/*
 *                             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);
}