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); }