diff bwa-0.6.2/bwtsw2.h @ 0:dd1186b11b3b draft

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/bwtsw2.h	Fri Jul 18 07:55:14 2014 -0400
@@ -0,0 +1,69 @@
+#ifndef LH3_BWTSW2_H
+#define LH3_BWTSW2_H
+
+#include <stdint.h>
+#include "bntseq.h"
+#include "bwt_lite.h"
+#include "bwt.h"
+
+#define BSW2_FLAG_MATESW  0x100
+#define BSW2_FLAG_TANDEM  0x200
+#define BSW2_FLAG_MOVED   0x400
+#define BSW2_FLAG_RESCUED 0x800
+
+typedef struct {
+	int skip_sw:16, hard_clip:16;
+	int a, b, q, r, t, qr, bw, max_ins;
+	int z, is, t_seeds, multi_2nd;
+	float mask_level, coef;
+	int n_threads, chunk_size;
+} bsw2opt_t;
+
+typedef struct {
+	bwtint_t k, l;
+	uint32_t flag:18, n_seeds:13, is_rev:1;
+	int len, G, G2;
+	int beg, end;
+} bsw2hit_t;
+
+typedef struct {
+	int flag, nn, n_cigar, chr, pos, qual, mchr, mpos, pqual, isize, nm;
+	uint32_t *cigar;
+} bsw2aux_t;
+
+typedef struct {
+	int n, max;
+	bsw2hit_t *hits;
+	bsw2aux_t *aux;
+} bwtsw2_t;
+
+typedef struct {
+	void *stack;
+	int max_l;
+	uint8_t *aln_mem;
+} bsw2global_t;
+
+typedef struct {
+	int l, tid;
+	char *name, *seq, *qual, *sam;
+} bsw2seq1_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	bsw2opt_t *bsw2_init_opt();
+	bwtsw2_t **bsw2_core(const bntseq_t *bns, const bsw2opt_t *opt, const bwtl_t *target, const bwt_t *query, bsw2global_t *pool);
+	void bsw2_aln(const bsw2opt_t *opt, const bntseq_t *bns, bwt_t * const target, const char *fn, const char *fn2);
+	void bsw2_destroy(bwtsw2_t *b);
+
+	bsw2global_t *bsw2_global_init();
+	void bsw2_global_destroy(bsw2global_t *_pool);
+
+	void bsw2_pair(const bsw2opt_t *opt, int64_t l_pac, const uint8_t *pac, int n, bsw2seq1_t *seq, bwtsw2_t **hit);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif