| 330 |
|
for (size_t i = 0; i < reads_file_names.size(); ++i) |
| 331 |
|
{ |
| 332 |
|
string fname=reads_file_names[i]; |
| 333 |
< |
string pipecmd=guess_packer(fname, true); |
| 334 |
< |
if (!pipecmd.empty()) pipecmd.append(" -cd"); |
| 335 |
< |
FZPipe seg_file(fname,pipecmd); |
| 333 |
> |
FZPipe seg_file(fname, true); //guess unpacker |
| 334 |
|
if (seg_file.file == NULL) { |
| 335 |
|
fprintf(stderr, "Error: cannot open reads file %s for reading\n", |
| 336 |
|
reads_file_names[i].c_str()); |
| 347 |
|
tokenize(quals_file_list, ",", quals_file_names); |
| 348 |
|
for (size_t i = 0; i < quals_file_names.size(); ++i) |
| 349 |
|
{ |
| 350 |
< |
string fname(quals_file_names[i]); |
| 353 |
< |
string pipecmd=guess_packer(fname, true); |
| 354 |
< |
FZPipe seg_file(fname, pipecmd); |
| 350 |
> |
FZPipe seg_file(quals_file_names[i], true); |
| 351 |
|
if (seg_file.file == NULL) |
| 352 |
|
{ |
| 353 |
|
fprintf(stderr, "Error: cannot open reads file %s for reading\n", |
