Mercurial > repos > ashvark > qiime_1_8_0
comparison bwa-0.6.2/bwase.h @ 2:a294fbfcb1db draft default tip
Uploaded BWA
author | ashvark |
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date | Fri, 18 Jul 2014 07:55:59 -0400 |
parents | dd1186b11b3b |
children |
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1:a9636dc1e99a | 2:a294fbfcb1db |
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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 bntseq_t *bns, const bwt_t* 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 bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int len, int *strand); | |
24 | |
25 #ifdef __cplusplus | |
26 } | |
27 #endif | |
28 | |
29 #endif // BWASE_H |