53 lines
2.0 KiB
C
Executable File
53 lines
2.0 KiB
C
Executable File
/* The MIT License
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Copyright (c) 2008 Genome Research Ltd (GRL).
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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*/
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#ifndef BWASE_H
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#define BWASE_H
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#include "bntseq.h"
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#include "bwt.h"
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#include "bwtaln.h"
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#ifdef __cplusplus
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extern "C" {
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#endif
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// Initialize mapping tables in the bwa single-end mapper.
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void bwase_initialize();
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// Calculate the approximate position of the sequence from the specified bwt with loaded suffix array.
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void bwa_cal_pac_pos_core(const bwt_t* forward_bwt, const bwt_t* reverse_bwt, bwa_seq_t* seq, const int max_mm, const float fnr);
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// Refine the approximate position of the sequence to an actual placement for the sequence.
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void bwa_refine_gapped(const bntseq_t *bns, int n_seqs, bwa_seq_t *seqs, ubyte_t *_pacseq, bntseq_t *ntbns);
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// Backfill certain alignment properties mainly centering around number of matches.
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void bwa_aln2seq(int n_aln, const bwt_aln1_t *aln, bwa_seq_t *s);
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// Calculate the end position of a read given a certain sequence.
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int64_t pos_end(const bwa_seq_t *p);
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#ifdef __cplusplus
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}
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#endif
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#endif // BWASE_H
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