int main(int argc, char **argv)
{
setvbuf(stdout, NULL, _IOLBF, 0);
CmdLine* cmd_line = cmd_line_alloc();
if (cmd_line==NULL)
{
return -1;
}
parse_cmdline(cmd_line, argc, argv, sizeof(Element));
dBGraph * db_graph = NULL;
//Create the de Bruijn graph/hash table
int max_retries=15;
db_graph = hash_table_new(cmd_line->mem_height,
cmd_line->mem_width,
max_retries,
cmd_line->kmer_size);
if (db_graph==NULL)
{
return -1;
}
//some setup
int file_reader_fasta(FILE * fp, Sequence * seq, int max_read_length, boolean new_entry, boolean * full_entry){
long long ret;
int offset = 0;
if (new_entry == false){
offset = db_graph->kmer_size;
//die("new_entry must be true in hsi test function");
}
ret = read_sequence_from_fasta(fp, seq, max_read_length,new_entry,full_entry,offset);
return ret;
}
int main(int argc, char **argv)
{
setvbuf(stdout, NULL, _IOLBF, 0);
CmdLine* cmd_line = cmd_line_alloc();
if (cmd_line==NULL)
{
return -1;
}
// VERSION_STR is passed from the makefile -- usually last commit hash
parse_cmdline(cmd_line, argc,argv,sizeof(Element));
if (cmd_line->format==Stdout){
printf("myKrobe.predictor for Staphylococcus, version %d.%d.%d.%d"VERSION_STR"\n",
VERSION, SUBVERSION, SUBSUBVERSION, SUBSUBSUBVERSION);
}
dBGraph * db_graph = NULL;
boolean (*subsample_function)();
//local func
boolean subsample_as_specified()
{
double ran = drand48();
if (ran <= cmd_line->subsample_propn)
{
return true;
}
return false;
}
//end of local func
if (cmd_line->subsample==true)
{
subsample_function = &subsample_as_specified;
}
else
{
subsample_function = &subsample_null;
}
// int lim = cmd_line->max_expected_sup_len;
/* CovgArray* working_ca_for_median=alloc_and_init_covg_array(lim);//will die if fails to alloc
if (working_ca_for_median==NULL)
{
return -1;
}*/
//Create the de Bruijn graph/hash table
int max_retries=15;
db_graph = hash_table_new(cmd_line->mem_height,
cmd_line->mem_width,
max_retries,
cmd_line->kmer_size);
if (db_graph==NULL)
{
return -1;
}
//some setup
int file_reader_fasta(FILE * fp, Sequence * seq, int max_read_length, boolean new_entry, boolean * full_entry){
long long ret;
int offset = 0;
if (new_entry == false){
offset = db_graph->kmer_size;
//die("new_entry must be true in hsi test function");
}
ret = read_sequence_from_fasta(fp,seq,max_read_length,new_entry,full_entry,offset);
return ret;
}
