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

Uploaded BWA

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bwa-0.6.2/stdaln.h	Fri Jul 18 07:55:14 2014 -0400
@@ -0,0 +1,162 @@
+/* The MIT License
+
+   Copyright (c) 2003-2006, 2008, by Heng Li <[e-mail]>
+
+   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.
+*/
+
+/*
+  2009-07-23, 0.10.0
+
+  - Use 32-bit to store CIGAR
+
+  - Report suboptimal aligments
+
+  - Implemented half-fixed-half-open DP
+
+  2009-04-26, 0.9.10
+
+  - Allow to set a threshold for local alignment
+
+  2009-02-18, 0.9.9
+
+  - Fixed a bug when no residue matches
+
+  2008-08-04, 0.9.8
+
+  - Fixed the wrong declaration of aln_stdaln_aux()
+
+  - Avoid 0 coordinate for global alignment
+
+  2008-08-01, 0.9.7
+
+  - Change gap_end penalty to 5 in aln_param_bwa
+
+  - Add function to convert path_t to the CIGAR format
+
+  2008-08-01, 0.9.6
+
+  - The first gap now costs (gap_open+gap_ext), instead of
+    gap_open. Scoring systems are modified accordingly.
+
+  - Gap end is now correctly handled. Previously it is not correct.
+
+  - Change license to MIT.
+
+ */
+
+#ifndef LH3_STDALN_H_
+#define LH3_STDALN_H_
+
+
+#define STDALN_VERSION 0.11.0
+
+#include <stdint.h>
+
+#define FROM_M 0
+#define FROM_I 1
+#define FROM_D 2
+#define FROM_S 3
+
+#define ALN_TYPE_LOCAL  0
+#define ALN_TYPE_GLOBAL 1
+#define ALN_TYPE_EXTEND 2
+
+/* This is the smallest integer. It might be CPU-dependent in very RARE cases. */
+#define MINOR_INF -1073741823
+
+typedef struct
+{
+	int gap_open;
+	int gap_ext;
+	int gap_end;
+
+	int *matrix;
+	int row;
+	int band_width;
+} AlnParam;
+
+typedef struct
+{
+	int i, j;
+	unsigned char ctype;
+} path_t;
+
+typedef struct
+{
+	path_t *path; /* for advanced users... :-) */
+	int path_len; /* for advanced users... :-) */
+	int start1, end1; /* start and end of the first sequence, coordinations are 1-based */
+	int start2, end2; /* start and end of the second sequence, coordinations are 1-based */
+	int score, subo; /* score */
+
+	char *out1, *out2; /* print them, and then you will know */
+	char *outm;
+
+	int n_cigar;
+	uint32_t *cigar32;
+} AlnAln;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	AlnAln *aln_stdaln_aux(const char *seq1, const char *seq2, const AlnParam *ap,
+						   int type, int do_align, int len1, int len2);
+	AlnAln *aln_stdaln(const char *seq1, const char *seq2, const AlnParam *ap, int type, int do_align);
+	void aln_free_AlnAln(AlnAln *aa);
+
+	int aln_global_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
+						path_t *path, int *path_len);
+	int aln_local_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
+					   path_t *path, int *path_len, int _thres, int *_subo);
+	int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap,
+						path_t *path, int *path_len, int G0, uint8_t *_mem);
+	uint16_t *aln_path2cigar(const path_t *path, int path_len, int *n_cigar);
+	uint32_t *aln_path2cigar32(const path_t *path, int path_len, int *n_cigar);
+
+#ifdef __cplusplus
+}
+#endif
+
+/********************
+ * global variables *
+ ********************/
+
+extern AlnParam aln_param_bwa;   /* = { 37,  9,  0, aln_sm_maq, 5, 50 }; */
+extern AlnParam aln_param_blast; /* = {  5,  2,  2, aln_sm_blast, 5, 50 }; */
+extern AlnParam aln_param_nt2nt; /* = { 10,  2,  2, aln_sm_nt, 16, 75 }; */
+extern AlnParam aln_param_aa2aa; /* = { 20, 19, 19, aln_sm_read, 16, 75 }; */
+extern AlnParam aln_param_rd2rd; /* = { 12,  2,  2, aln_sm_blosum62, 22, 50 }; */
+
+/* common nucleotide score matrix for 16 bases */
+extern int           aln_sm_nt[], aln_sm_bwa[];
+
+/* BLOSUM62 and BLOSUM45 */
+extern int           aln_sm_blosum62[], aln_sm_blosum45[];
+
+/* common read for 16 bases. note that read alignment is quite different from common nucleotide alignment */
+extern int           aln_sm_read[];
+
+/* human-mouse score matrix for 4 bases */
+extern int           aln_sm_hs[];
+
+#endif