void _setOptions(po::options_description &desc,
po::positional_options_description &p) {
po::options_description usage("Usage: DistributedNucleatingAssembly <options> [[--contig-file contigs.fa] [[--input-file input.fq ...]\n\tNote: --contig-file and --input-file can be specified either as a positional argument or within the options");
p.add("contig-file", 1);
p.add("input-file", -1);
desc.add(usage);
po::options_description opts("DistributedNucleatingAssembly Options");
opts.add_options()
("max-iterations", po::value<int>()->default_value(maxIterations), "the maximum number of rounds to extend the set of contigs")
("max-contigs-per-batch", po::value<int>()->default_value(maxContigsPerBatch), "the maximum number of assemblies (per mpi) to gather reads and execute per batch")
("max-contig-length", po::value<int>()->default_value(maxContigLength), "the maximum size of a contig to continue extending");
desc.add(opts);
MatcherInterfaceOptions::_setOptions(desc,p);
KmerMatchOptions::_setOptions(desc,p);
KmerBaseOptions::_setOptions(desc,p);
KmerSpectrumOptions::_setOptions(desc,p);
VmatchOptions::_setOptions(desc,p);
ContigExtenderBaseOptions::_setOptions(desc,p);
NewblerOptions::_setOptions(desc, p);
Cap3Options::_setOptions(desc,p);
MPIOptions::_setOptions(desc,p);
FilterKnownOdditiesOptions::_setOptions(desc,p);
GeneralOptions::_setOptions(desc,p);
};
void _setOptions(po::options_description &desc, po::positional_options_description &p) {
p.add("output-bam", 1);
p.add("input-bams", -1);
po::options_description opts("BamSort-P <options> output.bam input.bam [...]\n\nOptions");
opts.add_options()
("output-bam", po::value<std::string>())
("input-bams", po::value<FileListType>())
("unmapped-read-pairs", po::value<std::string>()->default_value(unmappedReadPairs), "gzipped file to place unmapped read Pairs Fastqs (can be same as --unmapped-reads)")
("unmapped-reads", po::value<std::string>()->default_value(unmappedReads), "gzipped file to place unmapped reads Fastqs (can be same as --unmapped-read-pairs)")
("keep-unmapped-paired-read", po::value<bool>()->default_value(keepUnmappedPairedRead), "if unmapped-read-pairs file is specified, keep an unmapped read in the bam if its pair is mapped")
("num-partitions", po::value<int>()->default_value(numPartitions), "The number of alignment-index partitions to merge. Input bams expected to come ordered grouped by in batches of num-partitions where each group has the exact same read counts in the exact same order");
desc.add(opts);
GeneralOptions::_setOptions(desc, p);
// Other *::_setOptions(desc,p);
}
void _setOptions(po::options_description &desc,
po::positional_options_description &p) {
p.add("kmer-size", 1);
p.add("input-file", -1);
po::options_description opts("EstimateSize Options");
opts.add_options()
("sample-partitions",po::value<long>()->default_value(samplePartitions),"The number of partitions to break up the file")
("max-sample-fraction", po::value<double>()->default_value(maxSampleFraction), "The maximum amount of data to read")
;
desc.add(opts);
KmerSpectrumOptions::_setOptions(desc, p);
MPIOptions::_setOptions(desc, p);
GeneralOptions::_setOptions(desc, p);
KmerBaseOptions::_setOptions(desc, p);
KmerSpectrumOptions::_setOptions(desc, p);
}
void _setOptions(po::options_description &desc, po::positional_options_description &p) {
// override the default output format!
// set options specific to this program
p.add("input-file", -1);
po::options_description opts("Fastq to Fasta Options");
opts.add_options()
("split-pairs", po::value<bool>()->default_value(splitPairs), "if set, pairs will be directed into separate files")
("split-size-mbase", po::value<int>()->default_value(splitSizeMbase), "maximum size of output fastas. requires --output-file");
desc.add(opts);
GeneralOptions::getOptions()._setOptions(desc, p);
}
void addPositional(po::positional_options_description& options) {
options.add("lower", 1);
options.add("upper", 1);
}