run.SATlotyper: A simple interface to run SATlotyper

In PolyHaplotyper: Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

Description

A simple interface to run SATlotyper

Usage

run.SATlotyper(path_to_SATlotyper, infile, outfile,
SAT_solver="sat4j.conf")

Arguments

path_to_SATlotyper	path to the folder where SATlotyper.jar and the *.conf files of the SAT-solvers are located
infile	name (and path) to the SATlotyper input file
outfile	name (and path) for the SATlotyper output file (an xml file)
SAT_solver	name of the *.conf file for the SAT-solver to use. Default "sat4j.conf" because this works under both Windows and Linux.

Details

This function issues a system command to invoke SATlotyper. Java and SATlotyper must be installed. This is just a simple interface for convenience; for more control run SATlotyper directly from the command window.

Value

The return is a list with elements:
$cmd : the command passed to the system
$result: screen output from SATlotyper; this contains some extra info not present in the output xml file)
The main result is the outfile

PolyHaplotyper documentation built on June 17, 2021, 5:12 p.m.