gistfile1.r

library(getopt)

options <- c('help', 'h', 0, 'logical',
             'reads', 'r', 1, 'character',
             'targets', 't', 1, 'character')

opt = getopt(matrix(options, ncol=4, byrow=T))

# Help was asked for.
if (!is.null(opt$help)) {
  # Print a friendly message and exit with a non-zero error code
  print('Usage: -[h] -reads|r -targets|t')
  q(status=1)
}

seqFile <- opt$reads
targetFile <- opt$targets

library('knitr')
knit2html('/n/home10/ohofmann/hsph/projects/dc_lung_cancer/scripts/teqc.Rmd')
#knit('teqc.Rmd')