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#include <alignment/files/BaseSequenceIO.hpp>
#include <cstdlib>
void BaseSequenceIO::SetFiles(FileType &pFileType, std::string &pFileName)
{
fileType = pFileType;
fileName = pFileName;
}
FileType BaseSequenceIO::GetFileType() { return fileType; }
int BaseSequenceIO::DetermineFileTypeByExtension(std::string &fileName, FileType &type,
bool exitOnFailure)
{
std::string::size_type dotPos = fileName.rfind(".");
if (dotPos != std::string::npos) {
std::string extension;
extension.assign(fileName, dotPos + 1, fileName.size() - (dotPos + 1));
if (extension == "fasta" || extension == "fa" || extension == "fas" ||
extension == "fsta" || extension == "screen") {
type = FileType::Fasta;
return 1;
} else if (extension == "h5") {
dotPos = fileName.rfind(".", dotPos - 1);
extension.assign(fileName, dotPos + 1, fileName.size() - (dotPos + 1));
if (extension == "pls.h5" || extension == "plx.h5") {
type = FileType::HDFPulse;
return 1;
} else if (extension == "bas.h5" || extension == "bax.h5") {
type = FileType::HDFBase;
return 1;
} else if (extension == "ccs.h5") {
type = FileType::HDFCCSONLY;
return 1;
} else {
type = FileType::None;
return 0;
}
} else if (extension == "fastq" || extension == "fq") {
type = FileType::Fastq;
return 1;
} else if (extension == "4bit" || extension == "fourbit") {
type = FileType::Fourbit;
assert("Four bit reading is not yet implemented for the reader agglomerate!" == 0);
return 1;
} else if (extension == "bam") {
type = FileType::PBBAM;
return 1;
} else if (extension == "xml") {
type = FileType::PBDATASET;
return 1;
} else {
type = FileType::None;
if (exitOnFailure) {
std::cout << "ERROR, file type '." << extension
<< "' is not understood to be one of pls.h5, fasta, fastq, nor bam. "
<< std::endl;
std::exit(EXIT_FAILURE);
}
return 0;
}
return 0;
}
return 0;
}
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