comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/bwase.h~ @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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1 #ifndef BWASE_H
2 #define BWASE_H
3
4 #include "bntseq.h"
5 #include "bwt.h"
6 #include "bwtaln.h"
7
8 #ifdef __cplusplus
9 extern "C" {
10 #endif
11
12 // Initialize mapping tables in the bwa single-end mapper.
13 void bwase_initialize();
14 // Calculate the approximate position of the sequence from the specified bwt with loaded suffix array.
15 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);
16 // Refine the approximate position of the sequence to an actual placement for the sequence.
17 void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, bntseq_t *ntbns);
18 // Backfill certain alignment properties mainly centering around number of matches.
19 void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
20 // Calculate the end position of a read given a certain sequence.
21 int64_t pos_end(const bwa_seq_t *p);
22
23 #ifdef __cplusplus
24 }
25 #endif
26
27 #endif // BWASE_H