int main (int argc, char **argv) { CallbackData data; parse_args (&data, &argc, &argv); load_fasta (&data); load_bsq (&data); rle_encode (&data); cleanup_data (&data); return 0; }
/// Check Correctness of the Output SA void CheckCorrectness (string ReferenceFile, string SuffixArrayFile) { vector<char> reference_array; vector<char> AlphapetChar; load_fasta(ReferenceFile, reference_array,AlphapetChar); FILE *aggr=fopen(SuffixArrayFile.c_str(),"r"); vector<int> Index; int returnValue=0; int temp; if (aggr==NULL) printf("Error while Opening File\n"); else { while(!feof(aggr)) { returnValue=fread(&temp,sizeof(int),1,aggr); Index.push_back(temp); } } printf("\n"); int TempIndex1; int TempIndex2; int count=0; for (int i=0;i<Index.size()-1;i++) { TempIndex1=Index[i]; TempIndex2=Index[i+1]; for (int j=0;(TempIndex1+j<reference_array.size())&&(TempIndex2+j<reference_array.size());j++) { if(reference_array[TempIndex1+j]<reference_array[TempIndex2+j]) break; if (reference_array[TempIndex1+j]>reference_array[TempIndex2+j]) { count++; printf("Check Failed at index= %d, in line= %d\n",TempIndex1,i+1); break; } } } if (count==0) printf("Check Succeed !!! \n"); }
int main(int argc, const char** argv) { const char* fasta_filename = argv[1]; const char* clustering_filename = argv[2]; // Init stuff. clusters = g_array_new(FALSE, FALSE, sizeof(GArray*)); GError* err = NULL; fasta = load_fasta(fasta_filename, &err); if (err != NULL){ g_critical("error while loading FASTA\n"); return 1; } g_print("now loading clustering...\n"); load_clustering(clustering_filename); calculate_CH(); return 0; }