142 lines
5.6 KiB
C
142 lines
5.6 KiB
C
/*
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Description: 通过fmt-idx数据结构对seed过程进行加速 (fm-index twice extend in one search step)
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2023/12/24
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*/
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#ifndef FMT_INDEX_H_
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#define FMT_INDEX_H_
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#include <stdint.h>
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#include <stddef.h>
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#include "bwt.h"
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#define FMT_OCC_INTV_SHIFT 8
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#define FMT_OCC_INTERVAL (1 << FMT_OCC_INTV_SHIFT)
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#define FMT_OCC_INTV_MASK (FMT_OCC_INTERVAL - 1)
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#define FMT_MID_INTV_SHIFT 6
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#define FMT_MID_INTERVAL (1 << FMT_MID_INTV_SHIFT)
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#define FMT_MID_INTV_MASK (FMT_MID_INTERVAL - 1)
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// #undef FMT_MID_INTERVAL
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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 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)
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// 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）
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#if FMT_MID_INTERVAL == 8
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#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 144))
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#elif FMT_MID_INTERVAL == 16
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#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 80))
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#elif FMT_MID_INTERVAL == 32
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#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 48))
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#elif FMT_MID_INTERVAL == 64
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#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 32))
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#elif FMT_MID_INTERVAL == 128
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#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 24))
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#else
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#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 20))
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#endif
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// 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，下边应该是计算扩展的两个碱基的occ和大于碱基的occ
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#define __fmt_occ_e2_aux2(fmt, b, val) \
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((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])
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#define __fmt_mid_sum(x) \
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((x) >> 24 & 0xff) + ((x) >> 16 & 0xff) + ((x) >> 8 & 0xff) + ((x) & 0xff)
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// sa存储的行间隔
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#define SA_INTV 2
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#define HASH_KMER_LEN 14
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#define BIT_KMER_LEN 17
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// 用来保存kmer对应的fmt的位置信息
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typedef struct
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{
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// 40+40+32 14个byte，这样好处理
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uint8_t intv_arr[14]; // 保存kmer中每扩展一个碱基对应的bwtintv_t数据
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} KmerEntry;
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typedef struct
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{
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uint8_t intv_arr[140]; // 保存长度为10的kmer，每个碱基对应的bwt匹配信息
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} KmerEntryArr;
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// 保存各个位置对应的bwt匹配信息
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typedef struct
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{
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KmerEntryArr *ke10;
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KmerEntry *ke11;
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KmerEntry *ke12;
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KmerEntry *ke13;
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KmerEntry *ke14;
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} KmerHash;
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// fm-index, extend twice in one search step (one memory access)
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typedef struct
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{
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bwtint_t primary; // S^{-1}(0), or the primary index of BWT
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bwtint_t sec_primary; // second primary line
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bwtint_t L2[5]; // C(), cumulative count
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bwtint_t seq_len; // sequence length
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bwtint_t bwt_size; // size of bwt, about seq_len/4
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uint32_t *bwt; // BWT
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// occurance array, separated to two parts
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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
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uint8_t sec_bcp; // base couple for sec primary line, AA=>0, AC=>1 ... TT=>15
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uint8_t first_base; // 序列的第一个碱基2bit的int类型，0,1,2,3
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uint8_t last_base; // dollar转换成的base
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// ref pac相关
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bwtint_t l_pac; // 参考序列长度
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uint8_t *pac; // 保存2bit编码的参考序列
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// 保存kmer对应的fmt位置信息
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KmerHash kmer_hash;
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// kmer_bit好像效果一般
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uint16_t *kmer_bit; // 用来检测特定长度序列有没有fm-index匹配
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int bit_kmer_len;
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// suffix array
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int sa_intv;
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bwtint_t n_sa;
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uint8_t *sa;
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} FMTIndex;
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// 将fmt结构数据写入到二进制文件
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void dump_fmt(const char *fn, const FMTIndex *fmt);
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// 从文件中读取fmt结构数据
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FMTIndex *fmt_restore_fmt(const char *fn);
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// 将kmer hash数据写入到文件
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void fmt_dump_kmer_idx(const char *fn, const KmerHash *kh);
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// 从文件中读取kmer hash信息
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KmerHash fmt_restore_kmer_idx(const char *fn);
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// 读取kmer bit数据
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uint16_t *fmt_restore_kmer_bit(const char *fn, int kmer_len);
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// 读取sa数据
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void fmt_restore_sa(const char *fn, FMTIndex *fmt);
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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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// 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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// 扩展两个碱基
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void fmt_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok1, bwtintv_t *ok2, int is_back, int b1, int b2);
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// 扩展一个碱基
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void fmt_extend1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok, int is_back, int b1);
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// 生成所有KMER_LEN长度的序列，字符串表示
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void gen_all_seq(char **seq_arr, int kmer_len);
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// 设置kmer第pos个碱基对应的fmt匹配信息
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void kmer_setval_at(uint8_t *mem_addr, bwtintv_t ik, int pos);
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// 获取kmer的fmt匹配信息
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void kmer_getval_at(uint8_t *mem_addr, bwtintv_t *ok, int pos);
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void fmt_kmer_get(const FMTIndex *fmt, bwtintv_t *ok, uint32_t qbit, int pos);
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// 找smem（seed）
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int fmt_smem(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv, bwtintv_v *mem, bwtintv_v *tmpvec[2]);
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int fmt_seed_strategy1(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_len, int max_intv, bwtintv_t *mem);
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bwtint_t fmt_sa(const FMTIndex *fmt, bwtint_t k);
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#endif |