108 lines
3.2 KiB
C
108 lines
3.2 KiB
C
#ifndef BWA_H_
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#define BWA_H_
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#include <stdint.h>
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#define BWA_DEF_MAX_SCORE 2048
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#define BWA_MAX_QUERY_LEN 1024
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// BWA index
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struct bwa_idx_t;
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typedef struct bwa_idx_t bwa_idx_t;
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// Buffer for BWA alignment
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struct bwa_buf_t;
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typedef struct bwa_buf_t bwa_buf_t;
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// BWA alignment options
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typedef struct {
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int s_gapo, s_gape; // gap open and extension penalties; the mismatch penalty is fixed at 3
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int max_diff, max_gapo, max_gape; // max differences (-1 to use fnr for length-adjusted max diff), gap opens and gap extensions
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int seed_len, max_seed_diff; // seed length and max differences allowed in the seed
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float fnr; // parameter for automatic length-adjusted max differences
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} bwa_opt_t;
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// default BWA alignment options
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extern bwa_opt_t bwa_def_opt; // = { 11, 4, -1, 1, 6, 32, 2, 0.04 }
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// an interval hit in the SA coordinate; basic unit in .sai files
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typedef struct {
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uint32_t n_mm:16, n_gapo:8, n_gape:8;
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int score;
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uint64_t k, l; // [k,l] is the SA interval; each interval has l-k+1 hits
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} bwa_sai1_t;
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// all interval hits in the SA coordinate
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typedef struct {
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int n; // number of interval hits
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bwa_sai1_t *sai;
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} bwa_sai_t;
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// an alignment
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typedef struct {
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uint32_t n_n:8, n_gap:12, n_mm:12; // number of ambiguous bases, gaps and mismatches in the alignment
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int32_t ref_id; // referece sequence index (the first seq is indexed by 0)
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uint32_t offset; // coordinate on the reference; zero-based
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uint32_t n_cigar:16, flag:16; // number of CIGAR operations; SAM flag
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uint32_t *cigar; // CIGAR in the BAM 28+4 encoding; having n_cigar operations
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} bwa_aln_t;
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typedef struct {
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int mapQs, mapQ, c1, c2;
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uint64_t sa;
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bwa_sai1_t *which;
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bwa_sai_t sai;
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bwa_aln_t one;
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} bwa_one_t;
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typedef struct {
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double avg, std, ap_prior;
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uint64_t low, high, high_bayesian;
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} bwa_pestat_t;
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#ifdef __cplusplus
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extern "C" {
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#endif
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// load a BWA index
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bwa_idx_t *bwa_idx_load(const char *prefix);
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void bwa_idx_destroy(bwa_idx_t *p);
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// allocate a BWA alignment buffer; if unsure, set opt to &bwa_def_opt and max_score to BWA_DEF_MAX_SCORE
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bwa_buf_t *bwa_buf_init(const bwa_opt_t *opt, int max_score);
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void bwa_buf_destroy(bwa_buf_t *p);
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/**
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* Find all the SA intervals
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*
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* @param idx BWA index; multiple threads can share the same index
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* @param buf BWA alignment buffer; each thread should have its own buffer
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* @param seq NULL terminated C string, consisting of A/C/G/T/N only
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*
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* @return SA intervals seq is matched to
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*/
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bwa_sai_t bwa_sai(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq);
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/**
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* Construct an alignment in the base-pair coordinate
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*
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* @param idx BWA index
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* @param buf BWA alignment buffer
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* @param seq NULL terinated C string
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* @param sa Suffix array value
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* @param n_gaps Number of gaps (typically equal to bwa_sai1_t::n_gapo + bwa_sai1_t::n_gape
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*
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* @return An alignment
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*/
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void bwa_sa2aln(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, uint64_t sa, int n_gaps, bwa_aln_t *aln);
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bwa_one_t *bwa_se(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, int gen_cigar);
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void bwa_one_destroy(bwa_one_t *one);
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#ifdef __cplusplus
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}
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#endif
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#endif
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