X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=kaln.h;fp=kaln.h;h=b04d8cc0b001c17c20654fc125e392b08aefb343;hp=0000000000000000000000000000000000000000;hb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351;hpb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a

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+/* The MIT License
+
+   Copyright (c) 2003-2006, 2008, 2009 by Heng Li <lh3@live.co.uk>
+
+   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.
+*/
+
+#ifndef LH3_KALN_H_
+#define LH3_KALN_H_
+
+#include <stdint.h>
+
+#define MINOR_INF -1073741823
+
+typedef struct {
+	int gap_open;
+	int gap_ext;
+	int gap_end;
+
+	int *matrix;
+	int row;
+	int band_width;
+} ka_param_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar);
+
+#ifdef __cplusplus
+}
+#endif
+
+extern ka_param_t ka_param_blast; /* = {  5,  2,  2, aln_sm_blast, 5, 50 }; */
+
+#endif