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#include "PbbamInternalConfig.h"
#include "DataSetIO.h"
#include <pbbam/StringUtilities.h>
#include "ErrnoReason.h"
#include "FileUtils.h"
#include "FofnReader.h"
#include "XmlReader.h"
#include "XmlWriter.h"
#include <boost/algorithm/string.hpp>
#include <algorithm>
#include <exception>
#include <fstream>
#include <ostream>
#include <sstream>
#include <stdexcept>
#include <cassert>
#include <cstddef>
namespace PacBio {
namespace BAM {
namespace {
struct DataSetFileException : public std::exception
{
DataSetFileException(std::string filename, std::string description) : std::exception{}
{
std::ostringstream s;
s << "[pbbam] dataset I/O ERROR: " << description << ":\n"
<< " file: " << filename;
MaybePrintErrnoReason(s);
msg_ = s.str();
}
const char* what() const noexcept override { return msg_.c_str(); }
std::string msg_;
};
std::unique_ptr<DataSetBase> DataSetFromXml(const std::string& xmlFn)
{
std::ifstream in{xmlFn};
if (!in) {
throw DataSetFileException{xmlFn, "could not open XML file for reading"};
}
return XmlReader::FromStream(in);
}
std::unique_ptr<DataSetBase> DataSetFromBam(const std::string& bamFn)
{
// peek at sort order to determine if file should be an AlignmentSet or else SubreadSet
const BamFile bamFile{bamFn};
const auto& header = bamFile.Header();
const auto aligned = header.SortOrder() == "coordinate";
std::unique_ptr<DataSetBase> dataset;
if (aligned) {
dataset = std::make_unique<AlignmentSet>();
} else {
dataset = std::make_unique<SubreadSet>();
}
auto& resources = dataset->ExternalResources();
resources.Add(ExternalResource(BamFile(bamFn)));
return
#ifdef __INTEL_COMPILER
std::move(
#endif
dataset
#ifdef __INTEL_COMPILER
)
#endif
;
}
std::unique_ptr<DataSetBase> DataSetFromFasta(const std::string& fasta)
{
// make FASTA data set
auto dataset = std::make_unique<ReferenceSet>();
auto& resources = dataset->ExternalResources();
resources.Add(ExternalResource("PacBio.ReferenceFile.ReferenceFastaFile", fasta));
return
#ifdef __INTEL_COMPILER
std::move(
#endif
dataset
#ifdef __INTEL_COMPILER
)
#endif
;
}
std::unique_ptr<DataSetBase> DataSetFromFofn(const std::string& fofn)
{
const auto fofnDir = FileUtils::DirectoryName(fofn);
std::ifstream in{fofn};
if (!in) {
throw DataSetFileException{fofn, "could not open FOFN for reading"};
}
auto filenames = FofnReader::Files(in);
std::transform(
filenames.begin(), filenames.end(), filenames.begin(),
[&fofnDir](const std::string fn) { return FileUtils::ResolvedFilePath(fn, fofnDir); });
return DataSetIO::FromUris(filenames);
}
std::unique_ptr<DataSetBase> DataSetFromUri(const std::string& uri)
{
// NOTE: this says URI, but we're not quite handling filenames as true URIs
// basically just treating as a regular filename for now
// handle on extension
if (boost::algorithm::iends_with(uri, ".xml")) {
return DataSetFromXml(uri);
} else if (boost::algorithm::iends_with(uri, ".bam")) {
return DataSetFromBam(uri);
} else if (boost::algorithm::iends_with(uri, ".fofn")) {
return DataSetFromFofn(uri);
} else if (boost::algorithm::iends_with(uri, ".fasta") ||
boost::algorithm::iends_with(uri, ".fsa") ||
boost::algorithm::iends_with(uri, ".fa")) {
return DataSetFromFasta(uri);
}
// unknown filename extension
throw std::runtime_error{"[pbbam] dataset I/O ERROR: unsupported extension:\n file: " + uri};
}
} // namespace
std::unique_ptr<DataSetBase> DataSetIO::FromUri(const std::string& uri)
{
return FromUris(std::vector<std::string>(1, uri));
}
std::unique_ptr<DataSetBase> DataSetIO::FromUris(const std::vector<std::string>& uris)
{
if (uris.empty()) {
throw std::runtime_error{"[pbbam] dataset I/O ERROR: empty input URI list"};
}
// create dataset(s) from URI(s)
std::vector<std::unique_ptr<DataSetBase> > datasets;
datasets.reserve(uris.size());
for (const auto& uri : uris) {
datasets.emplace_back(DataSetFromUri(uri));
}
assert(!datasets.empty());
// if only 1, just return
if (datasets.size() == 1) {
return std::unique_ptr<DataSetBase>(datasets.front().release());
// else merge
} else {
auto& result = datasets.at(0);
for (size_t i = 1; i < datasets.size(); ++i) {
const auto& next = datasets.at(i);
*result += *next;
}
return std::move(result);
}
}
std::unique_ptr<DataSetBase> DataSetIO::FromXmlString(const std::string& xml)
{
if (xml.empty()) {
throw std::runtime_error{"[pbbam] dataset I/O ERROR: cannot load from empty XML string"};
}
std::istringstream s{xml};
return XmlReader::FromStream(s);
}
void DataSetIO::ToFile(const std::unique_ptr<DataSetBase>& dataset, const std::string& fn,
DataSetPathMode pathMode)
{
DataSetIO::ToFile(*dataset, fn, pathMode);
}
void DataSetIO::ToStream(const std::unique_ptr<DataSetBase>& dataset, std::ostream& out,
DataSetPathMode pathMode)
{
DataSetIO::ToStream(*dataset, out, pathMode);
}
void DataSetIO::ToFile(DataSetBase& dataset, const std::string& fn, DataSetPathMode pathMode)
{
std::ofstream out(fn);
if (!out) {
throw DataSetFileException{fn, "could not open XML file for writing"};
}
XmlWriter::ToStream(dataset, out, pathMode);
}
void DataSetIO::ToStream(DataSetBase& dataset, std::ostream& out, DataSetPathMode pathMode)
{
XmlWriter::ToStream(dataset, out, pathMode);
}
} // namespace BAM
} // namespace PacBio
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