解决了各种bug，现在结果是准确的，比原始的扩展快了30%，比64间隔的扩展快了20%
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10
bwt.cpp
10
bwt.cpp
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@ -155,7 +155,7 @@ bwtint_t bwt_occ(const bwt_t *bwt, bwtint_t k, uint8_t c)
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// 统计k行（bwt mtx行）之前4种碱基累积数量，这里的k是bwt矩阵里的行，比bwt字符串多1
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void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
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{
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bwtint_t x;
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bwtint_t x = 0;
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uint32_t *p, tmp, *end;
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// bwtint_t bwt_k_base_line = k >> OCC_INTV_SHIFT << OCC_INTV_SHIFT;
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if (k == (bwtint_t)(-1))
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@ -165,7 +165,7 @@ void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
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}
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k -= (k >= bwt->primary); // because $ is not in bwt
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p = bwt_occ_intv(bwt, k);
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//cout << "k: " << k << "; occ: " << p[0] << ' ' << p[1] << ' ' << p[2] << ' ' << p[3] << endl;
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// cout << "k: " << k << "; occ: " << p[0] << ' ' << p[1] << ' ' << p[2] << ' ' << p[3] << endl;
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cnt[0] = p[0];
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cnt[1] = p[1];
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cnt[2] = p[2];
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@ -173,14 +173,14 @@ void bwt_occ4(const bwt_t *bwt, bwtint_t k, bwtint_t cnt[4])
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p += 4; // sizeof(bwtint_t) = 4*(sizeof(bwtint_t)/sizeof(uint32_t))
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end = p + ((k >> 4) - ((k & ~OCC_INTV_MASK) >> 4)); // this is the end point of the following loop
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//end = p + 1;
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//cout << "k - kbase: " << k - bwt_k_base_line << endl;
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for (x = 0; p < end; ++p)
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// cout << "k - kbase: " << k - bwt_k_base_line << endl;
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for (; p < end; ++p)
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{
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x += __occ_aux4(bwt, *p);
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//print_base_uint32(*p);
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}
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tmp = *p & ~((1U << ((~k & 15) << 1)) - 1);
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//print_base_uint32(tmp);
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// print_base_uint32(tmp);
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x += __occ_aux4(bwt, tmp) - (~k & 15); // 这里多算了A，要减去
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cnt[0] += x & 0xff;
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cnt[1] += x >> 8 & 0xff;
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2
bwt.h
2
bwt.h
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@ -7,7 +7,7 @@
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using std::string;
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// occ间隔对应的右移位数，5表示间隔32行保存一次
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#define OCC_INTV_SHIFT 6
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#define OCC_INTV_SHIFT 7
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#define OCC_INTERVAL (1LL << OCC_INTV_SHIFT)
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#define OCC_INTV_MASK (OCC_INTERVAL - 1)
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201
fmt_index.cpp
201
fmt_index.cpp
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@ -120,6 +120,23 @@ void fmt_gen_cnt_occ(FMTIndex *fmt)
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}
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}
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// fmt-index的count table，4对应着bwt碱基的累积量，0,1,2,3分别对应着bwt是A,C,G,T，pre-bwt的累积量
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void fmt_gen_cnt_table(uint32_t cnt_table[4][256])
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{
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int i, j, k;
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uint32_t x = 0;
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for (i = 0; i != 256; ++i) // 遍历单个字节的各种情况
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{
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for (k = 0; k < 4; ++k) // bwt碱基
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{
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x = 0; // for [A,C,G,T][A,C,G,T]
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for (j = 0; j != 4; ++j) // pre-bwt碱基
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x |= (((i >> 6 & 3) == j && (i >> 4 & 3) == k) + ((i >> 2 & 3) == j && (i & 3) == k)) << (j << 3);
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cnt_table[k][i] = x;
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}
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}
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}
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void dump_fmt(const char *fn, const FMTIndex *fmt)
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{
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FILE *fp;
