static
bam2sam::Settings fromCommandLine(optparse::OptionParser& parser,
int argc, char* argv[])
{
bam2sam::Settings settings;
const optparse::Values options = parser.parse_args(argc, argv);
// input
const std::vector<std::string> positionalArgs = parser.args();
const size_t numPositionalArgs = positionalArgs.size();
if (numPositionalArgs == 0)
settings.inputFilename_ = "-"; // stdin
else if (numPositionalArgs == 1)
settings.inputFilename_ = parser.args().front();
else {
assert(numPositionalArgs > 1);
settings.errors_.push_back("bam2sam does not support more than one input file per run");
}
// header options
if (options.is_set("no_header"))
settings.noHeader_ = options.get("no_header");
if (options.is_set("header_only"))
settings.printHeaderOnly_ = options.get("header_only");
if (settings.noHeader_ && settings.printHeaderOnly_)
settings.errors_.push_back("conflicting arguments requested: --no-header and --header-only");
return settings;
}
static
pbindexdump::Settings fromCommandLine(optparse::OptionParser& parser,
int argc,
char* argv[])
{
const optparse::Values options = parser.parse_args(argc, argv);
pbindexdump::Settings settings;
// input
const vector<string> positionalArgs = parser.args();
const size_t numPositionalArgs = positionalArgs.size();
if (numPositionalArgs == 0)
settings.inputPbiFilename_ = "-"; // stdin
else if (numPositionalArgs == 1)
settings.inputPbiFilename_ = parser.args().front();
else {
assert(numPositionalArgs > 1);
settings.errors_.push_back("pbindexdump does not support more than one input file per run");
}
// output format
if (options.is_set("format"))
settings.format_ = options["format"];
// JSON options
if (settings.format_ == "json") {
if (options.is_set("json_indent_level"))
settings.jsonIndentLevel_ = options.get("json_indent_level");
if (options.is_set("json_raw"))
settings.jsonRaw_ = options.get("json_raw");
} else {
if (options.is_set("json_indent_level") ||
options.is_set("json_raw"))
{
settings.errors_.push_back("JSON formatting options not valid on non-JSON output");
}
}
return settings;
}
Settings Settings::FromCommandLine(optparse::OptionParser& parser,
int argc,
char *argv[],
bool forcePulseMode)
{
Settings settings;
// general program info
settings.program = parser.prog();
settings.description = parser.description();
settings.version = parser.version();
for (int i = 1; i < argc; ++i) {
settings.args.append(argv[i]);
settings.args.append(" ");
}
const optparse::Values options = parser.parse_args(argc, argv);
// mode
settings.ignoreQV = options.is_set(Settings::Option::ignoreQV_);
const bool isBaseMode =
options.is_set(Settings::Option::baseMode_) ? options.get(Settings::Option::baseMode_) : false;
const bool isPulseMode =
options.is_set(Settings::Option::pulseMode_) ? options.get(Settings::Option::pulseMode_) : false;
int modeCount = 0;
if (isBaseMode) modeCount++;
if (isPulseMode) modeCount++;
if (modeCount == 0)
settings.mode = Settings::BaseMode;
else if (modeCount == 1)
if (isBaseMode)
settings.mode = Settings::BaseMode;
else
settings.mode = Settings::PulseMode;
else
settings.errors_.push_back("Unknown modes selected.");
if (forcePulseMode) settings.mode = Settings::PulseMode;
// BaseMap
if (not options[Settings::Option::baseMap_].empty()) {
settings.baseMap = options[Settings::Option::baseMap_];
std::transform(settings.baseMap.begin(), settings.baseMap.end(), settings.baseMap.begin(), ::toupper);
cout << settings.baseMap << endl;
std::string _baseMap = settings.baseMap;
std::sort(_baseMap.begin(), _baseMap.end());
if (_baseMap != "ACGT") { settings.errors_.push_back("Bad basemap."); }
}
// input
settings.inputBamFilenames = parser.args();
if (settings.inputBamFilenames.size() == 1) {
settings.polymeraseBamFilename = settings.inputBamFilenames[0];
if (settings.polymeraseBamFilename.find("polymerase.bam") == std::string::npos)
settings.errors_.push_back("missing input *.polymerase.bam.");
} else if (settings.inputBamFilenames.size() == 2) {
settings.subreadsBamFilename = settings.inputBamFilenames[0];
settings.scrapsBamFilename = settings.inputBamFilenames[1];
if (settings.subreadsBamFilename.find("subreads.bam") == std::string::npos)
settings.errors_.push_back("missing input *.subreads.bam.");
if (settings.scrapsBamFilename.find("scraps.bam") == std::string::npos)
settings.errors_.push_back("missing input *.scraps.bam.");
} else {
settings.errors_.push_back("missing input (polymerase.bam or subreads+scraps.bam.");
}
// output
settings.outputBaxPrefix = options[Settings::Option::output_];
if (settings.outputBaxPrefix.empty()) { // if output prefix not set.
if (not settings.subreadsBamFilename.empty()) {
settings.outputBaxPrefix = internal::GetMovienameFromFilename(settings.subreadsBamFilename);
} else if (not settings.polymeraseBamFilename.empty()) {
settings.outputBaxPrefix = internal::GetMovienameFromFilename(settings.polymeraseBamFilename);
}
}
if (settings.mode == Settings::BaseMode)
settings.outputBaxFilename = settings.outputBaxPrefix + ".bax.h5";
else if (settings.mode == Settings::PulseMode)
settings.outputBaxFilename = settings.outputBaxPrefix + ".plx.h5";
settings.outputRgnFilename = settings.outputBaxPrefix + ".rgn.h5";
// movie
settings.movieName = internal::GetMovienameFromFilename(settings.outputBaxPrefix);
if (options.is_set(Settings::Option::metadata_)) {
// metadata.xml will be placed at upper directory of bax.h5
settings.outputMetadataFilename = internal::DirectoryPath(settings.outputBaxPrefix) + "/../" +
settings.movieName + ".metadata.xml";
settings.outputAnalysisDirname = internal::ParentDirectoryName(internal::DirectoryPath(settings.outputBaxPrefix));
}
#ifdef DEBUG_SETTINGS
string modeString = "Unknown";
if (settings.mode == Settings::BaseMode)
modeString = "base";
else if (settings.mode == Settings::PulseMode)
modeString = "pulse";
cerr << "CommandLine: " << settings.program << " " << settings.args << endl
<< "Description: " << settings.description << endl
<< "Version : " << settings.version << endl
<< "Mode : " << modeString << endl
<< "BaseMap : " << settings.baseMap << endl
<< "Movie name : " << settings.movieName << endl
<< "Input files: " << endl;
if (not settings.subreadsBamFilename.empty())
cerr << " subreads : " << settings.subreadsBamFilename << endl;
if (not settings.scrapsBamFilename.empty())
cerr << " scraps : " << settings.scrapsBamFilename << endl;
if (not settings.polymeraseBamFilename.empty())
cerr << " polymerase: " << settings.polymeraseBamFilename << endl;
cerr << "Output h5 : " << settings.outputBaxFilename << endl
<< "Output xml : " << settings.outputMetadataFilename << endl;
#endif
return settings;
}