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#include "tools.h"
////////////////////////////////////
////////// SAM/BAM output //////////
////////////////////////////////////
seqan2::BamHeader getBamHeader() {
std::stringstream ss;
ss.str(std::string());
ss << HiLive_VERSION_MAJOR << "." << HiLive_VERSION_MINOR;
seqan2::BamHeader header;
resize(header, 2);
// @HD header.
seqan2::resize(header[0].tags, 2);
header[0].type = seqan2::BAM_HEADER_FIRST;
header[0].tags[0].i1 = "VN";
header[0].tags[0].i2 = "1.5";
header[0].tags[1].i1 = "GO";
header[0].tags[1].i2 = "query";
// @PG header.
seqan2::resize(header[1].tags, 3);
header[1].type = seqan2::BAM_HEADER_PROGRAM;
header[1].tags[0].i1 = "ID";
header[1].tags[0].i2 = "hilive";
header[1].tags[1].i1 = "PN";
header[1].tags[1].i2 = "HiLive";
header[1].tags[2].i1 = "VN";
header[1].tags[2].i2 = ss.str();
return header;
}
std::string reverse_mdz(std::string mdz) {
std::string reverse = "";
std::string next_match = "";
for ( auto string_it = mdz.rbegin(); string_it!=mdz.rend(); ++string_it) {
if ( seq_chars.find(*string_it) != std::string::npos ) {
std::reverse(next_match.begin(), next_match.end());
reverse += next_match;
next_match = "";
reverse += comp(*string_it);
}
else {
next_match += *string_it;
}
}
std::reverse(next_match.begin(), next_match.end());
reverse += next_match;
return reverse;
}
/////////////////////////////////
////////// Other stuff //////////
/////////////////////////////////
int atomic_rename( const char *oldname, const char *newname ) {
if ( !file_exists(oldname) )
throw file_not_exist_error("Can't rename file: " + std::string(oldname) + ". File does not exist.");
std::lock_guard<std::mutex> old_lock(fileLocks.at(std::string(oldname)));
std::lock_guard<std::mutex> new_lock(fileLocks.at(std::string(newname)));
return std::rename(oldname, newname);
}
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