout << "[time bwt search 2:] " << t4 << "s" << endl;
-
 	t3 = realtime();
 	for (int i = 0; i < (int)seed_arr.size(); ++i)
 		fmt_search(fmt, seed_arr[i]);
 	t3 = realtime() - t3;
 	cout << "[time fmt search:] " << t3 << "s" << endl;
  
-	cout << "bwt occ: " << t5 << "s; " << t7 << '\t' << t10 << endl;
+	//cout << "bwt occ: " << t5 << "s; " << t7 << '\t' << t10 << endl;
-	cout << "fmt occ: " << t6 << "s; " << t11 << '\t' << t8 << '\t' << t9 << endl;
+	//cout << "fmt occ: " << t6 << "s; " << t11 << '\t' << t8 << '\t' << t9 << endl;
 	// bwt_search(bwt, s);
 	// bwt_search2(bwt, s);
 	// for (int i = 0; i < 120; ++i)

fmt_index.h

@@ -11,6 +11,9 @@
 #define __fmt_occ_e2_aux4(fmt, b, val) \
     ((fmt)->cnt_table[(b)][(val) & 0xff] + (fmt)->cnt_table[b][(val) >> 8 & 0xff] + (fmt)->cnt_table[b][(val) >> 16 & 0xff] + (fmt)->cnt_table[b][(val) >> 24])
 
+#define __fmt_occ_e2_aux2(fmt, b, val) \
+    ((fmt)->cnt_occ[(b)][(val) & 0xff] + (fmt)->cnt_occ[b][(val) >> 8 & 0xff] + (fmt)->cnt_occ[b][(val) >> 16 & 0xff] + (fmt)->cnt_occ[b][(val) >> 24])
+
 // fm-index, extend twice in one search step (one memory access)
 struct FMTIndex
 {
@@ -22,6 +25,7 @@ struct FMTIndex
     uint32_t *bwt;        // BWT
     // occurance array, separated to two parts
     uint32_t cnt_table[5][256]; // 4对应原来的cnt_table，0,1,2,3,分别对应该碱基的扩展
+    uint32_t cnt_occ[16][256]; // 前16-24位表示b（碱基）的occ，8-16位表示大于b的occ，0-8表示大于a的occ，ba格式
     uint8_t sec_bcp;                // base couple for sec primary line, AA=>0, AC=>1 ... TT=>15
     uint8_t first_base;             // 序列的第一个碱基2bit的int类型，0,1,2,3
     uint8_t last_base;              // dollar转换成的base