add argument types

  cxxopts::Options options("chromap", "A short read mapper for chromatin biology");

  options.add_options("Indexing")

    ("i,build-index", "Build index")

    ("k,kmer", "Kmer length [17]", cxxopts::value<int>())

    ("w,window", "Window size [5]", cxxopts::value<int>());

    ("k,kmer", "Kmer length [17]", cxxopts::value<int>(), "INT")

    ("w,window", "Window size [5]", cxxopts::value<int>(), "INT");

  options.add_options("Mapping")

    ("m,map", "Map reads")

    ("e,error-threshold", "Max # errors allowed to map a read [3]", cxxopts::value<int>())

    ("A,match-score", "Match score [1]", cxxopts::value<int>())

    ("B,mismatch-penalty", "Mismatch penalty [4]", cxxopts::value<int>())

    ("O,gap-open-penalties", "Gap open penalty [6,6]", cxxopts::value<std::vector<int>>())

    ("E,gap-extension-penalties", "Gap extension penalty [1,1]", cxxopts::value<std::vector<int>>())

    ("s,min-num-seeds", "Min # seeds to try to map a read [2]", cxxopts::value<int>())

    ("f,max-seed-frequencies", "Max seed frequencies for a seed to be selected [1000,5000]", cxxopts::value<std::vector<int>>())

    ("n,max-num-best-mappings", "Only report n best mappings [10]", cxxopts::value<int>())

    ("l,max-insert-size", "Max insert size, only for paired-end read mapping [400]", cxxopts::value<int>())

    ("min-read-length", "Min read length [30]", cxxopts::value<int>())

    ("multi-mapping-allocation-distance", "Uni-mappings within this distance from any end of multi-mappings are used for allocation [0]", cxxopts::value<int>())

    ("multi-mapping-allocation-seed", "Seed for random number generator in multi-mapping allocation [11]", cxxopts::value<int>())

    ("drop-repetitive-reads", "Drop reads with too many best mappings [500000]", cxxopts::value<int>())

    ("e,error-threshold", "Max # errors allowed to map a read [3]", cxxopts::value<int>(), "INT")

    ("A,match-score", "Match score [1]", cxxopts::value<int>(), "INT")

    ("B,mismatch-penalty", "Mismatch penalty [4]", cxxopts::value<int>(), "INT")

    ("O,gap-open-penalties", "Gap open penalty [6,6]", cxxopts::value<std::vector<int>>(), "INT[,INT]")

    ("E,gap-extension-penalties", "Gap extension penalty [1,1]", cxxopts::value<std::vector<int>>(), "INT[,INT]")

    ("s,min-num-seeds", "Min # seeds to try to map a read [2]", cxxopts::value<int>(), "INT")

    ("f,max-seed-frequencies", "Max seed frequencies for a seed to be selected [1000,5000]", cxxopts::value<std::vector<int>>(), "INT[,INT]")

    ("n,max-num-best-mappings", "Only report n best mappings [10]", cxxopts::value<int>(), "INT")

    ("l,max-insert-size", "Max insert size, only for paired-end read mapping [400]", cxxopts::value<int>(), "INT")

    ("min-read-length", "Min read length [30]", cxxopts::value<int>(), "INT")

    ("multi-mapping-allocation-distance", "Uni-mappings within this distance from any end of multi-mappings are used for allocation [0]", cxxopts::value<int>(), "INT")

    ("multi-mapping-allocation-seed", "Seed for random number generator in multi-mapping allocation [11]", cxxopts::value<int>(), "INT")

    ("drop-repetitive-reads", "Drop reads with too many best mappings [500000]", cxxopts::value<int>(), "INT")

    ("trim-adapters", "Try to trim adapters on 3'")

    ("remove-pcr-duplicates", "Remove PCR duplicates")

    ("allocate-multi-mappings", "Allocate multi-mappings")

    ("unique-mappings", "Only output unique mappings")

    ("Tn5-shift", "Perform Tn5 shift")

    ("t,num-threads", "# threads for mapping [1]", cxxopts::value<int>());

    ("t,num-threads", "# threads for mapping [1]", cxxopts::value<int>(), "INT");

  options.add_options("Input")

    ("r,ref", "Reference file", cxxopts::value<std::string>())

    ("x,index", "Index file", cxxopts::value<std::string>())

    ("1,read1", "Single-end read file or paired-end read file 1", cxxopts::value<std::string>())

    ("2,read2", "Paired-end read file 2", cxxopts::value<std::string>())

    ("b,barcode", "Cell barcode file", cxxopts::value<std::string>());

    ("r,ref", "Reference file", cxxopts::value<std::string>(), "FILE")

    ("x,index", "Index file", cxxopts::value<std::string>(), "FILE")

    ("1,read1", "Single-end read file or paired-end read file 1", cxxopts::value<std::string>(), "FILE")

    ("2,read2", "Paired-end read file 2", cxxopts::value<std::string>(), "FILE")

    ("b,barcode", "Cell barcode file", cxxopts::value<std::string>(), "FILE");

  options.add_options("Output")

    ("o,output", "Output file", cxxopts::value<std::string>())

    ("o,output", "Output file", cxxopts::value<std::string>(), "FILE")

    ("BED", "Output mappings in BED/BEDPE format")

    ("TagAlign", "Output mappings in TagAlign/PairedTagAlign format")

    ("PAF", "Output mappings in PAF format");