解决了一些bug，目前看来fmt可以正常工作
This commit is contained in:
Gitea
parent
8e1576a2cd
commit
c69cb901bb
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@ -1,6 +1,7 @@
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# specific for bwa_perf
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*.txt
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fmtidx
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*.fmt
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# ---> C
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# Prerequisites
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17
bwt.cpp
17
bwt.cpp
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@ -10,6 +10,17 @@
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using namespace std;
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void bwt_dump_bwt(const char *fn, const bwt_t *bwt)
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{
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FILE *fp;
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fp = xopen(fn, "wb");
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err_fwrite(&bwt->primary, sizeof(bwtint_t), 1, fp);
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err_fwrite(bwt->L2 + 1, sizeof(bwtint_t), 4, fp);
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err_fwrite(bwt->bwt, 4, bwt->bwt_size, fp);
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err_fflush(fp);
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err_fclose(fp);
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}
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// 计算一个字节构成的T,G,C,A序列，对应的每个碱基的个数(按T,G,C,A顺序存储在32位整数中，每个占8位)
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void bwt_gen_cnt_table(bwt_t *bwt)
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{
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@ -23,8 +34,8 @@ void bwt_gen_cnt_table(bwt_t *bwt)
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}
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}
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// 解析两bit的bwt碱基序列
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bwt_t *restore_bwt_str(const char *fn)
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// 解析两bit的bwt碱基序列，这个只有bwt str，可以包含也可不包含occ check point
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bwt_t *restore_bwt(const char *fn)
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{
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bwt_t *bwt;
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bwt = (bwt_t *)calloc(1, sizeof(bwt_t));
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@ -202,6 +213,8 @@ void bwt_extend(const bwt_t *bwt, const bwtintv_t *ik, bwtintv_t ok[4], int is_b
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bwtint_t tk[4], tl[4];
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int i;
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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
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// cout << "bwt-1-d: " << ik->x[!is_back] - 1 << '\t' << tk[0] << '\t' << tk[1] << '\t' << tk[2] << '\t' << tk[3] << endl;
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// 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;
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// 这里是反向扩展
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for (i = 0; i != 4; ++i)
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{
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4
bwt.h
4
bwt.h
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@ -20,7 +20,7 @@ using std::string;
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// 从构建完成的bwt（包含occ check point）获取k行（不含$，这里的k不输出bwt mtx的行，是bwt字符串的行）的碱基
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#define bwt_B0(b, k) (bwt_bwt(b, k) >> ((~(k) & 0xf) << 1) & 3)
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// 获取碱基c（待查找序列的首）和对应的互补碱基对应的行，以及间隔
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// 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
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#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)
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// The following two lines are ONLY correct when OCC_INTERVAL==0x80
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@ -56,7 +56,7 @@ 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，包含k行本身）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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// 解析两bit的bwt碱基序列
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bwt_t *restore_bwt_str(const char *fn);
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bwt_t *restore_bwt(const char *fn);
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// 根据原始的字符串bwt创建interval-bwt
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void create_interval_occ_bwt(bwt_t *bwt);
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581
fmt_index.cpp
581
fmt_index.cpp
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@ -44,35 +44,44 @@ void print_base_uint32(uint32_t p)
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}
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}
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// 随机生成长度为len的序列
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string generate_rand_seq(int len)
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{
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string seq(len, 'A');
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for (int i = 0; i < len; ++i)
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{
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seq[i] = BASE[rand() % 4];
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}
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return seq;
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}
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// 创建bwt矩阵
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void create_bwt_mtx(string &seq)
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{
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cout << "seq size: " << seq.size() + 1 << endl;
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string sarr[seq.size() + 1];
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bwtint_t seq_len = seq.size() + 1;
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string sarr[seq_len];
