26 lines
917 B
C
26 lines
917 B
C
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#ifndef FMT_INDEX_H_
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#define FMT_INDEX_H_
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#include "bwt.h"
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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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int sec_bcp; // base couple for sec primary line, AA=>0, AC=>1 ... TT=>15
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int first_base; // 序列的第一个碱基2bit的int类型，0,1,2,3
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int 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
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