diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 7 |
1 files changed, 5 insertions, 2 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 461b4a1..91c1dd3 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -71,6 +71,7 @@ genRandomFileName <- function(prefix, string_size = 9, file_ext = ".txt") { # Generate control file path control_file_path <- file.path(opt$directory, genRandomFileName(prefix = "control", file_ext = ".json")) + cat("Generated the control file path at", control_file_path, "\n") # