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1 #ifndef BWASE_H
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2 #define BWASE_H
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3
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4 #include "bntseq.h"
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5 #include "bwt.h"
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6 #include "bwtaln.h"
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7
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8 #ifdef __cplusplus
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9 extern "C" {
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10 #endif
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11
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12 // Initialize mapping tables in the bwa single-end mapper.
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13 void bwase_initialize();
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14 // Calculate the approximate position of the sequence from the specified bwt with loaded suffix array.
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15 void bwa_cal_pac_pos_core(const bntseq_t *bns, const bwt_t* bwt, bwa_seq_t* seq, const int max_mm, const float fnr);
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16 // Refine the approximate position of the sequence to an actual placement for the sequence.
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17 void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, bntseq_t *ntbns);
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18 // Backfill certain alignment properties mainly centering around number of matches.
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19 void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
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20 // Calculate the end position of a read given a certain sequence.
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21 int64_t pos_end(const bwa_seq_t *p);
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22 //
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23 bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int len, int *strand);
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24
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25 #ifdef __cplusplus
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26 }
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27 #endif
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28
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29 #endif // BWASE_H
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