| 353 | } |
| 354 | |
| 355 | long getLineNumber(std::string const& fileName, std::string const& refFileName, const std::string& pathToSamtools, const std::string& pathToSambamba, const std::string& SambambaThreads) { |
| 356 | string line ; |
| 357 | long count = 0; |
| 358 | FILE *stream; |
| 359 | char buffer[MAX_BUFFER]; |
| 360 | |
| 361 | if (fileName.substr(fileName.size()-3,3).compare(".gz")==0) { |
| 362 | string command = "gzip -cd "+fileName; |
| 363 | stream = |
| 364 | #if defined(_WIN32) |
| 365 | _popen(command.c_str(), "r"); |
| 366 | #else |
| 367 | popen(command.c_str(), "r"); |
| 368 | #endif |
| 369 | while ( fgets(buffer, MAX_BUFFER, stream) != NULL ) { |
| 370 | count++; |
| 371 | } |
| 372 | #if defined(_WIN32) |
| 373 | _pclose(stream); |
| 374 | #else |
| 375 | pclose(stream); |
| 376 | #endif |
| 377 | } |
| 378 | else if (fileName.substr(fileName.size()-4,4).compare(".bam")==0) { |
| 379 | string command = ""; |
| 380 | if (pathToSambamba != "") |
| 381 | { |
| 382 | command = pathToSambamba + " view -t " + SambambaThreads + " " +fileName; |
| 383 | //myInputFormat="sam"; //will try to use existing samtools |
| 384 | cout << "..sambamba should be installed to be able to read BAM files\n"; |
| 385 | } |
| 386 | else |
| 387 | { |
| 388 | command = pathToSamtools + " view -@ "+ SambambaThreads + " " + fileName; |
| 389 | //myInputFormat="sam"; //will try to use existing samtools |
| 390 | cout << "..samtools should be installed to be able to read BAM files\n"; |
| 391 | } |
| 392 | stream = |
| 393 | #if defined(_WIN32) |
| 394 | _popen(command.c_str(), "r"); |
| 395 | #else |
| 396 | popen(command.c_str(), "r"); |
| 397 | #endif |
| 398 | |
| 399 | while ( fgets(buffer, MAX_BUFFER, stream) != NULL ) { |
| 400 | count++; |
| 401 | } |
| 402 | #if defined(_WIN32) |
| 403 | _pclose(stream); |
| 404 | #else |
| 405 | pclose(stream); |
| 406 | #endif |
| 407 | } |
| 408 | else if (fileName.substr(fileName.size()-5,5).compare(".cram")==0) { |
| 409 | string command = ""; |
| 410 | if (refFileName == "") |
| 411 | { |
| 412 | cout << "..Reference FASTA file (config.fastaFile) should be given to be able to read CRAM files\n"; |