Mercurial > repos > ashvark > qiime_1_8_0
view bwa-0.6.2/bwase.h @ 2:a294fbfcb1db draft default tip
Uploaded BWA
author | ashvark |
---|---|
date | Fri, 18 Jul 2014 07:55:59 -0400 |
parents | dd1186b11b3b |
children |
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#ifndef BWASE_H #define BWASE_H #include "bntseq.h" #include "bwt.h" #include "bwtaln.h" #ifdef __cplusplus extern "C" { #endif // Initialize mapping tables in the bwa single-end mapper. void bwase_initialize(); // Calculate the approximate position of the sequence from the specified bwt with loaded suffix array. 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); // Refine the approximate position of the sequence to an actual placement for the sequence. void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, bntseq_t *ntbns); // Backfill certain alignment properties mainly centering around number of matches. void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s); // Calculate the end position of a read given a certain sequence. int64_t pos_end(const bwa_seq_t *p); // bwtint_t bwa_sa2pos(const bntseq_t *bns, const bwt_t *bwt, bwtint_t sapos, int len, int *strand); #ifdef __cplusplus } #endif #endif // BWASE_H