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sarr[0] = seq + '$';
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for (int i = 1; i < sarr[0].size(); ++i)
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for (int i = 1; i < seq_len; ++i)
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{
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sarr[i] = sarr[0].substr(i) + sarr[0].substr(0, i);
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}
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std::sort(sarr, sarr + seq.size() + 1);
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// bwt matrix
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for (int i = 0; i < sarr[0].size(); ++i)
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{
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// cout << i << ' ' << sarr[i] << endl;
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cout << sarr[i] << endl;
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}
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std::sort(sarr, sarr + seq_len);
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// print bwt matrix
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// for (int i = 0; i < seq_len; ++i)
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//{
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// // cout << i << ' ' << sarr[i] << endl;
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// cout << sarr[i] << endl;
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//}
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// cout << "bwt string" << endl;
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// for (int i = 0; i < sarr[0].size(); ++i)
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// for (int i = 0; i < seq_len; ++i)
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// {
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// cout << sarr[i].back();
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// }
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// cout << endl;
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// cout << "pre bwt string" << endl;
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// for (int i = 0; i < sarr[0].size(); ++i)
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// for (int i = 0; i < seq_len; ++i)
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// {
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// cout << sarr[i][sarr[0].size() - 2];
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// cout << sarr[i][seq_len - 2];
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// }
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// cout << endl;
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}
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@ -98,7 +107,43 @@ void fmt_gen_cnt_table(FMTIndex *fmt)
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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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fp = xopen(fn, "wb");
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err_fwrite(&fmt->primary, sizeof(bwtint_t), 1, fp);
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err_fwrite(&fmt->sec_primary, sizeof(bwtint_t), 1, fp);
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err_fwrite(&fmt->sec_bcp, sizeof(uint8_t), 1, fp);
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err_fwrite(&fmt->first_base, sizeof(uint8_t), 1, fp);
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err_fwrite(&fmt->last_base, sizeof(uint8_t), 1, fp);
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err_fwrite(fmt->L2 + 1, sizeof(bwtint_t), 4, fp);
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err_fwrite(fmt->bwt, 4, fmt->bwt_size, fp);
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err_fflush(fp);
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err_fclose(fp);
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}
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FMTIndex *restore_fmt(const char *fn)
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{
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FMTIndex *fmt;
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fmt = (FMTIndex *)calloc(1, sizeof(FMTIndex));
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FILE *fp = fopen(fn, "rb");
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fseek(fp, 0, SEEK_END);
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fmt->bwt_size = (ftell(fp) - sizeof(bwtint_t) * 6 - 3) >> 2; // 以32位word为单位计算的size
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fmt->bwt = (uint32_t *)calloc(fmt->bwt_size, 4);
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fseek(fp, 0, SEEK_SET);
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fread(&fmt->primary, sizeof(bwtint_t), 1, fp);
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fread(&fmt->sec_primary, sizeof(bwtint_t), 1, fp);
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fread(&fmt->sec_bcp, sizeof(uint8_t), 1, fp);
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fread(&fmt->first_base, sizeof(uint8_t), 1, fp);
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fread(&fmt->last_base, sizeof(uint8_t), 1, fp);
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fread(fmt->L2 + 1, sizeof(bwtint_t), 4, fp);
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fread_fix(fp, fmt->bwt_size << 2, fmt->bwt);
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fmt->seq_len = fmt->L2[4];
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fclose(fp);
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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
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return fmt;
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}
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// 根据interval-bwt创建fmt-index
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FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
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@ -108,13 +153,13 @@ FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
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fmt_gen_cnt_table(fmt);
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bwtint_t i, j, k, m, n, n_occ, cnt[4], cnt2[4];
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uint32_t c[4], c2[16] /*保存AA..TT*/;
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uint32_t *buf;
