94 lines
3.6 KiB
C
94 lines
3.6 KiB
C
#ifndef FMT_INDEX_H_
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#define FMT_INDEX_H_
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#define FMT_OCC_INTV_SHIFT 8
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#define FMT_OCC_INTERVAL (1LL << 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 (1LL << 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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#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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// 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
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#define __fmt_occ_e2_aux4(fmt, b, val) \
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((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])
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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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#define XMER_LEN 14
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// sa存储的行间隔
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#define SA_INTV 4
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#define SA_BYTES(n_sa) ((((33 * (n_sa) + 7) / 8) & (~7L)) + 8)
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// x-mer entry, 1 - 14个碱基组成的hash key
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struct XmerEntry
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{
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uint8_t intv_arr[14];
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};
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struct XmerEntryArr
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{
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uint8_t intv_arr[140];
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};
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struct XmerHash
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{
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XmerEntryArr *xe10;
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XmerEntry *xe11;
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XmerEntry *xe12;
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XmerEntry *xe13;
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XmerEntry *xe14;
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};
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// fm-index, extend twice in one search step (one memory access)
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struct FMTIndex
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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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XmerHash xmer_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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};
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#endif |