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@ -169,6 +186,13 @@ FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
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uint32_t c[4], c2[16]; /*c用来保存原来的bwt碱基串的累积值，c2用来保存pre-bwt和bwt碱基对的累计值，如AA..TT*/
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uint32_t *buf; /* 计算之后变成fmt结构中bwt部分 */
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#ifdef FMT_MID_INTERVAL
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// 加入中间的check point
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uint32_t mc[4] = {0};
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uint32_t cnt_table[4][256]; // 4对应原来的cnt_table，0,1,2,3,分别对应该碱基的扩展
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fmt_gen_cnt_table(cnt_table);
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#endif
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fmt->seq_len = bwt->seq_len; // bwt碱基序列的长度，不包含$字符，也就是该长度比bwt matrix长度少1
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for (i = 0; i < 5; ++i)
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fmt->L2[i] = bwt->L2[i]; // 每个碱基的总累积值
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@ -177,6 +201,14 @@ FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
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n_occ = (bwt->seq_len + FMT_OCC_INTERVAL - 1) / FMT_OCC_INTERVAL + 1; // check point 个数
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fmt->bwt_size = (fmt->seq_len * 2 + 15) >> 4; // 要保存最后两列碱基
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fmt->bwt_size += n_occ * 20; // A,C,G,T和AA,AC.....TG,TT共20个
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#ifdef FMT_MID_INTERVAL
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bwtint_t mn_occ = (bwt->seq_len >> FMT_OCC_INTV_SHIFT) * (FMT_OCC_INTERVAL / FMT_MID_INTERVAL - 1);
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bwtint_t last_seq_len = bwt->seq_len % FMT_OCC_INTERVAL;
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mn_occ += (last_seq_len + FMT_MID_INTERVAL - 1) / FMT_MID_INTERVAL - 1;
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fmt->bwt_size += mn_occ * 4;
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#endif
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buf = (uint32_t *)calloc(fmt->bwt_size, 4); // 开辟计算fmt用到的缓存
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c[0] = c[1] = c[2] = c[3] = 0;
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@ -198,6 +230,7 @@ FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
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k += 4;
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memcpy(buf + k, c2, sizeof(uint32_t) * 16); // pre-bwt:bwt碱基对的occ
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k += 16;
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mc[0] = mc[1] = mc[2] = mc[3] = 0;
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}
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// 每个32位整数保存8个倒数第二列碱基（pre-bwt）和8个倒数第一列(bwt)碱基
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if (i % 16 == 0) // 每个32位整数可以包含16个碱基，每次需要处理16个碱基，也就是间隔最小可以设置为16
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@ -257,6 +290,7 @@ FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
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}
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// 保存bwt和pre_bwt
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uint32_t pre_and_bwt_seq = 0;
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uint32_t pre_and_bwt_seq_2 = 0;
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for (m = 0; m < 8; ++m)
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{
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int lshift_bit = 30 - 2 * m;
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@ -265,14 +299,28 @@ FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
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buf[k++] = pre_and_bwt_seq;
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if (j > 8)
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{
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pre_and_bwt_seq = 0;
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for (m = 8; m > 0; --m)
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{
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int lshift_bit = 2 * m - 2;
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pre_and_bwt_seq |= (((pre_bwt_16_seq & (3 << lshift_bit)) << (m * 2)) | ((bwt_16_seq & (3 << lshift_bit)) << (m * 2 - 2)));
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pre_and_bwt_seq_2 |= (((pre_bwt_16_seq & (3 << lshift_bit)) << (m * 2)) | ((bwt_16_seq & (3 << lshift_bit)) << (m * 2 - 2)));
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}
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buf[k++] = pre_and_bwt_seq;
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buf[k++] = pre_and_bwt_seq_2;
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}
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#ifdef FMT_MID_INTERVAL
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// 加入中间的check point
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for (m = 0; m < 4; ++m)
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{
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uint32_t s1 = pre_and_bwt_seq;
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mc[m] += cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24];
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s1 = pre_and_bwt_seq_2;
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mc[m] += cnt_table[m][s1 & 0xff] + cnt_table[m][s1 >> 8 & 0xff] + cnt_table[m][s1 >> 16 & 0xff] + cnt_table[m][s1 >> 24];
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}
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if ((i + 16) % FMT_OCC_INTERVAL != 0 && j > 8) // 序列最后的部分不用保存
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{
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for (m = 0; m < 4; ++m)
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buf[k++] = mc[m];
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}
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#endif
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}
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}
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// the last element
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@ -291,8 +339,8 @@ FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
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// 扩展两个个碱基，计算bwt base为b的pre-bwt str中各个碱基的occ
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void fmt_e2_occ(const FMTIndex *fmt, bwtint_t k, int b1, int b2, bwtint_t cnt[4])
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{
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uint32_t x;
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uint32_t *p, *q, tmp, *end;
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uint32_t x = 0;
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uint32_t *p, *q, tmp;
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bwtint_t bwt_k_line = k, bwt_k_base_line = k >> FMT_OCC_INTV_SHIFT << FMT_OCC_INTV_SHIFT;
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int i, ti;
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cnt[0] = 0;
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@ -301,25 +349,80 @@ void fmt_e2_occ(const FMTIndex *fmt, bwtint_t k, int b1, int b2, bwtint_t cnt[4]
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if (k == (bwtint_t)(-1))
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{
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p = fmt->bwt + 4 + b1 * 4;
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for (i = 3; i > b2; --i) cnt[2] += p[i];
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for (i = b2 + 1; i < 4; ++i) cnt[2] += p[i];
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cnt[3] = p[b2];
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return;
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}
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ti = b1 << 2 | b2;
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// _mm_prefetch((const char *)(&fmt->cnt_occ[ti]), _MM_HINT_T0);
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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）
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p = fmt_occ_intv(fmt, k);
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// cout << "k-base: " << k << "; occ: " << p[0] << ' ' << p[1] << ' ' << p[2] << ' ' << p[3] << endl;
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for (i = 3; i > b1; --i) cnt[0] += p[i];
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cnt[1] = p[b1];
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for (i = b1 + 1; i < 4; ++i) cnt[0] += p[i]; // 大于b1的碱基的occ之和
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cnt[1] = p[b1]; // b1的occ
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q = p + 4 + b1 * 4;
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for (i = 3; i > b2; --i) cnt[2] += q[i];
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cnt[3] = q[b2];
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p += 20; // 该地址是bwt和pre_bwt字符串数据的首地址
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end = p + ((k >> 3) - ((k & ~FMT_OCC_INTV_MASK) >> 3)); // this is the end point of the following loop
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//p = end - (end - p) / 4;
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for (i = b2 + 1; i < 4 ; ++i) cnt[2] += q[i]; // 大于b2的occ之和
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cnt[3] = q[b2]; // b2的occ
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p += 20;
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#ifdef FMT_MID_INTERVAL
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// 使用mid interval信息
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int mk = k % FMT_OCC_INTERVAL;
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int n_mintv = mk >> FMT_MID_INTV_SHIFT;
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//if (k == 3137454504)
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//{
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// for (i = 0; i < n_mintv; ++i)
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// {
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// q = p + i * 6;
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// print_base_uint32(*q);
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// print_base_uint32(*(q + 1));
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// x = *(q + 2);
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// cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl;
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// x = *(q + 3);
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// cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl;
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// x = *(q + 4);
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// cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl;
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// x = *(q + 5);
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// cout << ((x) >> 24 & 0xff) << ' ' << ((x) >> 16 & 0xff) << ' ' << ((x) >> 8 & 0xff) << ' ' << ((x) & 0xff) << ' ' << __fmt_mid_sum(x) << endl;
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// }
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// x = 0;
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//}
