34 lines
1.7 KiB
C
34 lines
1.7 KiB
C
#ifndef FMT_INDEX_H_
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#define FMT_INDEX_H_
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#include "bwt.h"
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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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#define fmt_occ_intv(b, k) ((b)->bwt + (k) / OCC_INTERVAL * (OCC_INTERVAL / 8 + 20))
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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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// 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_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
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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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// 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 |