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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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fmt->seq_len = bwt->seq_len;
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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];
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fmt->primary = bwt->primary;
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fmt->L2[i] = bwt->L2[i]; // 每个碱基的总累积值
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fmt->primary = bwt->primary; // $在末尾的行，在bwt matrix行中的排序位置
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n_occ = (bwt->seq_len + OCC_INTERVAL - 1) / 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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@ -129,146 +174,95 @@ FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
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bwt_occ4(bwt, before_first_line, cnt);
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for (j = i * 4, k = 0; k < 4; ++j, ++k)
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c2[j] = cnt[k];
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// cout << "start: " << BASE[i] << " line: " << before_first_line << " occ: " << cnt[0] << '\t' << cnt[1] << '\t' << cnt[2] << '\t' << cnt[3] << endl;
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}
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// cout << "c2: ";
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// for (m = 0; m < 16; ++m)
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// cout << c2[m] << ' ';
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// cout << endl;
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// k表示buf存储的偏移量
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for (i = k = 0; i < bwt->seq_len; ++i)
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{
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// 记录occ
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if (i % OCC_INTERVAL == 0)
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{
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memcpy(buf + k, c, sizeof(uint32_t) * 4); // 保存occ
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memcpy(buf + k, c, sizeof(uint32_t) * 4); // bwt str中各个碱基的occ
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k += 4;
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memcpy(buf + k, c2, sizeof(uint32_t) * 16); // 二次计算的occ
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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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}
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// 每个32位整数保存8个倒数第二列碱基和8个倒数第一列(bwt)碱基
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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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{
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uint32_t bwt_16_seq = bwt->bwt[i / 16];
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uint32_t pre_bwt_16_seq = 0;
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uint32_t *bwt_addr = bwt_occ_intv(bwt, i) + 8; // bwt字符串i对应的基准行
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int offset = (i % OCC_INTERVAL) / 16;
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bwt_16_seq = *(bwt_addr + offset);
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for (j = 0; j < 16; ++j)
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uint32_t pre_bwt_16_seq = 0; // 16个pre-bwt碱基串
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uint32_t *bwt_addr = bwt_occ_intv(bwt, i) + 8; // bwt字符串i对应的基准行，因为原始的bwt-cp（check point）包含由4个uint64_t(8个uint32_t)组成的occ信息
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int offset = (i % OCC_INTERVAL) / 16; // 每OCC_INTERVAL个碱基共享同一个基准地址，每16个碱基共用一个uint32整型，因此需要偏移量来获取当前碱基串的首地址
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uint32_t bwt_16_seq = *(bwt_addr + offset); // 待处理的当前16个碱基串的首地址
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for (j = 0; j < 16; ++j) // 对于bwt碱基串，一个一个碱基分别处理
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{
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bwtint_t cur_line = i + j;
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if (cur_line < bwt->seq_len) // 因为bwt序列里除去了$符号，所以bwt序列个数比原版bwt少1
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bwtint_t cur_str_line = i + j; // 当前碱基在bwt str中的行排序
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if (cur_str_line < bwt->seq_len) // 当前碱基行不应超出bwt str总碱基长度（bwt str长度比bwt matrix长度少1，因为bwt str不包含$）
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{
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uint8_t bwt_base = bwt_B0(bwt, cur_line); // 对应行的bwt的碱基
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// 先求出该碱基对应在第一列的行
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if (cur_line >= bwt->primary) // 因为bwt序列里除去了$符号，所以，超过$所在行之后，对应的seq位置应该加一，才是真正对应的行
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cur_line += 1;
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bwtint_t origin_base_line = bwt->L2[bwt_base] + 1 + bwt_occ(bwt, cur_line - 1, bwt_base); // bwt矩阵行
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bwtint_t base_line = origin_base_line;
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if (base_line >= bwt->primary) // base_line表示在bwt字符中的位置，所以超出$为最尾所在行之后，要减掉1
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base_line -= 1; // bwt碱基序列行（不包含$）
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uint32_t pre_bwt_base = bwt_B0(bwt, base_line); // bwt列碱基对应的前一个碱基
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if (origin_base_line == bwt->primary)
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uint8_t bwt_base = bwt_B0(bwt, cur_str_line); // 对应行的bwt的碱基
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// 先求出该碱基对应在第一列的行（对应的bwt matrix行）
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bwtint_t cur_mtx_line = cur_str_line;
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if (cur_str_line >= bwt->primary) // 因为bwt序列里除去了$符号，所以，超过$所在行之后，对应的seq位置应该加一，才是真正对应bwt matrix的行
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cur_mtx_line += 1;
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bwt_occ4(bwt, cur_mtx_line, cnt); // 获取原来bwt-checkpoint中的occ值
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for (m=0; m<4; ++m)
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c[m] = (uint32_t)cnt[m]; // 碱基m在cur_bwt_mtx_line(包含)之前的累积值，直接拷贝原bwt中的occ即可