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if (n_mintv > 0) // 至少超过了第一个mid interval
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{
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p += n_mintv * 6 - 4; // 对应的mid interval check point的首地址，即A C G T的局部累积量
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q = p + b1;
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for (i = b1 + 1; i < 4; ++i)
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x += p[i]; // 大于b1的碱基的occ之和
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cnt[0] += __fmt_mid_sum(x);
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x = *q;
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// if (k == 3137454504)
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// {
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// cout << ((x) >> 24 & 0xff) << '\t' << ((x) >> 16 & 0xff)
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// << '\t' << ((x) >> 8 & 0xff) << '\t' << ((x) & 0xff) << endl;
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// cout << __fmt_mid_sum(x) << endl;
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// }
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cnt[1] += __fmt_mid_sum(x); // b1的occ
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for (i = 3; i > b2; --i)
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cnt[2] += x >> (i << 3) & 0xff; // 大于b2的occ之和
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cnt[3] += x >> (b2 << 3) & 0xff; // b2的occ
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x = 0;
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p += 4;
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}
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// cout << "k: " << k << ' ' << cnt[1] << endl;
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if ((mk & FMT_MID_INTV_MASK) >> 3)
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{
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x += __fmt_occ_e2_aux2(fmt, ti, *p);
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// print_base_uint32(*p);
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++p;
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}
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tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
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// print_base_uint32(tmp);
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x += __fmt_occ_e2_aux2(fmt, ti, tmp);
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#else // 该地址是bwt和pre_bwt字符串数据的首地址
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uint32_t *end = p + ((k >> 3) - ((k & ~FMT_OCC_INTV_MASK) >> 3)); // this is the end point of the following loop
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// p = end - (end - p) / 8;
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// cout << "k - kbase: " << k - bwt_k_base_line << endl;
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for (x = 0; p < end; ++p)
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for (; p < end; ++p)
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{
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x += __fmt_occ_e2_aux2(fmt, ti, *p);
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// print_base_uint32(*p);
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@ -327,14 +430,7 @@ void fmt_e2_occ(const FMTIndex *fmt, bwtint_t k, int b1, int b2, bwtint_t cnt[4]
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tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
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// print_base_uint32(tmp);
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x += __fmt_occ_e2_aux2(fmt, ti, tmp);
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// end = p + (end - p) / 4;
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// end = p + 2;
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// p = end - (end - p) / 32;
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// if (k % 2 == 0)
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// x += __fmt_occ_e2_aux2(fmt, ti, *p);
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// p += 1;
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// tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
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// x += __fmt_occ_e2_aux2(fmt, ti, tmp);
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#endif
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if (b1 == 0)
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{
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@ -345,10 +441,10 @@ void fmt_e2_occ(const FMTIndex *fmt, bwtint_t k, int b1, int b2, bwtint_t cnt[4]
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// 如果跨过了second_primary,那么可能需要减掉一次累积值
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if (b1 == fmt->first_base && bwt_k_base_line < fmt->sec_primary && bwt_k_line >= fmt->sec_primary)
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{
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if (b2 == fmt->last_base)
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x -= 1 << 24;
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else if (b2 < fmt->last_base)
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if (b2 < fmt->last_base)
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x -= 1 << 16;
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else if (b2 == fmt->last_base)
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x -= 1 << 24;
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}
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cnt[0] += x & 0xff;
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cnt[1] += x >> 8 & 0xff;
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@ -405,13 +501,12 @@ bwtintv_t fmt_search(FMTIndex *fmt, const string &q)
