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;
}
