Usage: ./phi_analysis.R [options] file1 file2 ...
Options:
--phi=CHARACTER
comma separated string defining phi values: [default= 0.177,0.0442]
-c CHARACTER, --col=CHARACTER
collection table with name and collection columns
-h, --help
Show this help message and exit
Usage: ./duplicate_analisys.R [options] file1 file2 ...
Options:
-t OPTION, --phi=OPTION
phi threshold to infer duplication [default= 0.45]
-v OPTION, --vertexinfo=OPTION
tab delimited file, minimum 2 columns: name collection
-r OPTION, --resultsdir=OPTION
results directory [default= results]
-h, --help
Show this help message and exit
Usage: ./fastivs_analysis.R [options] file
Options:
-t OPTION, --phi=OPTION
phi threshold to infer independence [default= 0.0442]
-n OPTION, --nreq=OPTION
number of ivs requested to fastindep [default= 2]
-m OPTION, --nread=OPTION
number of ivs to read from fastindep [default= 2]
-v OPTION, --vertexinfo=OPTION
tab delimited file, minimum 2 columns: name collection
-r OPTION, --resultsdir=OPTION
results directory [default= fastivs]
-h, --help
Show this help message and exit