FileStringParser myFileParser = FileStringParser.getParser();
myFileParser.setMustBeFile(true);
myFileParser.setMustExist(true);
// build the jsap object
SimpleJSAP jsap = new SimpleJSAP(
"spectralHMM",
"Analyze temporal data using a spectral HMM method.",
new Parameter[] {
new FlaggedOption( "inputFile", myFileParser, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'f', "inputFile", "Specify an input file. See documentation for formatting." ),
new Switch ("mutSelBalance", 'j', "mutSelBalance", "Set the initial condition to be selection-drift balance."),
new Switch ("mutDriftBalance", 'd', "mutDriftBalance", "Set the initial condition to be mutation-drift balance."),
new FlaggedOption( "initFrequency", JSAP.BIGDECIMAL_PARSER, "-0.5", JSAP.NOT_REQUIRED, 'i', "initFrequency", "Set the initial frequency." ),
new FlaggedOption( "initTime", JSAP.BIGDECIMAL_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 't', "initTime", "The initial time. If not given, the initial time is expected to be in the file with each dataset. Also, this only works with multiplexing." ),
new FlaggedOption( "mutToBenef", JSAP.BIGDECIMAL_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'a', "mutToBenef", "The mutation rate from the wild type allele to the selected allele." ),
new FlaggedOption( "mutFromBenef", JSAP.BIGDECIMAL_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'b', "mutFromBenef", "The mutation rate from the selected allele to the wild-type allele." ),
new FlaggedOption( "selection", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 's', "selection", "Selection coefficient s (can be a range: [start:step:stop])." ),
new FlaggedOption( "dominance", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 'h', "dominance", "Dominance parameter h (can be a range: [start:step:stop])." ),
new FlaggedOption( "hetF", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 'w', "hetF", "Fitness of the heterozygote (can be a range: [start:step:stop])." ),
new FlaggedOption( "homF", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.NOT_REQUIRED, 'v', "homF", "Fitness of the homozygote (can be a range: [start:step:stop])." ),
new FlaggedOption( "effPopSize", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'e', "effPopSize", "The effective population size (diploid)." ),
new FlaggedOption( "yearsPerGen", JSAP.STRING_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'y', "yearsPerGen", "Specify how many years a generation takes." ),
new FlaggedOption( "matrixCutoff", JSAP.INTEGER_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'c', "matrixCutoff", "The cutoff for the matrix whose eigenvectors yield the coefficients for the eigenfunctions." ),
new FlaggedOption( "maxM", JSAP.INTEGER_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'm', "maxM", "Specify how many summands to use in the infinite sum for each eigenfunction." ),
new FlaggedOption( "maxN", JSAP.INTEGER_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'n', "maxN", "Specify how many eigenfunctions/-values to use in the computations." ),
new FlaggedOption( "precision", JSAP.INTEGER_PARSER, JSAP.NO_DEFAULT, JSAP.REQUIRED, 'p', "precision", "Specify a precision to be used for the computations. This gives the number of significant digits used." ),
new Switch ("ignoreBinomials", 'z', "ignoreBinomials", "If set, the likelihood is calculated without the binomial coefficients required to make it a probability."),
new Switch ("multiplex", JSAP.NO_SHORTFLAG, "multiplex", "Analyze each of the multiple datasests given in the input file using all the selection parameters specified."),
new Switch ("condOnLastSegregating", JSAP.NO_SHORTFLAG, "condOnLastSegregating", "When set, condition on the last sample being segregating."),
}
);
JSAPResult config = jsap.parse(args);
if (jsap.messagePrinted()) { System.exit(1); }
// what about the binomials
boolean ignoreBinomials = config.getBoolean ("ignoreBinomials");
// what about multiplexing
boolean multiplex = config.getBoolean ("multiplex");