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#include "tools_static.h"
///////////////////////////////////
////////// File handling //////////
///////////////////////////////////
std::vector<char> read_binary_file(const std::string &fname) {
// get file size
uint64_t size = get_filesize(fname);
// open binary file
FILE* f;
f = fopen(fname.c_str(), "rb");
if (!f) {
std::stringstream error;
error << "Error reading binary file " << fname << ": Could not open file.";
throw std::ios::failure ( error.str() );
}
// allocate memory
std::vector<char> data (size);
// read all data at once
uint64_t read = fread(data.data(), 1, size, f);
if (read != size){
std::stringstream error;
error << "Error reading binary file " << fname << ": Read " << read << " bytes while file has " << size << " bytes.";
throw std::ios::failure ( error.str() );
}
fclose(f);
return data;
}
uint64_t write_binary_file(const std::string &fname, const std::vector<char> & data) {
// open binary file
FILE* ofile;
ofile = fopen(fname.c_str(), "wb");
if (!ofile) {
std::stringstream error;
error << "Error serializing object to file " << fname << ": Could not open file for writing.";
throw std::ios::failure ( error.str() );
}
// write all data
uint64_t written = fwrite(data.data(), 1, data.size(), ofile);
// close file
fclose(ofile);
if (written != data.size()){
std::stringstream error;
error << "Error serializing object to file " << fname << ": Wrote " << written << " bytes while data contains " << data.size() << " bytes.";
throw std::ios::failure ( error.str() );
}
return written;
}
std::string get_file_suffix ( OutputFormat format ) {
switch ( format ) {
case OutputFormat::SAM:
return ".sam";
break;
case OutputFormat::BAM:
return ".bam";
break;
case OutputFormat::CRAM:
return ".cram";
break;
default:
return ".txt";
break;
}
}
////////////////////////////////////////////////
////////// Property trees / XML files //////////
////////////////////////////////////////////////
bool read_xml(boost::property_tree::ptree & xml_in, std::string xml_fname) {
if ( !file_exists(xml_fname) ) {
std::cout << "XML file not found: " << xml_fname << std::endl;
return false;
}
try {
boost::property_tree::read_xml (xml_fname, xml_in);
} catch ( const std::exception &ex) {
std::cerr << "Error loading xml file " << xml_fname << ": " << std::endl << ex.what() << std::endl;
return false;
}
return true;
}
bool write_ini(boost::property_tree::ptree & ini_out, std::string ini_fname) {
try {
boost::property_tree::write_ini( ini_fname, ini_out );
} catch ( const std::exception &ex ) {
std::cerr << "Error writing config file " << ini_fname << ": " << std::endl << ex.what() << std::endl;
return false;
}
return true;
}
/////////////////////////////////
////////// Other stuff //////////
/////////////////////////////////
uint32_t num_reads_from_bcl(std::string bcl) {
// open BCL file of first cycle
FILE* ifile;
ifile = fopen(bcl.c_str(), "rb");
if (!ifile) {
std::cerr << "Error reading BCL file " << bcl << ": Could not open file." << std::endl;
return 0;
}
// extract the number of reads
uint32_t num_reads;
bool res = fread(&num_reads, 1, sizeof(uint32_t), ifile);
if (!res) {
std::cerr << "Error extracting number of reads from BCL file " << bcl << std::endl;
return 0;
}
// close file
fclose (ifile);
return num_reads;
}
AlignmentMode to_alignmentMode ( std::string value ) {
if ( std::toupper(value[0]) == 'B' )
return BALANCED;
if ( std::toupper(value[0]) == 'A' )
return ACCURATE;
if ( std::toupper(value[0]) == 'F' )
return FAST;
if ( std::toupper(value[0]) == 'V' ) {
if ( std::toupper(value[1]) == 'F' || std::toupper(value[5]) == 'F')
return VERYFAST;
if ( std::toupper(value[1]) == 'A' || std::toupper(value[5]) == 'A')
return VERYACCURATE;
}
throw std::runtime_error("Invalid alignment mode " + value + ".");
}
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