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cnt[bwt_base] -= 1; // 得到cur_bwt_mtx_line(不包含)之前的累积量，即bwt_occ4(bwt, cur_bwt_mtx_line-1, cnt)
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bwtint_t bwt_base_mtx_line = bwt->L2[bwt_base] + 1 + cnt[bwt_base]; // bwt_base对应的bwt matrix行（LF变换）
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bwt_occ4(bwt, bwt_base_mtx_line, cnt2); // 计算bwt_base_mtx_line之前的occ
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for (n = 0; n < 4; ++n)
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{
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int c2_idx = bwt_base << 2 | n; // bwt base放在前边
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c2[c2_idx] = (uint32_t)cnt2[n]; // pre-bwt:bwt 碱基对的累计值
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}
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bwtint_t bwt_base_str_line = bwt_base_mtx_line; // bwt-str中对应的行排序
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if (bwt_base_str_line >= bwt->primary) // base_line表示在bwt str中的位置，所以超出$为最尾所在行之后，要减掉1
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bwt_base_str_line -= 1; // bwt碱基序列行（不包含$）
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uint32_t pre_bwt_base = bwt_B0(bwt, bwt_base_str_line); // bwt列碱基对应的前一个碱基pre-bwt
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// 此时，bwt_base对应的bwt matrix首行，是$排在最尾的行，说明bwt_base就是序列的第一个碱基，
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// 此时计算出来的pre_bwt_base就是primary前一行的bwt base，以此来代替$字符，在后续的计算过程中需要考虑
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if (bwt_base_mtx_line == bwt->primary)
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{
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// 计算sec_bcp
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fmt->sec_bcp = pre_bwt_base << 2 | bwt_base; // 因为把$当成A处理了
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fmt->sec_primary = cur_line;
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fmt->first_base = bwt_base;
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fmt->last_base = pre_bwt_base;
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fmt->sec_primary = cur_mtx_line; // pre-bwt base为$的行排序（bwt-matrix行）
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fmt->first_base = bwt_base; // 原始序列第一个碱基
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fmt->last_base = pre_bwt_base; // 计算后替代$字符的碱基（应该是primary行上边一行对应的bwt base）
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}
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// 暂存
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pre_bwt_16_seq = pre_bwt_16_seq | (pre_bwt_base << (15-j)*2);
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if (base_line >= bwt->primary)
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base_line += 1; // bwt矩阵行
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bwtint_t pre_base_line = bwt->L2[pre_bwt_base] + 1 + bwt_occ(bwt, base_line - 1, pre_bwt_base);
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// 获取c
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bwt_occ4(bwt, cur_line, cnt);
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for (m = 0; m < 4; ++m)
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{
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c[m] = (uint32_t)cnt[m]; // 碱基m在cur_line(包含)之前的累积值
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}
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// 求出c2
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||||
cnt[bwt_base] -= 1; // 得到cur_line(不包含)之前的累积量
|
||||
// bwtint_t m_first_line = bwt->L2[bwt_base] + cnt[bwt_base]; // 该bwt_base对应的在bwt矩阵中行的前一行
|
||||
// bwt_occ4(bwt, m_first_line, cnt2);
|
||||
// for (n = 0; n < 4; ++n) // 只计算bwt_base对应的二级occ，其他用之前的值
|
||||
// {
|
||||
// int c2_idx = bwt_base << 2 | n;
|
||||
// c2[c2_idx] = (uint32_t)cnt2[n];
|
||||
// }
|
||||
// 暂存 pre-bwt碱基序列
|
||||
pre_bwt_16_seq = pre_bwt_16_seq | (pre_bwt_base << (15-j)*2); // 序列靠前的碱基排在uint32_t数据中的高位
|
||||
|
||||
for (m = 0; m < 4; ++m)
|
||||
{
|
||||
bwtint_t m_first_line = -1;
|
||||
|
||||
// if (m == bwt_base || cnt[m] > 0)
|
||||
if (m == bwt_base)
|
||||
{
|
||||
m_first_line = bwt->L2[m] + 1 + cnt[m]; // m是否与bwt_base相同，这里需要想清楚，情况不一样的
|
||||
if (m_first_line >= bwt->seq_len)
|
||||
m_first_line = bwt->seq_len;
|
||||
// cout << cur_line << '\t' << BASE[m] << '\t' << m_first_line << endl;
|
||||
bwt_occ4(bwt, m_first_line, cnt2);
|
||||
for (n = 0; n < 4; ++n)
|
||||
{
|
||||
int c2_idx = m << 2 | n;
|
||||
c2[c2_idx] = (uint32_t)cnt2[n];
|
||||
}
|
||||
}
|
||||
}
|
||||
cnt[bwt_base] += 1; // cur_line(包含)之前
|
||||
// cout << cur_line << '\t'
|
||||
// << base_line << '\t'
|
||||
// << pre_base_line << '\t'
|
||||
// << BASE[pre_bwt_base] << '\t'
|
||||
// << BASE[bwt_base] << '\t'
|
||||
// << cnt[0] << ' ' << cnt[1] << ' ' << cnt[2] << ' ' << cnt[3] << "\t\t";
|
||||
// 输出调试信息
|
||||
// cout << "mtx line: " << cur_mtx_line << ' ' << c[0] << ' ' << c[1] << ' ' << c[2] << ' ' << c[3] << ' ';
|
||||
// for (m = 0; m < 16; ++m)
|
||||
// cout << c2[m] << ' ';
|
||||
// cout << endl;
|
||||
// for (m = 0; m < 16; ++m)
|
||||
// fprintf(fmt_out, "%-4d", c2[m]);
|
||||
// fprintf(fmt_out, "\n");
|
||||
}
|
||||
else
|
||||
break;
|
||||
}
|
||||
//print_base_uint32(pre_bwt_16_seq);
|
||||
//cout << endl;
|
||||
//print_base_uint32(bwt_16_seq);
|
||||
// 保存bwt和pre_bwt
|
||||
uint32_t tmp_seq = 0;
|
||||
tmp_seq = (((pre_bwt_16_seq & (3 << 30)) >> 0) | ((bwt_16_seq & (3 << 30)) >> 2))
|
||||
| (((pre_bwt_16_seq & (3 << 28)) >> 2) | ((bwt_16_seq & (3 << 28)) >> 4))
|
||||
| (((pre_bwt_16_seq & (3 << 26)) >> 4) | ((bwt_16_seq & (3 << 26)) >> 6))
|
||||
| (((pre_bwt_16_seq & (3 << 24)) >> 6) | ((bwt_16_seq & (3 << 24)) >> 8))
|
||||
| (((pre_bwt_16_seq & (3 << 22)) >> 8) | ((bwt_16_seq & (3 << 22)) >> 10))
|
||||
| (((pre_bwt_16_seq & (3 << 20)) >> 10) | ((bwt_16_seq & (3 << 20)) >> 12))
|
||||
| (((pre_bwt_16_seq & (3 << 18)) >> 12) | ((bwt_16_seq & (3 << 18)) >> 14))
|
||||
| (((pre_bwt_16_seq & (3 << 16)) >> 14) | ((bwt_16_seq & (3 << 16)) >> 16));
|
||||
buf[k++] = tmp_seq;
|
||||
//cout << i << endl;
|
||||
//print_base_uint32(tmp_seq);
|
||||
uint32_t pre_and_bwt_seq = 0;
|
||||
for (m = 0; m < 8; ++m)
|
||||
{
|
||||
int lshift_bit = 30 - 2 * m;
|
||||
pre_and_bwt_seq |= (((pre_bwt_16_seq & (3 << lshift_bit)) >> (m * 2)) | ((bwt_16_seq & (3 << lshift_bit)) >> ((m * 2) + 2)));
