28 lines
960 B
C
28 lines
960 B
C
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#ifndef BWASE_H
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#define BWASE_H
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#include "bntseq.h"
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#include "bwt.h"
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#include "bwtaln.h"
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#ifdef __cplusplus
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extern "C" {
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#endif
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// Initialize mapping tables in the bwa single-end mapper.
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void bwase_initialize();
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// Calculate the approximate position of the sequence from the specified bwt with loaded suffix array.
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void bwa_cal_pac_pos_core(const bwt_t* forward_bwt, const bwt_t* reverse_bwt, bwa_seq_t* seq, const int max_mm, const float fnr);
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// Refine the approximate position of the sequence to an actual placement for the sequence.
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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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// Backfill certain alignment properties mainly centering around number of matches.
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void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
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// Calculate the end position of a read given a certain sequence.
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int64_t pos_end(const bwa_seq_t *p);
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#ifdef __cplusplus
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}
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#endif
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#endif // BWASE_H
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