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/*
* The MIT License
*
* Wavefront Alignment Algorithms
* Copyright (c) 2017 by Santiago Marco-Sola <santiagomsola@gmail.com>
*
* This file is part of Wavefront Alignment Algorithms.
*
* 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.
*
* PROJECT: Wavefront Alignment Algorithms
* AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
* DESCRIPTION: WFA Sample-Code
*/
#include "utils/commons.h"
#include "wavefront/wavefront_align.h"
int main(int argc,char* argv[]) {
// Patter & Text
char* pattern = "TCTTTACTCGCGCGTTGGAGAAATACAATAGT";
char* text = "TCTATACTGCGCGTTTGGAGAAATAAAATAGT";
// Configure alignment attributes
wavefront_aligner_attr_t attributes = wavefront_aligner_attr_default;
attributes.distance_metric = gap_affine;
attributes.affine_penalties.match = 0;
attributes.affine_penalties.mismatch = 4;
attributes.affine_penalties.gap_opening = 6;
attributes.affine_penalties.gap_extension = 2;
// Set heuristic wf-adaptive
attributes.heuristic.strategy = wf_heuristic_wfadaptive;
attributes.heuristic.min_wavefront_length = 10;
attributes.heuristic.max_distance_threshold = 50;
attributes.heuristic.steps_between_cutoffs = 1;
// Initialize Wavefront Aligner
wavefront_aligner_t* const wf_aligner = wavefront_aligner_new(&attributes);
// Align
wavefront_align(wf_aligner,pattern,strlen(pattern),text,strlen(text));
fprintf(stderr,"WFA-Alignment returns score %d\n",wf_aligner->cigar->score);
// Count mismatches, deletions, and insertions
int i, misms=0, ins=0, del=0;
cigar_t* const cigar = wf_aligner->cigar;
for (i=cigar->begin_offset;i<cigar->end_offset;++i) {
switch (cigar->operations[i]) {
case 'M': break;
case 'X': ++misms; break;
case 'D': ++del; break;
case 'I': ++ins; break;
}
}
fprintf(stderr,"Alignment contains %d mismatches, "
"%d insertions, and %d deletions\n",misms,ins,del);
// Free
wavefront_aligner_delete(wf_aligner);
}
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