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comparison PsiCLASS-1.0.2/samtools-0.1.19/kaln.h @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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1 /* The MIT License
2
3 Copyright (c) 2003-2006, 2008, 2009 by Heng Li <lh3@live.co.uk>
4
5 Permission is hereby granted, free of charge, to any person obtaining
6 a copy of this software and associated documentation files (the
7 "Software"), to deal in the Software without restriction, including
8 without limitation the rights to use, copy, modify, merge, publish,
9 distribute, sublicense, and/or sell copies of the Software, and to
10 permit persons to whom the Software is furnished to do so, subject to
11 the following conditions:
12
13 The above copyright notice and this permission notice shall be
14 included in all copies or substantial portions of the Software.
15
16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
17 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
18 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
20 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
21 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
22 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
23 SOFTWARE.
24 */
25
26 #ifndef LH3_KALN_H_
27 #define LH3_KALN_H_
28
29 #include <stdint.h>
30
31 #define MINOR_INF -1073741823
32
33 typedef struct {
34 int gap_open;
35 int gap_ext;
36 int gap_end_open;
37 int gap_end_ext;
38
39 int *matrix;
40 int row;
41 int band_width;
42 } ka_param_t;
43
44 typedef struct {
45 int iio, iie, ido, ide;
46 int eio, eie, edo, ede;
47 int *matrix;
48 int row;
49 int band_width;
50 } ka_param2_t;
51
52 #ifdef __cplusplus
53 extern "C" {
54 #endif
55
56 uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap,
57 int *_score, int *n_cigar);
58 int ka_global_score(const uint8_t *_seq1, int len1, const uint8_t *_seq2, int len2, const ka_param2_t *ap);
59 #ifdef __cplusplus
60 }
61 #endif
62
63 extern ka_param_t ka_param_blast; /* = { 5, 2, 5, 2, aln_sm_blast, 5, 50 }; */
64 extern ka_param_t ka_param_qual; // only use this for global alignment!!!
65 extern ka_param2_t ka_param2_qual; // only use this for global alignment!!!
66
67 #endif