func init() {
cmd.Run = runAlign
cmd.Flag.Var(&alignersFlag, "aligner", "comma-separated list of aligners")
cmd.Flag.BoolVar(&dryRunFlag, "dry-run", true, "write the job script, but do not run it")
cmd.Flag.StringVar(&referenceFlag, "reference", "", "path to the reference fasta")
cmd.Flag.StringVar(&jobManagerFlag, "job-manager", "", "SLURM|PBS|SGE|NONE")
command.Register(cmd)
}
func init() {
// break init cycle
cmd.Run = func(cmd *command.Command, args []string) error {
return Run(numThreads, dtoFile, refPath, dupPath, statsPath, matrixPath, minCoverage, minProportion, args...)
}
cmd.Flag.IntVar(&numThreads, "num-threads", runtime.NumCPU(), "Max number of CPUs that can be executing simultaneously")
cmd.Flag.StringVar(&dtoFile, "dto-file", "", "Path to the matrix_dto.xml file")
cmd.Flag.StringVar(&refPath, "reference-fasta", "", "Path to the reference.fasta against which samples are compared")
cmd.Flag.StringVar(&dupPath, "reference-dups", "", "Path to the duplicates.txt file marking duplicated positions")
cmd.Flag.StringVar(&statsPath, "stats-folder", "", "Path to the output folder for statistics")
cmd.Flag.StringVar(&matrixPath, "matrix-folder", "", "Path to the output folder for matrices")
cmd.Flag.IntVar(&minCoverage, "minimum-coverage", -1, "Filter positions below this coverage/depth threshold")
cmd.Flag.Float64Var(&minProportion, "minimum-proportion", -1.0, "Filter positions below this proportion threshold")
cmd.Flag.BoolVar(&withAllRefPos, "withallrefpos", false, "Include the withallrefpos matrix")
command.Register(cmd)
}
func init() {
// TODO: Update Run interface to be a function that returns an error
cmd.Run = run
cmd.Flag.StringVar(&typeFlag, "type", "vcf", "")
command.Register(cmd)
}