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