diff --git a/.gitignore b/.gitignore index 9999bc1..4aff00b 100644 --- a/.gitignore +++ b/.gitignore @@ -1,6 +1,6 @@ # specific for bwa_perf *.txt -fmtidx +bwa_perf *.fmt # ---> C diff --git a/Makefile b/Makefile index 27f3eef..54ddc26 100644 --- a/Makefile +++ b/Makefile @@ -7,7 +7,7 @@ SHOW_PERF= -DSHOW_PERF AR= ar DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) $(SHOW_PERF) AOBJS= util.o sa.o fmt_index.o bwt.o -PROG= fmtidx +PROG= bwa_perf INCLUDES= LIBS= -lm -lz -lpthread SUBDIRS= . @@ -23,7 +23,7 @@ endif all:$(PROG) -fmtidx:$(AOBJS) main.o +$(PROG):$(AOBJS) main.o $(CC) $(CFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. $(LIBS) clean: diff --git a/bwt.cpp b/bwt.cpp index 5ed0cb9..1177ef6 100644 --- a/bwt.cpp +++ b/bwt.cpp @@ -15,7 +15,6 @@ const static char BASE[4] = {'A', 'C', 'G', 'T'}; // 打印32位整型数据中包含的pre-bwt：bwt static void print_base_uint32(uint32_t p) { - const char BASE[4] = {'A', 'C', 'G', 'T'}; for (int i = 30; i > 0; i -= 2) { int b1 = p >> i & 3; @@ -23,6 +22,7 @@ static void print_base_uint32(uint32_t p) } } +// 保存bwt数据 void dump_bwt(const char *fn, const bwt_t *bwt) { FILE *fp; @@ -90,11 +90,6 @@ void create_interval_occ_bwt(bwt_t *bwt) // 计算occ，生成naive bwt for (i = k = 0; i < bwt->seq_len; ++i) { - if (i % 1000000 == 0) - { - cout << "line: " << i << '\t' << ((uint64_t)c[0] + c[1] + c[2] + c[3]) << '\t'; - cout << c[0] << ' ' << c[1] << ' ' << c[2] << ' ' << c[3] << endl; - } if (i % OCC_INTERVAL == 0) { memcpy(buf + k, c, sizeof(uint32_t) * 4); @@ -105,7 +100,6 @@ void create_interval_occ_bwt(bwt_t *bwt) ++c[bwt_B00(bwt, i)]; } // the last element - // cout << c[0] << '\t' << c[1] << '\t' << c[2] << '\t' << c[3] << endl; memcpy(buf + k, c, sizeof(uint32_t) * 4); xassert(k + 4 == bwt->bwt_size, "inconsistent bwt_size"); // update bwt @@ -137,7 +131,6 @@ bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, uint8_t c) // retrieve Occ at k/OCC_INTERVAL n = ((bwtint_t *)(p = bwt_occ_intv(bwt, k)))[c]; - // cout << "bwt_occ - 1: " << (int)c << '\t' << k << '\t' << n << endl; p += sizeof(bwtint_t); // jump to the start of the first BWT cell // calculate Occ up to the last k/32 @@ -145,12 +138,10 @@ bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, uint8_t c) for (; p < end; p += 2) n += __occ_aux((uint64_t)p[0] << 32 | p[1], c); - // cout << "bwt_occ - 2: " << (int)c << '\t' << k << '\t' << n << endl; // calculate Occ n += __occ_aux(((uint64_t)p[0] << 32 | p[1]) & ~((1ull << ((~k & 31) << 1)) - 1), c); if (c == 0) n -= ~k & 31; // corrected for the masked bits - // cout << "bwt_occ - 3: " << (int)c << '\t' << k << '\t' << n << endl; return n; } @@ -167,37 +158,27 @@ 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 << "k: " << k << "; occ: " << p[0] << ' ' << p[1] << ' ' << p[2] << ' ' << p[3] << endl; cnt[0] = p[0]; cnt[1] = p[1]; cnt[2] = p[2]; cnt[3] = p[3]; - p += 4; // sizeof(bwtint_t) = 4*(sizeof(bwtint_t)/sizeof(uint32_t)) + p += 4; // check point之后的bwt字符串首地址 end = p + ((k >> 4) - ((k & ~OCC_INTV_MASK) >> 4)); // this is the end point of the following loop - //end = p + 1; - // cout << "k - kbase: " << k - bwt_k_base_line << endl; for (; p < end; ++p) { x += __occ_aux4(bwt, *p); - //if (k == 3965453116 || k == 3965453672 || k == 2668688087 || k == 2668688550) - // print_base_uint32(*p); } tmp = *p & ~((1U << ((~k & 15) << 1)) - 1); - //if (k == 3965453116 || k == 3965453672 || k == 2668688087 || k == 2668688550) - // print_base_uint32(tmp); x += __occ_aux4(bwt, tmp) - (~k & 15); // 这里多算了A，要减去 cnt[0] += x & 0xff; cnt[1] += x >> 8 & 0xff; cnt[2] += x >> 16 & 0xff; cnt[3] += x >> 24; - //if (k == 3965453116 || k == 3965453672 || k == 2668688087 || k == 2668688550) - // cout << "final-occ: " << cnt[0] << ' ' << cnt[1] << ' ' << cnt[2] << ' ' << cnt[3] << endl; } -// an analogy to bwt_occ4() but more efficient, requiring k <= l +// an analogy to bwt_occ4() but more efficient, requiring k <= l，有提升，但不大 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; @@ -220,7 +201,7 @@ void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtin cntk[1] = p[1]; cntk[2] = p[2]; cntk[3] = p[3]; - p += 4; // sizeof(bwtint_t) = 4*(sizeof(bwtint_t)/sizeof(uint32_t)) + p += 4; // prepare cntk[] endk = p + ((k >> 4) - ((k & ~OCC_INTV_MASK) >> 4)); endl = p + ((l >> 4) - ((l & ~OCC_INTV_MASK) >> 4)); @@ -244,8 +225,6 @@ void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtin cntl[2] += y >> 16 & 0xff; cntl[3] += y >> 24; } - // t5 += realtime() - tm_t; - // f1 += 1; } void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_back) @@ -253,9 +232,7 @@ void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_b bwtint_t tk[4], tl[4]; 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 - // cout << "bwt-1-d: " << ik->x[!is_back] - 1 << '\t' << tk[0] << '\t' << tk[1] << '\t' << tk[2] << '\t' << tk[3] << endl; - // cout << "bwt-1-d: " << ik->x[!is_back] - 1 + ik->x[2] << '\t' << tl[0] << '\t' << tl[1] << '\t' << tl[2] << '\t' << tl[3] << endl; - // 这里是反向扩展 + // 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 @@ -276,7 +253,6 @@ void bwt_search(bwt_t *bwt, const string &q) 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 < (int)q.size(); ++i) { @@ -286,7 +262,6 @@ void bwt_search(bwt_t *bwt, const string &q) bwt_extend(bwt, &ik, ok, 0); ik = ok[c]; ik.info = i + 1; - // cout << "bwt-1: " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl; } } } @@ -295,8 +270,6 @@ void bwt_search(bwt_t *bwt, const string &q) 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]; - // oc1, oc2; - // int int1 = 0, int2 = 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 @@ -312,17 +285,8 @@ void bwt_extend2(const bwt_t *bwt, bwtintv_t *ik, bwtintv_t ok[4], int is_back, 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]; - //oc1 = oc2 = 0; - //for (i = 3; i > c1; --i) - //{ - // int1 += tl[i] - tk[i]; - // oc1 += tk[i]; - // oc2 += tl[i]; - //} - //cout << "bwt-2 interval-1: " << int1 << ' ' << oc1 << ' ' << oc2 << endl; + *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) @@ -335,15 +299,6 @@ void bwt_extend2(const bwt_t *bwt, bwtintv_t *ik, bwtintv_t ok[4], int is_back, 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]; - - // oc1 = oc2 = 0; - // for (i = 3; i > c2; --i) - // { - // int2 += tl[i] - tk[i]; - // oc1 += tk[i]; - // oc2 += tl[i]; - // } - // cout << "bwt-2 interval-2: " << int2 << ' ' << oc1 << ' ' << oc2 << endl; } // 每次扩展两步 @@ -354,7 +309,6 @@ bwtintv_t bwt_search2(bwt_t *bwt, const string &q) bwt_set_intv(bwt, bval(q[x]), ik); ik.info = x + 1; - //cout << "bwt-2: " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl; for (i = x + 1; i + 1 < (int)q.size(); i += 2) { @@ -364,14 +318,10 @@ bwtintv_t bwt_search2(bwt_t *bwt, const string &q) c1 = cbval(q[i]); c2 = cbval(q[i + 1]); - // double tm_t = realtime(); - //cout << BASE[c2] << BASE[c1] << endl; bwt_extend2(bwt, &ik, ok, 0, c1, c2); - // t7 += realtime() - tm_t; ik = ok[c2]; ik.info = i + 1; - //cout << "bwt-2: " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl; } else { @@ -381,13 +331,9 @@ bwtintv_t bwt_search2(bwt_t *bwt, const string &q) if (i < (int)q.size() && bval(q[i]) < 4) { // 最后一次扩展 c1 = cbval(q[i]); - // double tm_t = realtime(); bwt_extend(bwt, &ik, ok, 0); - // t10 += realtime() - tm_t; ik = ok[c1]; ik.info = i + 1; - //cout << "bwt-2: " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl; } - // cout << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl; return ik; } \ No newline at end of file diff --git a/bwt.h b/bwt.h index faae948..d13d900 100644 --- a/bwt.h +++ b/bwt.h @@ -7,7 +7,7 @@ using std::string; // occ间隔对应的右移位数，5表示间隔32行保存一次 -#define OCC_INTV_SHIFT 7 +#define OCC_INTV_SHIFT 6 #define OCC_INTERVAL (1LL << OCC_INTV_SHIFT) #define OCC_INTV_MASK (OCC_INTERVAL - 1) @@ -23,10 +23,6 @@ using std::string; // 获取碱基c（待查找序列的首个碱基）和对应的互补碱基对应的行，以及间隔 #define bwt_set_intv(bwt, c, ik) ((ik).x[0] = (bwt)->L2[(int)(c)] + 1, (ik).x[2] = (bwt)->L2[(int)(c) + 1] - (bwt)->L2[(int)(c)], (ik).x[1] = (bwt)->L2[3 - (c)] + 1, (ik).info = 0) -// The following two lines are ONLY correct when OCC_INTERVAL==0x80 -// #define bwt_bwt(b, k) ((b)->bwt[((k) >> 7 << 4) + sizeof(bwtint_t) + (((k) & 0x7f) >> 4)]) -// #define bwt_occ_intv(b, k) ((b)->bwt + ((k) >> 7 << 4)) -///* For general OCC_INTERVAL, the following is correct: // k行对应的bwt str碱基，对应的check point bwt str数据起始地址 #define bwt_bwt(b, k) ((b)->bwt[(k) / OCC_INTERVAL * (OCC_INTERVAL / 16 + 4) + 4 + (k) % OCC_INTERVAL / 16]) // k行（bwt str行（不包含$））对应的check point occ数据起始地址（小于k且是OCC_INTERVAL的整数倍） diff --git a/fmt_index.cpp b/fmt_index.cpp index 30114ac..365c137 100644 --- a/fmt_index.cpp +++ b/fmt_index.cpp @@ -315,13 +315,13 @@ FMTIndex *create_fmt_from_bwt(bwt_t *bwt) pre_and_bwt_seq_2 |= (((pre_bwt_16_seq & (3 << lshift_bit)) << (m * 2)) | ((bwt_16_seq & (3 << lshift_bit)) << (m * 2 - 2))); } -#ifdef FMT_MID_INTERVAL +#ifdef FMT_MID_INTERVAL // 计算前边8+8个碱基的mid interval occ s1 = pre_and_bwt_seq; for (m = 0; m < 4; ++m) mc[m] += cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24]; #endif -#if FMT_MID_INTERVAL == 8 +#if FMT_MID_INTERVAL == 8 // 如果mid interval是8的话，这里要保存一次 for (m = 0; m < 4; ++m) buf[k++] = mc[m]; #endif @@ -458,13 +458,7 @@ void fmt_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok, int is_back, // 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_occ(fmt, ik->x[!is_back] - 1, b1, b2, tk); fmt_e2_occ(fmt, ik->x[!is_back] - 1 + ik->x[2], b1, b2, tl); - - //fmt_e2_occ_2way(fmt, ik->x[!is_back] - 1, b1, b2, tk); - //fmt_e2_occ_2way(fmt, ik->x[!is_back] - 1 + ik->x[2], b1, b2, tl); // 这里是反向扩展 - //cout << BASE[b1] << BASE[b2] << endl; - //cout << "fmt: interval-1: " << tl[0] - tk[0] << ' ' << tl[0] << ' ' << tk[0] << endl; - //cout << "fmt: interval-2: " << tl[2] - tk[2] << ' ' << tl[2] << ' ' << tk[2] << endl; ok->x[!is_back] = fmt->L2[b2] + 1 + tk[3]; ok->x[2] = tl[3] - tk[3]; // 第一次正向扩展 @@ -478,12 +472,10 @@ void fmt_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok, int is_back, void fmt_extend1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok, int is_back, int b1) { bwtint_t tk[4], tl[4]; - int b2 = 3; + int b2 = 3; // 如果只扩展一次，那么第二个碱基设置成T，可以减小一些计算量，如计算大于b2的累积数量 // 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_occ(fmt, ik->x[!is_back] - 1, b1, b2, tk); fmt_e2_occ(fmt, ik->x[!is_back] - 1 + ik->x[2], b1, b2, tl); - //fmt_e2_occ_2way(fmt, ik->x[!is_back] - 1, b1, b2, tk); - //fmt_e2_occ_2way(fmt, ik->x[!is_back] - 1 + ik->x[2], b1, b2, tl); // 这里是反向扩展 ok->x[!is_back] = fmt->L2[b1] + 1 + tk[1]; ok->x[2] = tl[1] - tk[1]; @@ -501,21 +493,17 @@ bwtintv_t fmt_search(FMTIndex *fmt, const string &q) fmt_set_intv(fmt, bval(q[x]), ik); ik.info = x + 1; - //cout << "fmt : " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl; + // 每次扩展两个碱基 for (i = x + 1; i + 1 < qlen; i += 2) { if (bval(q[i]) < 4 && bval(q[i + 1]) < 4) { c1 = cbval(q[i]); c2 = cbval(q[i + 1]); - //cout << BASE[c2] << BASE[c1] << endl; - //double tm_t = realtime(); fmt_extend2(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; } else { @@ -525,14 +513,10 @@ bwtintv_t fmt_search(FMTIndex *fmt, const string &q) if (i < qlen && bval(q[i]) < 4) { // 最后一次扩展 c1 = cbval(q[i]); - // double tm_t = realtime(); fmt_extend1(fmt, &ik, &ok, 0, c1); ik = ok; - // t9 += realtime() - tm_t; ik.info = i + 1; - //cout << "fmt : " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl; } - // cout << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl; return ik; } @@ -544,36 +528,14 @@ uint32_t str2bit(string &str) return pac; } +#define GEN_BWT_IDX 0 +#define GEN_FMT_IDX 0 +#define CMP_FMT_BWT_TIME 1 +#define CMP_FMT_BWT_RESULT 1 + +// argv[1] 应该是索引的前缀 int main_fmtidx(int argc, char **argv) { - // string seq("ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA"); - //string seq("ACCCT"); - //string rseq = calc_reverse_seq(seq); - //seq = seq + rseq; - //create_bwt_mtx(seq); - //cout << seq << endl; - - // uint32_t cnt_table[4][256]; - // fmt_gen_cnt_table(cnt_table); - // string ss1("ATATATCAATTCTCTT"); - // string ss2("ATTGCCTCTGAATTAC"); - // uint32_t bs1 = str2bit(ss1), bs2 = str2bit(ss2); - // uint32_t s1 = bs1; - // uint32_t x = 0; - // for (int m = 0; m < 4; ++m) - // { - // x = cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24]; - // cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl; - // } - // x = 0; - // s1 = bs2; - // for (int m = 0; m < 4; ++m) - // { - // x = cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24]; - // cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl; - // } - - // return 0; string prefix = argv[1]; string bwt_str = prefix + ".bwt.str"; string bwt_idx, fmt_idx; @@ -594,7 +556,7 @@ int main_fmtidx(int argc, char **argv) // 生成或读取bwt索引文件 double time_read_bwt = realtime(); -#if 0 +#if GEN_BWT_IDX bwt = restore_bwt(bwt_str.c_str()); create_interval_occ_bwt(bwt); dump_bwt(bwt_idx.c_str(), bwt); @@ -606,7 +568,7 @@ int main_fmtidx(int argc, char **argv) // 生成或读取fmt索引文件 double time_read_fmt = realtime(); -#if 0 +#if GEN_FMT_IDX fmt = create_fmt_from_bwt(bwt); dump_fmt(fmt_idx.c_str(), fmt); #else @@ -618,9 +580,9 @@ 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 = 11; vector seq_arr(seq_size); - seq_arr[0] = "GCGATACTAAGA"; + // seq_arr[0] = "GCGATACTAAGA"; // seq_arr[0] = "GAGAGCTGTTCCCGTGTTTTCCATGGTTT"; #if 1 srand(time(NULL)); @@ -632,7 +594,7 @@ int main_fmtidx(int argc, char **argv) #endif // 对比bwt和fmt搜索的时间 -#if 1 +#if CMP_FMT_BWT_TIME double time_bwt_search = realtime(); for (int i = 0; i < (int)seq_arr.size(); ++i) bwt_search(bwt, seq_arr[i]); @@ -647,9 +609,9 @@ int main_fmtidx(int argc, char **argv) #endif // 对比bwt和fmt搜索的结果 -#if 1 +#if CMP_FMT_BWT_RESULT double time_cmp = realtime(); - for (int i = 0; i < (int)seq_arr.size(); ++i) + for (int i = 0; i < (int)seq_arr.size() / 100; ++i) { bwtintv_t p1 = bwt_search2(bwt, seq_arr[i]); bwtintv_t p2 = fmt_search(fmt, seq_arr[i]); diff --git a/fmt_index.h b/fmt_index.h index aca2472..8d525a2 100644 --- a/fmt_index.h +++ b/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 7 +#define FMT_MID_INTV_SHIFT 5 #define FMT_MID_INTERVAL (1LL << FMT_MID_INTV_SHIFT) #define FMT_MID_INTV_MASK (FMT_MID_INTERVAL - 1) diff --git a/main.cpp b/main.cpp index 6d763da..2788d71 100644 --- a/main.cpp +++ b/main.cpp @@ -10,10 +10,19 @@ using namespace std; int main_sa(int argc, char **argv); int main_fmtidx(int argc, char **argv); +#define TEST_SA 0 +#define TEST_FMT 1 + // 整个程序的入口 int main(int argc, char **argv) { - // main_sa(argc, argv); +#if TEST_SA + main_sa(argc, argv); +#endif + +#if TEST_FMT main_fmtidx(argc, argv); +#endif + return 0; } \ No newline at end of file diff --git a/sa.cpp b/sa.cpp index 044086a..5eb2683 100644 --- a/sa.cpp +++ b/sa.cpp @@ -8,6 +8,7 @@ using namespace std; +// 由33bit表示的bwt行对应的所在序列位置信息 inline void bwt_set_sa_33(uint8_t *sa_arr, bwtint_t k, bwtint_t val) { const bwtint_t block_idx = (k >> 3) * 33; // 8个数为一组，共享33个字节 @@ -66,6 +67,8 @@ static inline uint64_t get_sa_val_40(uint8_t *sa_arr, uint64_t idx) { return sa_val; } +#define TEST_RAND_READ 1 + int main_sa(int argc, char **argv) { double timeRead40, timeWrite40, @@ -73,20 +76,25 @@ int main_sa(int argc, char **argv) timeRead401, timeWrite401, timeRead64, timeWrite64; double timeStart; - int saLen = 1 << 25; - bwtint_t diffPos = 0; + int saLen = 1 << 25; // 对应于bwt字符串长度 + bwtint_t diffPos = 0; // 用来显示结果不一致时候的出错位置 vector valArr(saLen); vector ri(saLen); - uint8_t *sa33 = (uint8_t*)calloc(SA_BYTES_40(saLen), 1); + uint8_t *sa33 = (uint8_t*)calloc(SA_BYTES_33(saLen), 1); uint8_t *sa40 = (uint8_t*)calloc(SA_BYTES_40(saLen), 1); uint8_t *sa401 = (uint8_t*)calloc(SA_BYTES_40(saLen), 1); bwtint_t *sa64 = (bwtint_t*)calloc(saLen, sizeof(bwtint_t)); + for (int i=0; i< saLen; ++i) { valArr[i] = rand(); valArr[i] <<= 1; + #if TEST_RAND_READ ri[i] = rand() % saLen; - // ri[i] = i; + #else + ri[i] = i; + #endif } + // 33 test timeStart = realtime(); for (int i=0; i