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

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/bntseq.h	Fri Jul 18 07:55:14 2014 -0400
@@ -0,0 +1,85 @@
+/* The MIT License
+
+   Copyright (c) 2008 Genome Research Ltd (GRL).
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Contact: Heng Li <[e-mail]> */
+
+#ifndef BWT_BNTSEQ_H
+#define BWT_BNTSEQ_H
+
+#include <stdint.h>
+#include <zlib.h>
+
+#ifndef BWA_UBYTE
+#define BWA_UBYTE
+typedef uint8_t ubyte_t;
+#endif
+
+typedef struct {
+	int64_t offset;
+	int32_t len;
+	int32_t n_ambs;
+	uint32_t gi;
+	char *name, *anno;
+} bntann1_t;
+
+typedef struct {
+	int64_t offset;
+	int32_t len;
+	char amb;
+} bntamb1_t;
+
+typedef struct {
+	int64_t l_pac;
+	int32_t n_seqs;
+	uint32_t seed;
+	bntann1_t *anns; // n_seqs elements
+	int32_t n_holes;
+	bntamb1_t *ambs; // n_holes elements
+	FILE *fp_pac;
+} bntseq_t;
+
+extern unsigned char nst_nt4_table[256];
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	void bns_dump(const bntseq_t *bns, const char *prefix);
+	bntseq_t *bns_restore(const char *prefix);
+	bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename);
+	void bns_destroy(bntseq_t *bns);
+	int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only);
+	int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id);
+
+#ifdef __cplusplus
+}
+#endif
+
+static inline int64_t bns_depos(const bntseq_t *bns, int64_t pos, int *is_rev)
+{
+	return (*is_rev = (pos >= bns->l_pac))? (bns->l_pac<<1) - 1 - pos : pos;
+}
+
+#endif