|
||||
}
|
||||
buf[k++] = pre_and_bwt_seq;
|
||||
if (j > 8)
|
||||
{
|
||||
// cout << "j: " << j << endl;
|
||||
tmp_seq = (((pre_bwt_16_seq & (3 << 14)) << 16) | ((bwt_16_seq & (3 << 14)) << 14))
|
||||
| (((pre_bwt_16_seq & (3 << 12)) << 14) | ((bwt_16_seq & (3 << 12)) << 12))
|
||||
| (((pre_bwt_16_seq & (3 << 10)) << 12) | ((bwt_16_seq & (3 << 10)) << 10))
|
||||
| (((pre_bwt_16_seq & (3 << 8)) << 10) | ((bwt_16_seq & (3 << 8)) << 8))
|
||||
| (((pre_bwt_16_seq & (3 << 6)) << 8) | ((bwt_16_seq & (3 << 6)) << 6))
|
||||
| (((pre_bwt_16_seq & (3 << 4)) << 6) | ((bwt_16_seq & (3 << 4)) << 4))
|
||||
| (((pre_bwt_16_seq & (3 << 2)) << 4) | ((bwt_16_seq & (3 << 2)) << 2))
|
||||
| (((pre_bwt_16_seq & (3 << 0)) << 2) | ((bwt_16_seq & (3 << 0)) << 0));
|
||||
|
||||
buf[k++] = tmp_seq;
|
||||
//print_base_uint32(tmp_seq);
|
||||
pre_and_bwt_seq = 0;
|
||||
for (m = 8; m > 0; --m)
|
||||
{
|
||||
int lshift_bit = 2 * m - 2;
|
||||
pre_and_bwt_seq |= (((pre_bwt_16_seq & (3 << lshift_bit)) << (m * 2)) | ((bwt_16_seq & (3 << lshift_bit)) << (m * 2 - 2)));
|
||||
}
|
||||
buf[k++] = pre_and_bwt_seq;
|
||||
}
|
||||
}
|
||||
}
|
||||
// the last element
|
||||
// cout << c[0] << '\t' << c[1] << '\t' << c[2] << '\t' << c[3] << endl;
|
||||
memcpy(buf + k, c, sizeof(uint32_t) * 4);
|
||||
k += 4;
|
||||
memcpy(buf + k, c2, sizeof(uint32_t) * 16);
|
||||
|
|
@ -278,103 +272,149 @@ FMTIndex *create_fmt_from_bwt(bwt_t *bwt)
|
|||
xassert(k == fmt->bwt_size, "inconsistent bwt_size");
|
||||
// update fmt
|
||||
fmt->bwt = buf;
|
||||
|
||||
return fmt;
|
||||
}
|
||||
|
||||
|
||||
|
||||
#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)
|
||||
#define fmt_occ_intv(b, k) ((b)->bwt + (k) / OCC_INTERVAL * (OCC_INTERVAL / 8 + 20))
|
||||
|
||||
void fmt_occ4(const FMTIndex *fmt, bwtint_t k, int b, uint32_t cnt1[4], uint32_t cnt2[4])
|
||||
// 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_occ4(const FMTIndex *fmt, bwtint_t k, int b, uint32_t cnt1[4], uint32_t cnt2[4])
|
||||
{
|
||||
bwtint_t x;
|
||||
uint32_t x1, x2;
|
||||
uint32_t *p, tmp, *end;
|
||||
bwtint_t bwt_k_line = k, bwt_k_base_line = k >> OCC_INTV_SHIFT << OCC_INTV_SHIFT;
|
||||
if (k == (bwtint_t)(-1))
|
||||
{
|
||||
p = fmt->bwt + 4 + b * 4;
|
||||
memset(cnt1, 0, 4 * sizeof(uint32_t));
|
||||
memset(cnt2, 0, 4 * sizeof(uint32_t));
|
||||
memcpy(cnt2, p, 4 * sizeof(uint32_t));
|
||||
return;
|
||||
}
|
||||
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 << "base: " << BASE[b] << endl;
|
||||
cout << "k: " << k << "; p: " << (uint64_t)p << endl;
|
||||
// cout << "0: " << (uint64_t)fmt_occ_intv(fmt, 0)
|
||||
// << " ;31: " << (uint64_t)fmt_occ_intv(fmt, 31)
|
||||
// << " ;32: " << (uint64_t)fmt_occ_intv(fmt, 32)
|
||||
// << " ;64: " << (uint64_t)fmt_occ_intv(fmt, 64)
|
||||
// << " ;96: " << (uint64_t)fmt_occ_intv(fmt, 96) << endl;
|
||||
|
||||
|
||||
memcpy(cnt1, p, 4 * sizeof(uint32_t));
|
||||
memcpy(cnt2, p + 4 + b * 4, 4 * sizeof(uint32_t));
|
||||
cout << "cnt1: " << cnt1[0] << '\t' << cnt1[1] << '\t' << cnt1[2] << '\t' << cnt1[3] << endl;
|
||||
cout << "cnt2: " << cnt2[0] << '\t' << cnt2[1] << '\t' << cnt2[2] << '\t' << cnt2[3] << endl;
|
||||
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
|
||||
|
||||
p += 20; // 该地址是bwt和pre_bwt字符串数据的首地址
|
||||
end = p + ((k >> 4) - ((k & ~OCC_INTV_MASK) >> 4)); // this is the end point of the following loop
|
||||
// for (x = 0; p < end; ++p)
|
||||
// x += __occ_aux4(bwt, *p);
|
||||
// tmp = *p & ~((1U << ((~k & 15) << 1)) - 1);
|
||||
// x += __occ_aux4(bwt, tmp) - (~k & 15);
|
||||
// cnt[0] += x & 0xff;
|
||||
// cnt[1] += x >> 8 & 0xff;
|
||||
// cnt[2] += x >> 16 & 0xff;
|
||||
// cnt[3] += x >> 24;
|
||||
for (x1 = 0, x2 = 0; p < end; ++p)
|
||||
{
|
||||
x1 += __fmt_occ_e2_aux4(fmt, 4, *p);
|
||||
x2 += __fmt_occ_e2_aux4(fmt, b, *p);
|
||||
}
|
||||
tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
|
||||
x1 += __fmt_occ_e2_aux4(fmt, 4, tmp) - (~k & 7);
|
||||
x2 += __fmt_occ_e2_aux4(fmt, b, tmp);
|
||||
if (b == 0)
|
||||
x2 -= ~k & 7;
|
||||
// 如果跨过了second_primary,那么可能需要减掉一次累积值
|
||||
if (b == fmt->first_base && bwt_k_base_line < fmt->sec_primary && bwt_k_line >= fmt->sec_primary)
|
||||
{
|
||||
x2 -= 1 << (fmt->last_base << 3);
|
||||
}
|
||||
|
||||
cnt1[0] += x1 & 0xff;
|
||||
cnt1[1] += x1 >> 8 & 0xff;
|
||||
cnt1[2] += x1 >> 16 & 0xff;
|
||||
cnt1[3] += x1 >> 24;
|
||||
cnt2[0] += x2 & 0xff;
|
||||
cnt2[1] += x2 >> 8 & 0xff;
|
||||
cnt2[2] += x2 >> 16 & 0xff;
|
||||
cnt2[3] += x2 >> 24;
|
||||
|
||||
// cout << "fmt-occ: " << k << '\t' << cnt1[0] << '\t' << cnt1[1] << '\t' << cnt1[2] << '\t' << cnt1[3] << endl;
|
||||
// cout << "fmt-occ-2: " << k << '\t' << cnt2[0] << '\t' << cnt2[1] << '\t' << cnt2[2] << '\t' << cnt2[3] << endl;
|
||||
// cout << "bwt_k_base_line: " << bwt_k_base_line << endl;
|
||||
// cout << "bwt_k_line: " << bwt_k_line << endl;
|
||||
// cout << "sec_primary: " << fmt->sec_primary << endl;
|
||||
}
|
||||
|
||||
void fmt_2occ4(const FMTIndex *fmt, bwtint_t k, bwtint_t l, int b,
|
||||
uint32_t cntk1[4], uint32_t cntl1[4], uint32_t cntk2[4], uint32_t cntl2[4])
|
||||
// 对k行和l行同时计算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_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, l, b, cntl1, cntl2);
|
||||
// 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_occ4(fmt, k, b, cntk1, cntk2);
|
||||
fmt_occ4(fmt, l, b, cntl1, cntk1);
|
||||
// }
|
||||
// else
|
||||
// {
|
||||
// bwtint_t x, y;
|
||||
// uint32_t *p, tmp, *endk, *endl;
|
||||
// k -= (k >= bwt->primary); // because $ is not in bwt
|
||||
// l -= (l >= bwt->primary);
|
||||
// p = bwt_occ_intv(bwt, k);
|
||||
// memcpy(cntk, p, 4 * sizeof(bwtint_t));
|
||||
// p += sizeof(bwtint_t); // sizeof(bwtint_t) = 4*(sizeof(bwtint_t)/sizeof(uint32_t))
|
||||
// // prepare cntk[]
|
||||
// endk = p + ((k >> 4) - ((k & ~OCC_INTV_MASK) >> 4));
|
||||
// endl = p + ((l >> 4) - ((l & ~OCC_INTV_MASK) >> 4));
|
||||
// for (x = 0; p < endk; ++p)
|
||||
// x += __occ_aux4(bwt, *p);
|
||||
// y = x;
|
||||
// tmp = *p & ~((1U << ((~k & 15) << 1)) - 1);
|
||||
// x += __occ_aux4(bwt, tmp) - (~k & 15);
|
||||
// // calculate cntl[] and finalize cntk[]
|
||||
// for (; p < endl; ++p)
|
||||
// y += __occ_aux4(bwt, *p);
|
||||
// tmp = *p & ~((1U << ((~l & 15) << 1)) - 1);
|
||||
// y += __occ_aux4(bwt, tmp) - (~l & 15);
|
||||
// memcpy(cntl, cntk, 4 * sizeof(bwtint_t));
|
||||
// cntk[0] += x & 0xff;
|
||||
// cntk[1] += x >> 8 & 0xff;
|
||||
// cntk[2] += x >> 16 & 0xff;
|
||||
// cntk[3] += x >> 24;
|
||||
// cntl[0] += y & 0xff;
|
||||
// cntl[1] += y >> 8 & 0xff;
|
||||
// cntl[2] += y >> 16 & 0xff;
|
||||
// cntl[3] += y >> 24;
|
||||
// }
|
||||
if (_l >> OCC_INTV_SHIFT != _k >> OCC_INTV_SHIFT || k == (bwtint_t)(-1) || l == (bwtint_t)(-1))
|
||||
{
|
||||
fmt_e2_occ4(fmt, k, b, cntk1, cntk2);
|
||||
fmt_e2_occ4(fmt, l, b, cntl1, cntl2);
|
||||
}
|
||||
else
|
||||
{
|
||||
uint32_t x1, x2, y1, y2;
|
||||
uint32_t *p, tmp, *ek, *el;
|
||||
bwtint_t bwt_k_line = k, bwt_l_line = l, bwt_base_line = k >> OCC_INTV_SHIFT << OCC_INTV_SHIFT;
|
||||
|
||||
k -= (k >= fmt->primary); // because $ is not in bwt
|
||||
l -= (l >= fmt->primary);
|
||||
p = fmt_occ_intv(fmt, k);
|
||||
memcpy(cntk1, p, 4 * sizeof(uint32_t));
|
||||
memcpy(cntk2, p + 4 + b * 4, 4 * sizeof(uint32_t));
|
||||
memcpy(cntl1, cntk1, 4 * sizeof(uint32_t));
|
||||
memcpy(cntl2, cntk2, 4 * sizeof(uint32_t));
|
||||
p += 20;
|
||||
// prepare cntk[]
|
||||
ek = p + ((k >> 3) - ((k & ~OCC_INTV_MASK) >> 3));
|
||||
el = p + ((l >> 3) - ((l & ~OCC_INTV_MASK) >> 3));
|
||||
for (x1 = 0, x2 = 0; p < ek; ++p)
|
||||
{
|
||||
x1 += __fmt_occ_e2_aux4(fmt, 4, *p);
|
||||
x2 += __fmt_occ_e2_aux4(fmt, b, *p);
|
||||
}
|
||||
y1 = x1;
|
||||
y2 = x2;
|
||||
tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
|
||||
x1 += __fmt_occ_e2_aux4(fmt, 4, tmp) - (~k & 7);
|
||||
x2 += __fmt_occ_e2_aux4(fmt, b, tmp);
|
||||
if (b == 0)
|
||||
x2 -= ~k & 7;
|
||||
for (; p < el; ++p)
|
||||
{
|
||||
y1 += __fmt_occ_e2_aux4(fmt, 4, *p);
|
||||
y2 += __fmt_occ_e2_aux4(fmt, b, *p);
|
||||
}
|
||||
tmp = *p & ~((1U << ((~l & 7) << 2)) - 1);
|
||||
y1 += __fmt_occ_e2_aux4(fmt, 4, tmp) - (~l & 7);
|
||||
y2 += __fmt_occ_e2_aux4(fmt, b, tmp);
|
||||
if (b == 0)
|
||||
y2 -= ~l & 7;
|
||||
// 如果跨过了second_primary,那么可能需要减掉一次累积值
|
||||
if (b == fmt->first_base && bwt_base_line < fmt->sec_primary)
|
||||
{
|
||||
if (bwt_k_line >= fmt->sec_primary)
|
||||
x2 -= 1 << (fmt->last_base << 3);
|
||||
if (bwt_l_line >= fmt->sec_primary)
|
||||
y2 -= 1 << (fmt->last_base << 3);
|
||||
}
|
||||
cntk1[0] += x1 & 0xff;
|
||||
cntk1[1] += x1 >> 8 & 0xff;
|
||||
cntk1[2] += x1 >> 16 & 0xff;
|
||||
cntk1[3] += x1 >> 24;
|
||||
cntk2[0] += x2 & 0xff;
|
||||
cntk2[1] += x2 >> 8 & 0xff;
|
||||
cntk2[2] += x2 >> 16 & 0xff;
|
||||
cntk2[3] += x2 >> 24;
|
||||
|
||||
cntl1[0] += y1 & 0xff;
|
||||
cntl1[1] += y1 >> 8 & 0xff;
|
||||
cntl1[2] += y1 >> 16 & 0xff;
|
||||
cntl1[3] += y1 >> 24;
|
||||
cntl2[0] += y2 & 0xff;
|
||||
cntl2[1] += y2 >> 8 & 0xff;
|
||||
cntl2[2] += y2 >> 16 & 0xff;
|
||||
cntl2[3] += y2 >> 24;
|
||||
|
||||
// cout << "fmt-occ: " << k << '\t' << cntk1[0] << '\t' << cntk1[1] << '\t' << cntk1[2] << '\t' << cntk1[3] << endl;
|
||||
// cout << "fmt-occ-2: " << k << '\t' << cntk2[0] << '\t' << cntk2[1] << '\t' << cntk2[2] << '\t' << cntk2[3] << endl;
|
||||
// cout << "fmt-occ: " << l << '\t' << cntl1[0] << '\t' << cntl1[1] << '\t' << cntl1[2] << '\t' << cntl1[3] << endl;
|
||||
// cout << "fmt-occ-2: " << l << '\t' << cntl2[0] << '\t' << cntl2[1] << '\t' << cntl2[2] << '\t' << cntl2[3] << endl;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
#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])
|
||||
|
||||
// 扩展一个碱基，计算bwt str中各个碱基的occ
|
||||
void fmt_e1_occ4(const FMTIndex *fmt, bwtint_t k, uint32_t cnt[4])
|
||||
{
|
||||
uint32_t x;
|
||||
|
|
@ -402,69 +442,58 @@ void fmt_e1_occ4(const FMTIndex *fmt, bwtint_t k, uint32_t cnt[4])
|
|||
cnt[3] += x >> 24;
|
||||
}
|
||||
|
||||
void fmt_e2_occ4(const FMTIndex *fmt, bwtint_t k, int b, uint32_t cnt1[4], uint32_t cnt2[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])
|
||||
{
|
||||
uint32_t x1, x2;
|
||||
uint32_t *p, tmp, *end;
|
||||
bwtint_t bwt_k_line = k, bwt_k_base_line = k >> OCC_INTV_SHIFT << OCC_INTV_SHIFT;
|
||||
if (k == (bwtint_t)(-1))
|
||||
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))
|
||||
{
|
||||
p = fmt->bwt + 4 + b * 4;
|
||||
memset(cnt1, 0, 4 * sizeof(uint32_t));
|
||||
memcpy(cnt2, p, 4 * sizeof(uint32_t));
|
||||
return;
|
||||
fmt_e1_occ4(fmt, k, cntk);
|
||||
fmt_e1_occ4(fmt, l, cntl);
|
||||
}
|
||||
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 << "base: " << BASE[b] << endl;
|
||||
// cout << "k: " << k << "; c 0 cnt: " << p[0] << '\t' << p[1] << '\t' << p[2] << '\t' << p[3] << endl;
|
||||
memcpy(cnt1, p, 4 * sizeof(uint32_t));
|
||||
memcpy(cnt2, p + 4 + b * 4, 4 * sizeof(uint32_t));
|
||||
// cout << "[start: ] k: " << k << "; k line cnt: " << cnt[0] << '\t' << cnt[1] << '\t' << cnt[2] << '\t' << cnt[3] << endl;
|
||||
|
||||
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
|
||||
|
||||
for (x1 = 0, x2 = 0; p < end; ++p)
|
||||
else
|
||||
{
|
||||
x1 += __fmt_occ_e2_aux4(fmt, 4, *p);
|
||||
x2 += __fmt_occ_e2_aux4(fmt, b, *p);
|
||||
}
|
||||
//{
|
||||
// x += fmt->cnt_table[b][*p & 0xff]
|
||||
// + fmt->cnt_table[b][*p >> 8 & 0xff]
|
||||
// + fmt->cnt_table[b][*p >> 16 & 0xff]
|
||||
// + fmt->cnt_table[b][*p >> 24 & 0xff];
|
||||
// // cout << "p: " << *p << endl;
|
||||
// // print_base_uint32(*p);
|
||||
// // cout << (fmt->cnt_table[b][*p & 0xff] >> 24) << ' '
|
||||
// // << fmt->cnt_table[b][*p >> 24 & 0xff]
|
||||
// // << endl;
|
||||
//}
|
||||
uint32_t x1, y1;
|
||||
uint32_t *p, tmp, *endk, *endl;
|
||||
|
||||
tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
|
||||
x1 += __fmt_occ_e2_aux4(fmt, 4, tmp) - (~k & 7);
|
||||
x2 += __fmt_occ_e2_aux4(fmt, b, tmp);
|
||||
if (b == 0)
|
||||
x2 -= ~k & 7;
|
||||
// 如果跨过了second_primary,那么可能需要减掉一次累积值
|
||||
if (b == fmt->first_base && bwt_k_base_line < fmt->sec_primary && bwt_k_line >= fmt->sec_primary)
|
||||
{
|
||||
x2 -= 1 << (fmt->last_base << 3);
|
||||
k -= (k >= fmt->primary); // because $ is not in bwt
|
||||
l -= (l >= fmt->primary);
|
||||
p = fmt_occ_intv(fmt, k);
|
||||
memcpy(cntk, p, 4 * sizeof(uint32_t));
|
||||
memcpy(cntl, p, 4 * sizeof(uint32_t));
|
||||
p += 20;
|
||||
// prepare cntk[]
|
||||
endk = p + ((k >> 3) - ((k & ~OCC_INTV_MASK) >> 3));
|
||||
endl = p + ((l >> 3) - ((l & ~OCC_INTV_MASK) >> 3));
|
||||
for (x1 = 0; p < endk; ++p)
|
||||
{
|
||||
x1 += __fmt_occ_e2_aux4(fmt, 4, *p);
|
||||
}
|
||||
y1 = x1;
|
||||
tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
|
||||
x1 += __fmt_occ_e2_aux4(fmt, 4, tmp) - (~k & 7);
|
||||
for (; p < endl; ++p)
|
||||
{
|
||||
y1 += __fmt_occ_e2_aux4(fmt, 4, *p);
|
||||
}
|
||||
tmp = *p & ~((1U << ((~k & 7) << 2)) - 1);
