diff bwa-0.6.2/bwa.h @ 2:a294fbfcb1db draft default tip

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/bwa.h	Fri Jul 18 07:55:59 2014 -0400
@@ -0,0 +1,107 @@
+#ifndef BWA_H_
+#define BWA_H_
+
+#include <stdint.h>
+
+#define BWA_DEF_MAX_SCORE 2048
+#define BWA_MAX_QUERY_LEN 1024
+
+// BWA index
+struct bwa_idx_t;
+typedef struct bwa_idx_t bwa_idx_t;
+
+// Buffer for BWA alignment
+struct bwa_buf_t;
+typedef struct bwa_buf_t bwa_buf_t;
+
+// BWA alignment options
+typedef struct {
+	int s_gapo, s_gape;               // gap open and extension penalties; the mismatch penalty is fixed at 3
+	int max_diff, max_gapo, max_gape; // max differences (-1 to use fnr for length-adjusted max diff), gap opens and gap extensions
+	int seed_len, max_seed_diff;      // seed length and max differences allowed in the seed
+	float fnr;                        // parameter for automatic length-adjusted max differences
+} bwa_opt_t;
+
+// default BWA alignment options
+extern bwa_opt_t bwa_def_opt; // = { 11, 4, -1, 1, 6, 32, 2, 0.04 }
+
+// an interval hit in the SA coordinate; basic unit in .sai files
+typedef struct {
+	uint32_t n_mm:16, n_gapo:8, n_gape:8;
+	int score;
+	uint64_t k, l; // [k,l] is the SA interval; each interval has l-k+1 hits
+} bwa_sai1_t;
+
+// all interval hits in the SA coordinate
+typedef struct {
+	int n; // number of interval hits
+	bwa_sai1_t *sai;
+} bwa_sai_t;
+
+// an alignment
+typedef struct {
+	uint32_t n_n:8, n_gap:12, n_mm:12; // number of ambiguous bases, gaps and mismatches in the alignment
+	int32_t ref_id;                    // referece sequence index (the first seq is indexed by 0)
+	uint32_t offset;                   // coordinate on the reference; zero-based
+	uint32_t n_cigar:16, flag:16;      // number of CIGAR operations; SAM flag
+	uint32_t *cigar;                   // CIGAR in the BAM 28+4 encoding; having n_cigar operations
+} bwa_aln_t;
+
+typedef struct {
+	int mapQs, mapQ, c1, c2;
+	uint64_t sa;
+	bwa_sai1_t *which;
+	bwa_sai_t sai;
+	bwa_aln_t one;
+} bwa_one_t;
+
+typedef struct {
+	double avg, std, ap_prior;
+	uint64_t low, high, high_bayesian;
+} bwa_pestat_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	// load a BWA index
+	bwa_idx_t *bwa_idx_load(const char *prefix);
+	void bwa_idx_destroy(bwa_idx_t *p);
+
+	// allocate a BWA alignment buffer; if unsure, set opt to &bwa_def_opt and max_score to BWA_DEF_MAX_SCORE
+	bwa_buf_t *bwa_buf_init(const bwa_opt_t *opt, int max_score);
+	void bwa_buf_destroy(bwa_buf_t *p);
+
+	/**
+	 * Find all the SA intervals
+	 *
+	 * @param idx    BWA index; multiple threads can share the same index
+	 * @param buf    BWA alignment buffer; each thread should have its own buffer
+	 * @param seq    NULL terminated C string, consisting of A/C/G/T/N only
+	 *
+	 * @return       SA intervals seq is matched to
+	 */
+	bwa_sai_t bwa_sai(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq);
+
+	/**
+	 * Construct an alignment in the base-pair coordinate
+	 *
+	 * @param idx     BWA index
+	 * @param buf     BWA alignment buffer
+	 * @param seq     NULL terinated C string
+	 * @param sa      Suffix array value
+	 * @param n_gaps  Number of gaps (typically equal to bwa_sai1_t::n_gapo + bwa_sai1_t::n_gape
+	 *
+	 * @return        An alignment
+	 */
+	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);
+
+	bwa_one_t *bwa_se(const bwa_idx_t *idx, bwa_buf_t *buf, const char *seq, int gen_cigar);
+
+	void bwa_one_destroy(bwa_one_t *one);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif