libwfa2 0.1.1

Bindings to the C implementation of WFA2-lib
Documentation 
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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;
  // 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);
  // Display alignment
  fprintf(stderr,"  PATTERN  %s\n",pattern);
  fprintf(stderr,"  TEXT     %s\n",text);
  fprintf(stderr,"  SCORE (RE)COMPUTED %d\n",
      cigar_score_gap_affine(wf_aligner->cigar,&attributes.affine_penalties));
  cigar_print_pretty(stderr,wf_aligner->cigar,
      pattern,strlen(pattern),text,strlen(text));
  // Free
  wavefront_aligner_delete(wf_aligner);
}