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fmt_set_intv(fmt, bval(q[x]), ik);
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ik.info = x + 1;
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// cout << "fmt : " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl;
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// cout << "fmt : " << ik.x[0] << '\t' << ik.x[1] << '\t' << ik.x[2] << endl;
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for (i = x + 1; i + 1 < qlen; i += 2)
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{
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if (bval(q[i]) < 4 && bval(q[i + 1]) < 4)
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{
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c1 = cbval(q[i]);
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c2 = cbval(q[i + 1]);
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//double tm_t = realtime();
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@ -440,6 +535,14 @@ bwtintv_t fmt_search(FMTIndex *fmt, const string &q)
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return ik;
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}
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uint32_t str2bit(string &str)
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{
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uint32_t pac = 0;
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for (int i = 0; i < 16; ++i)
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pac = (pac << 2) | bval(str[i]);
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return pac;
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}
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int main_fmtidx(int argc, char **argv)
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{
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// string seq("ACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTA");
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@ -449,9 +552,31 @@ int main_fmtidx(int argc, char **argv)
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//create_bwt_mtx(seq);
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//cout << seq << endl;
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||||
|
||||
//string bwt_str = string(argv[1]) + ".bwt.str";
|
||||
// string bwt_idx = string(argv[1]) + ".128.bwt";
|
||||
string bwt_idx = string(argv[1]) + ".64.bwt";
|
||||
// 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 bwt_str = string(argv[1]) + ".bwt.str";
|
||||
string bwt_idx = string(argv[1]) + ".128.bwt";
|
||||
//string bwt_idx = string(argv[1]) + ".64.bwt";
|
||||
// string bwt_idx = string(argv[1]) + ".16.bwt";
|
||||
// string bwt_idx = string(argv[1]) + ".bwt";
|
||||
//bwt_t *bwt = restore_bwt(bwt_str.c_str());
|
||||
|
|
@ -459,17 +584,21 @@ int main_fmtidx(int argc, char **argv)
|
|||
//dump_bwt(bwt_idx.c_str(), bwt);
|
||||
|
||||
//string fmt_idx = string(argv[1]) + ".fmt";
|
||||
// string fmt_idx = string(argv[1]) + ".256.fmt";
|
||||
string fmt_idx = string(argv[1]) + ".256.fmt";
|
||||
// string fmt_idx = string(argv[1]) + ".128.fmt";
|
||||
string fmt_idx = string(argv[1]) + ".64.fmt";
|
||||
// string fmt_idx = string(argv[1]) + ".64.fmt";
|
||||
// string fmt_idx = string(argv[1]) + ".32.fmt";
|
||||
|
||||
|
||||
|
||||
t11 = realtime();
|
||||
bwt_t *bwt = restore_bwt(bwt_idx.c_str());
|
||||
t11 = realtime() - t11;
|
||||
cout << "[time read bwt:] " << t11 << "s" << endl;
|
||||
t10 = realtime();
|
||||
FMTIndex *fmt = restore_fmt(fmt_idx.c_str());
|
||||
// FMTIndex *fmt = create_fmt_from_bwt(bwt);
|
||||
// dump_fmt(fmt_idx.c_str(), fmt);
|
||||
t10 = realtime() - t10;
|
||||
cout << "[time gen fmt:] " << t10 << "s" << endl;
|
||||
|
||||
vector<string> seed_arr(10000000);
|
||||
seed_arr[0] = "GCGATACTAAGA";
|
||||
|
|
@ -492,6 +621,8 @@ int main_fmtidx(int argc, char **argv)
|
|||
t3 = realtime() - t3;
|
||||
cout << "[time fmt search:] " << t3 << "s" << endl;
|
||||
|
||||
return 0;
|
||||
|
||||
t4 = realtime();
|
||||
for (int i = 0; i < (int)seed_arr.size(); ++i)
|
||||
{
|
||||
|
|
|
|||
15
fmt_index.h
15
fmt_index.h
|
|
@ -1,16 +1,23 @@
|
|||
#ifndef FMT_INDEX_H_
|
||||
#define FMT_INDEX_H_
|
||||
|
||||
#define FMT_OCC_INTV_SHIFT 6
|
||||
#define FMT_OCC_INTV_SHIFT 8
|
||||
#define FMT_OCC_INTERVAL (1LL << FMT_OCC_INTV_SHIFT)
|
||||
#define FMT_OCC_INTV_MASK (FMT_OCC_INTERVAL - 1)
|
||||
|
||||
#define FMT_MID_INTV 16
|
||||
#define FMT_MID_INTV_SHIFT 4
|
||||
#define FMT_MID_INTERVAL (1LL << FMT_MID_INTV_SHIFT)
|
||||
#define FMT_MID_INTV_MASK (FMT_MID_INTERVAL - 1)
|
||||
|
||||
// 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 fmt_set_intv(fmt, c, ik) ((ik).x[0] = (fmt)->L2[(int)(c)] + 1, (ik).x[2] = (fmt)->L2[(int)(c) + 1] - (fmt)->L2[(int)(c)], (ik).x[1] = (fmt)->L2[3 - (c)] + 1, (ik).info = 0)
|
||||
// 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）
|
||||
#ifdef FMT_MID_INTERVAL
|
||||
// 包含mid interval
|
||||
#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 80))
|
||||
#else
|
||||
#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 20))
|
||||
#endif
|
||||
// 字节val中包含bwt base为b的pre-bwt中T G C A（按顺序保存在32位整数里（每个占8bit））的数量
|
||||
#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])
|
||||
|
|
@ -18,6 +25,9 @@
|
|||
#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])
|
||||
|
||||
#define __fmt_mid_sum(x) \
|
||||
((x) >> 24 & 0xff) + ((x) >> 16 & 0xff) + ((x) >> 8 & 0xff) + ((x) & 0xff)
|
||||
|
||||
// fm-index, extend twice in one search step (one memory access)
|
||||
struct FMTIndex
|
||||
{
|
||||
|
|
@ -28,7 +38,6 @@ struct FMTIndex
|
|||
bwtint_t bwt_size; // size of bwt, about seq_len/4
|
||||
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
|
||||
|
|
|
|||
Loading…
Reference in New Issue