121 lines
4.9 KiB
C
121 lines
4.9 KiB
C
/*
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Description: fmt-idxseed (fm-index twice extend in one search step)
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Copyright : All right reserved by
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Author :
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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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#include "utils.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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// c（），
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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（bwt str（$））check point occ（kOCC_INTERVAL）
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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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#define fmt_occ_intv(b, k) ((b)->bwt + ((k) >> 8) * 80)
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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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#define fmt_occ_intv(b, k) ((b)->bwt + ((k) >> 8 << 6))
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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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// valbwt basebpre-bwtT G C A（32（8bit）），occocc
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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
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#define SA_INTV 4
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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]; // 16-24b（）occ，8-16bocc，0-8aocc，ba
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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; // 2bitint，0,1,2,3
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uint8_t last_base; // dollarbase
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// ref pac
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bwtint_t l_pac; //
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uint8_t *pac; // 2bit
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// kmerfmt
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KmerHash kmer_hash;
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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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// fmt
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void dump_fmt(const char *fn, const FMTIndex *fmt);
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// fmt
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FMTIndex *fmt_restore_fmt(const char *fn);
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void fmt_create_kmer_index(FMTIndex *fmt);
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// kmer hash
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void fmt_dump_kmer_idx(const char *fn, const KmerHash *kh);
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// kmer hash
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KmerHash fmt_restore_kmer_idx(const char *fn);
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// sa
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void fmt_restore_sa(const char *fn, FMTIndex *fmt);
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// interval-bwtfmt-index
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FMTIndex *create_fmt_from_bwt(bwt_t *bwt);
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// ，bwt basebpre-bwt strocc
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void fmt_direct_e2_occ(const FMTIndex *fmt, bwtint_t k, int b1, int b2, bwtint_t cnt[4]);
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void fmt_direct2_e2_occ(const FMTIndex *fmt, bwtint_t k, int b1, int b2, bwtint_t cnt[4]);
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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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void fmt_direct2_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok1, bwtintv_t *ok2, int is_back, int b1, int b2);
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void fmt_direct_extend2(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok1, bwtintv_t *ok2, int is_back, int b1, int b2);
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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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//
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void fmt_direct_extend1(const FMTIndex *fmt, bwtintv_t *ik, bwtintv_t *ok, int is_back, int b1);
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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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// KMER_LEN，
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// void gen_all_seq(char **seq_arr, int kmer_len);
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// kmerposfmt
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void kmer_setval_at(uint8_t *mem_addr, bwtintv_t ik, int pos);
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// kmerfmt
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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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// smem（seed）
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int fmt_smem(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv, int min_seed_len, bwtintv_t *lm, bwtintv_v *mem, bwtintv_v *tmpvec);
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int fmt_smem_2(const FMTIndex *fmt, int len, const uint8_t *q, int x, int min_intv, int min_seed_len, bwtintv_t *lm, bwtintv_v *mem, bwtintv_v *tmpvec, uint32_v qev);
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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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bwtint_t fmt_sa_offset(const FMTIndex *fmt, bwtint_t k);
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void fmt_gen_cnt_occ(FMTIndex *fmt);
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#endif |