|
||||
y1 += __fmt_occ_e2_aux4(fmt, 4, tmp) - (~k & 7);
|
||||
|
||||
cntk[0] += x1 & 0xff;
|
||||
cntk[1] += x1 >> 8 & 0xff;
|
||||
cntk[2] += x1 >> 16 & 0xff;
|
||||
cntk[3] += x1 >> 24;
|
||||
|
||||
cntl[0] += y1 & 0xff;
|
||||
cntl[1] += y1 >> 8 & 0xff;
|
||||
cntl[2] += y1 >> 16 & 0xff;
|
||||
cntl[3] += y1 >> 24;
|
||||
}
|
||||
// x += __occ_aux4(bwt, tmp) - (~k & 15);
|
||||
// cout << "x: " << x << " b:" << b << endl;
|
||||
cnt1[0] += x1 & 0xff;
|
||||
cnt1[1] += x1 >> 8 & 0xff;
|
||||
cnt1[2] += x1 >> 16 & 0xff;
|
||||
cnt1[3] += x1 >> 24;
|
||||
cnt2[0] += x2 & 0xff;
|
||||
cnt2[1] += x2 >> 8 & 0xff;
|
||||
cnt2[2] += x2 >> 16 & 0xff;
|
||||
cnt2[3] += x2 >> 24;
|
||||
// cout << "[end : ]k: " << k << "; k line cnt: " << cnt[0] << '\t' << cnt[1] << '\t' << cnt[2] << '\t' << cnt[3] << endl;
|
||||
}
|
||||
|
||||
// 扩展一个碱基
|
||||
void fmt_extend1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_back, int b1)
|
||||
{
|
||||
uint32_t tk[4], tl[4];
|
||||
|
|
@ -472,6 +501,7 @@ void fmt_extend1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_bac
|
|||
|
||||
fmt_e1_occ4(fmt, ik->x[!is_back] - 1, tk);
|
||||
fmt_e1_occ4(fmt, ik->x[!is_back] - 1 + ik->x[2], tl);
|
||||
fmt_e1_2occ4(fmt, 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] = fmt->L2[i] + 1 + tk[i]; // 起始行位置，互补链
|
||||
|
|
@ -483,19 +513,22 @@ void fmt_extend1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_bac
|
|||
*ik = ok[b1];
|
||||
}
|
||||
|
||||
// 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)
|
||||
{
|
||||
uint32_t tk1[4], tl1[4], tk2[4], tl2[4];
|
||||
int i;
|
||||
|
||||
// fmt_e2_occ4(fmt, ik->x[!is_back] - 1, b1, tk1, tk2);
|
||||
// fmt_e2_occ4(fmt, ik->x[!is_back] - 1 + ik->x[2], b1, tl1, tl2);
|
||||
// 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_2occ4(fmt, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], b1, tk1, tk2, tl1, tl2);
|
||||
|
||||
// fmt_2occ4(fmt, ik->x[!is_back] - 1, ik->x[!is_back] - 1 + ik->x[2], b1, tk1, tl1, tk2, tl2); // 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 << "k: " << tk1[0] << '\t' << tk1[1] << '\t' << tk1[2] << '\t' << tk1[3] << endl;
|
||||
// cout << "l: " << tl1[0] << '\t' << tl1[1] << '\t' << tl1[2] << '\t' << tl1[3] << endl;
|
||||
// cout << "k: " << tk2[0] << '\t' << tk2[1] << '\t' << tk2[2] << '\t' << tk2[3] << endl;
|
||||
// cout << "l: " << tl2[0] << '\t' << tl2[1] << '\t' << tl2[2] << '\t' << tl2[3] << endl;
|
||||
|
||||
fmt_e2_occ4(fmt, ik->x[!is_back] - 1, b1, tk1, tk2);
|
||||
fmt_e2_occ4(fmt, ik->x[!is_back] - 1 + ik->x[2], b1, tl1, tl2);
|
||||
|
||||
// fmt_e2_occ(fmt, -1, 0, tk);
|
||||
|
||||
// 这里是反向扩展
|
||||
for (i = 0; i != 4; ++i)
|
||||
{
|
||||
|
|
@ -505,11 +538,17 @@ void fmt_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t ok[4], int is_bac
|
|||
// 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] <= fmt->primary && ik->x[!is_back] + ik->x[2] - 1 >= fmt->primary);
|
||||
for (i = 2; i >= b1; --i)
|
||||
ok[i].x[is_back] = ok[i + 1].x[is_back] + tl1[i + 1] - tk1[i + 1];
|
||||
ok[2].x[is_back] = ok[3].x[is_back] + tl1[3] - tk1[3];
|
||||
ok[1].x[is_back] = ok[2].x[is_back] + tl1[2] - tk1[2];
|
||||
ok[0].x[is_back] = ok[1].x[is_back] + tl1[1] - tk1[1];
|
||||
|
||||
cout << "fmt-d: " << BASE[b1] << '\t' << ok[b1].x[is_back] << '\t' << ok[b1].x[2] << endl;
|
||||
|
||||
ok[3].x[is_back] = ok[b1].x[is_back] + (ok[b1].x[!is_back] <= fmt->primary && ok[b1].x[!is_back] + ok[b1].x[2] - 1 >= fmt->primary);
|
||||
for (i = 2; i >= b2; --i)
|
||||
ok[i].x[is_back] = ok[i + 1].x[is_back] + ok[i + 1].x[2];
|
||||
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[b2];
|
||||
}
|
||||
// 利用fmt搜索seed，完整搜索，只需要单向搜索
|
||||
|
|
@ -557,13 +596,18 @@ int main_fmtidx(int argc, char **argv)
|
|||
//create_bwt_mtx(seq);
|
||||
//cout << seq << endl;
|
||||
|
||||
bwt_t *bwt = restore_bwt_str(argv[1]); // 读取bwt原始字符串（带ACGT总的累积量）
|
||||
create_interval_occ_bwt(bwt); // 根据bwt字符串创建包含interval occ的bwt（128碱基+ACGT累积量）
|
||||
bwt_t *bwt = restore_bwt(argv[1]); // 读取bwt原始字符串（带ACGT总的累积量）
|
||||
// create_interval_occ_bwt(bwt); // 根据bwt字符串创建包含interval occ的bwt（128碱基+ACGT累积量）
|
||||
cout << "L2: " << bwt->L2[0] << '\t' << bwt->L2[1] << '\t' << bwt->L2[2] << '\t'
|
||||
<< bwt->L2[3] << '\t' << bwt->L2[4] << endl;
|
||||
|
||||
string s = "AACCCTAA";
|
||||
|
||||
srand(time(NULL));
|
||||
s = generate_rand_seq(10);
|
||||
cout << "seq: " << s << endl;
|
||||
// s = "TTC";
|
||||
|
||||
bwt_search(bwt, s);
|
||||
bwt_search2(bwt, s);
|
||||
|
||||
|
|
@ -573,6 +617,9 @@ int main_fmtidx(int argc, char **argv)
|
|||
// }
|
||||
// TGGGAT
|
||||
FMTIndex *fmt = create_fmt_from_bwt(bwt);
|
||||
dump_fmt("ref.fmt", fmt);
|
||||
// FMTIndex *fmt = restore_fmt("tiny.fmt");
|
||||
|
||||
fmt_search(fmt, s);
|
||||
// cout << bwt->bwt_size << endl;
|
||||
// cout << bwt->seq_len << endl;
|
||||
|
|
|
|||
14
fmt_index.h
14
fmt_index.h
|
|
@ -3,6 +3,14 @@
|
|||
|
||||
#include "bwt.h"
|
||||
|
||||
// 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）
|
||||
#define fmt_occ_intv(b, k) ((b)->bwt + (k) / OCC_INTERVAL * (OCC_INTERVAL / 8 + 20))
|
||||
// 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])
|
||||
|
||||
// fm-index, extend twice in one search step (one memory access)
|
||||
struct FMTIndex
|
||||
{
|
||||
|
|
@ -14,9 +22,9 @@ 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
|
||||
int sec_bcp; // base couple for sec primary line, AA=>0, AC=>1 ... TT=>15
|
||||
int first_base; // 序列的第一个碱基2bit的int类型，0,1,2,3
|
||||
int last_base; // dollar转换成的base
|
||||
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
|
||||
// suffix array
|
||||
int sa_intv;
|
||||
bwtint_t n_sa;
|
||||
|
|
|
|||
100
util.cpp
100
util.cpp
|
|
@ -1,7 +1,16 @@
|
|||
#define FSYNC_ON_FLUSH
|
||||
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <sys/time.h>
|
||||
|
||||
#include <string.h>
|
||||
#include <errno.h>
|
||||
#ifdef FSYNC_ON_FLUSH
|
||||
#include <sys/types.h>
|
||||
#include <sys/stat.h>
|
||||
#include <unistd.h>
|
||||
#endif
|
||||
#include <stdarg.h>
|
||||
#include "util.h"
|
||||
|
||||
// base转成2bit值
|
||||
|
|
@ -39,6 +48,48 @@ void _err_fatal_simple_core(const char *func, const char *msg)
|
|||
abort();
|
||||
}
|
||||
|
||||
// 打印信息并停止运行
|
||||
void _err_fatal_simple(const char *func, const char *msg)
|
||||
{
|
||||
fprintf(stderr, "[%s] %s\n", func, msg);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
void err_fatal(const char *header, const char *fmt, ...)
