int main (int argc, char** argv) {
if (argc != 7) usage(argc, argv);
string fasta_filename = argv[1];
string masks_filename = argv[2];
string scov_filename = argv[3];
out_file = argv[4];
window_size = atoi(argv[5]);
num_bins = atoi(argv[6]);
//fprintf(stderr,"Using window_size %d, num_bins %d\n",window_size,num_bins);
double bins_lambdas[num_bins];
sequence = read_genome(fasta_filename); //read in fasta file
//printf("Read in %d chars from %s\n",sequence_length,fasta_filename);
ifstream inf;
open_file_binary(inf, scov_filename);
scov = new double[sequence.length()];
inf.read((char *) scov, sizeof(double) * sequence.length());
inf.close();
//read in the masks
open_file_binary(inf, masks_filename);
masks = new char[sequence.length()];
if (masks ==NULL) {
fprintf(stderr,"Problem with allocating memory!\n");
exit(1);
}
inf.read(masks, sequence.length());
inf.close();
build_gc_bins(bins_lambdas);
delete[] scov;
delete[] masks;
return 0;
}
int main (int argc, char** argv) {
if (argc != 5) usage(argc, argv);
string rmap_filename = argv[1];
string scov_filename = argv[2];
string ref_name = argv[3];
uint64_t ref_len = atol(argv[4]);
double * sum_normodds = new double[ref_len];
for (int i = 0; i < ref_len; i++) sum_normodds[i] = 0;
//Read in rmap file
ifstream inf;
open_file_binary(inf, rmap_filename);
Map_t mapt;
while (inf) {
inf.read((char*) & mapt, sizeof(mapt));
if (mapt.ref_name == ref_name) {
if (mapt.ref_pos > ref_len) {
cerr << argv[0] << ": Error, out of range position " << mapt.ref_pos << " on ref " << ref_name << " of size " << ref_len << ".\n";
exit(1);
}
sum_normodds[mapt.ref_pos - 1] += mapt.normodds;
}
}
inf.close();
//Write out scov file
ofstream outf;
open_file_binary(outf, scov_filename);
outf.write((char*) sum_normodds, ref_len * sizeof(double));
if (outf.bad()) {
cerr << argv[0] << ": Error writing scov file " << scov_filename << ".\n";
exit(1);
}
outf.close();
delete[] sum_normodds;
return 0;
}
