44 lines
1.1 KiB
C
44 lines
1.1 KiB
C
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/*
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Description: 通过fmt-idx数据结构对seed过程进行加速（fm-index twice search in one time）
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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 BWA_FMT_IDX_H
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#define BWA_FMT_IDX_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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typedef uint64_t bwtint_t;
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/*
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ignore the first 12 bases, and give the entrence directly
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*/
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typedef struct {
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uint8_t range[9]; // 前36位表示起始行，后36位表示结束行（fm-index索引行）
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} kmer_range_t;
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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 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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// kmer entry
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kmer_range_t *kmer_range;
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// occurance array, separated to two parts
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uint32_t cnt_table[256];
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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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bwtint_t *sa;
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} bwtd_t;
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// 创建fmt-index索引数据
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void BuildBwtdFromBwt(bwt_t *bwt, bwtd_t **bwtd_p);
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#endif
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