diff options
Diffstat (limited to 'scripts/rqtl_wrapper.R')
| -rw-r--r-- | scripts/rqtl_wrapper.R | 8 |
1 files changed, 7 insertions, 1 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R index 31c1277..0b39a6a 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -4,6 +4,9 @@ library(stringi) library(stringr) + +cat("Running the qtl script.\n") + tmp_dir = Sys.getenv("TMPDIR") if (!dir.exists(tmp_dir)) { tmp_dir = "/tmp" @@ -24,7 +27,7 @@ option_list = list( make_option(c("--control"), type="character", default=NULL, help="Name of marker (contained in genotype file) to be used as a control"), make_option(c("-o", "--outdir"), type="character", default=file.path(tmp_dir, "gn3"), help="Directory in which to write result file"), make_option(c("-f", "--filename"), type="character", default=NULL, help="Name to use for result file"), - make_option(c("-v", "--verbose"), action="store_true", default=NULL, help="Show extra information") + make_option(c("-v", "--verbose"), action="store_true", default=TRUE, help="Show extra information") ); opt_parser = OptionParser(option_list=option_list); @@ -353,5 +356,8 @@ if (!is.null(opt$pairscan)) { colnames(qtl_results)[4:7] <- c("AC", "AD", "BC", "BD") } + write.csv(qtl_results, out_file) } + +cat("End of script. Now working on processing the results.\n") |