Mercurial > repos > siyuan > prada
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 |
| parents | |
| children |
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| -1:000000000000 | 0:acc2ca1a3ba4 |
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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, int n_seqs, 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 |