|
||||
{
|
||||
va_list args;
|
||||
va_start(args, fmt);
|
||||
fprintf(stderr, "[%s] ", header);
|
||||
vfprintf(stderr, fmt, args);
|
||||
fprintf(stderr, "\n");
|
||||
va_end(args);
|
||||
exit(EXIT_FAILURE);
|
||||
}
|
||||
|
||||
void err_fatal_core(const char *header, const char *fmt, ...)
|
||||
{
|
||||
va_list args;
|
||||
va_start(args, fmt);
|
||||
fprintf(stderr, "[%s] ", header);
|
||||
vfprintf(stderr, fmt, args);
|
||||
fprintf(stderr, " Abort!\n");
|
||||
va_end(args);
|
||||
abort();
|
||||
}
|
||||
|
||||
// 打开文件流
|
||||
FILE *err_xopen_core(const char *func, const char *fn, const char *mode)
|
||||
{
|
||||
FILE *fp = 0;
|
||||
if (strcmp(fn, "-") == 0)
|
||||
return (strstr(mode, "r")) ? stdin : stdout;
|
||||
if ((fp = fopen(fn, mode)) == 0)
|
||||
{
|
||||
err_fatal(func, "fail to open file '%s' : %s", fn, strerror(errno));
|
||||
}
|
||||
return fp;
|
||||
}
|
||||
|
||||
// 读取数据
|
||||
bwtint_t fread_fix(FILE *fp, bwtint_t size, void *a)
|
||||
{ /* Mac/Darwin has a bug when reading data longer than 2GB. This function fixes this issue by reading data in small chunks */
|
||||
|
|
@ -53,4 +104,51 @@ bwtint_t fread_fix(FILE *fp, bwtint_t size, void *a)
|
|||
offset += x;
|
||||
}
|
||||
return offset;
|
||||
}
|
||||
|
||||
// 写二进制文件
|
||||
size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream)
|
||||
{
|
||||
size_t ret = fwrite(ptr, size, nmemb, stream);
|
||||
if (ret != nmemb)
|
||||
_err_fatal_simple("fwrite", strerror(errno));
|
||||
return ret;
|
||||
}
|
||||
|
||||
// 刷新文件流
|
||||
int err_fflush(FILE *stream)
|
||||
{
|
||||
int ret = fflush(stream);
|
||||
if (ret != 0)
|
||||
_err_fatal_simple("fflush", strerror(errno));
|
||||
|
||||
#ifdef FSYNC_ON_FLUSH
|
||||
/* Calling fflush() ensures that all the data has made it to the
|
||||
kernel buffers, but this may not be sufficient for remote filesystems
|
||||
(e.g. NFS, lustre) as an error may still occur while the kernel
|
||||
is copying the buffered data to the file server. To be sure of
|
||||
catching these errors, we need to call fsync() on the file
|
||||
descriptor, but only if it is a regular file. */
|
||||
{
|
||||
struct stat sbuf;
|
||||
if (0 != fstat(fileno(stream), &sbuf))
|
||||
_err_fatal_simple("fstat", strerror(errno));
|
||||
|
||||
if (S_ISREG(sbuf.st_mode))
|
||||
{
|
||||
if (0 != fsync(fileno(stream)))
|
||||
_err_fatal_simple("fsync", strerror(errno));
|
||||
}
|
||||
}
|
||||
#endif
|
||||
return ret;
|
||||
}
|
||||
|
||||
// 关闭文件流
|
||||
int err_fclose(FILE *stream)
|
||||
{
|
||||
int ret = fclose(stream);
|
||||
if (ret != 0)
|
||||
_err_fatal_simple("fclose", strerror(errno));
|
||||
return ret;
|
||||
}
|
||||
12
util.h
12
util.h
|
|
@ -10,7 +10,9 @@ typedef uint64_t bwtint_t;
|
|||
if ((cond) == 0) \
|
||||
_err_fatal_simple_core(__func__, msg)
|
||||
|
||||
double realtime(void);
|
||||
#define xopen(fn, mode) err_xopen_core(__func__, fn, mode)
|
||||
|
||||
double realtime(void);
|
||||
|
||||
// 在fm-indexv(或者bwt)查找过程中，记录结果
|
||||
struct bwtintv_t
|
||||
|
|
@ -27,5 +29,13 @@ void _err_fatal_simple_core(const char *func, const char *msg);
|
|||
int bval(char b);
|
||||
// 互补碱基值
|
||||
int cbval(char b);
|
||||
// 打开文件流
|
||||
FILE *err_xopen_core(const char *func, const char *fn, const char *mode);
|
||||
// 写二进制文件
|
||||
size_t err_fwrite(const void *ptr, size_t size, size_t nmemb, FILE *stream);
|
||||
// 刷新文件流
|
||||
int err_fflush(FILE *stream);
|
||||
// 关闭文件流
|
||||
int err_fclose(FILE *stream);
|
||||
|
||||
#endif
|
||||
Loading…
Reference in New Issue