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);
	}
示例#5
0
 void addPositional(po::positional_options_description& options) {
   options.add("lower", 1);
   options.add("upper", 1);
 }