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6 ChromoCombineUsage: chromocombine [OPTIONS] -o <outputfileroot> <listofinputfiles> Remember to set <outputfileroot>. Additionally, you must supply at least one inputfile. Inputfiles can be specified in the following forms: a) ChromoPainter root file name b) ChromoPainter ⋆full⋆ file names, with any combination of endings. Repeated roots will be kept only once. Note that you must not have changed the file name endings. Options: -o <outputfileroot>Set the output file root name (default: output) -d Specify that the input is a directory, and that ⋆all⋆ valid file roots ending in <ending> are of interest. -l Specify that length matrices should be IGNORED. -m Specify that mutation matrices should be IGNORED. -f <forcefile> Process a continental forcing file. "c" will be calculated for this file separately, and stored in it. The other output files will not be changed by this. Therefore, fineSTRUCTURE will use the correct "c" when run on the dataset without a forcefile, as well as when one is provided. You must however use the force file on the dataset for which "c" was calculated. -F <forceoutput> By default, the force file is ⋆updated⋆ with the correct value of c. This instead writes a ⋆new⋆ force file that contains the important sections (in case you want to use the. same force file on many datasets). -e <ending> Set the inputfile ending (default: ".out") Remember the dot! -E <ending> Set the outputfile ending (default: ".out") -C Instead of smallish regions, use complete genomic segments for calculation of c. (Currently only valid if you provide a number of input files and that each has approximately the same recombination distance) -i <file> The id file from ChromoPainter. This is needed to provide the correct column headers if donorfiles have been used to exclude some individuals, but the individuals were themselves the populations. -t Test: print the files that will be processed. and additionally test that they exist. -u Unsafe mode; when summing individuals from different files, the default is to stop if some are seen more often than others. Use this option to override. -v Verbose mode. -h This help message. |