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

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/bwtgap.h	Fri Jul 18 07:55:59 2014 -0400
@@ -0,0 +1,39 @@
+#ifndef BWTGAP_H_
+#define BWTGAP_H_
+
+#include "bwt.h"
+#include "bwtaln.h"
+
+typedef struct { // recursion stack
+	u_int32_t info; // score<<21 | i
+	u_int32_t n_mm:8, n_gapo:8, n_gape:8, state:2, n_seed_mm:6;
+	bwtint_t k, l; // (k,l) is the SA region of [i,n-1]
+	int last_diff_pos;
+} gap_entry_t;
+
+typedef struct {
+	int n_entries, m_entries;
+	gap_entry_t *stack;
+} gap_stack1_t;
+
+typedef struct {
+	int n_stacks, best, n_entries;
+	gap_stack1_t *stacks;
+} gap_stack_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	gap_stack_t *gap_init_stack2(int max_score);
+	gap_stack_t *gap_init_stack(int max_mm, int max_gapo, int max_gape, const gap_opt_t *opt);
+	void gap_destroy_stack(gap_stack_t *stack);
+	bwt_aln1_t *bwt_match_gap(bwt_t *const bwt, int len, const ubyte_t *seq, bwt_width_t *w,
+							  bwt_width_t *seed_w, const gap_opt_t *opt, int *_n_aln, gap_stack_t *stack);
+	void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif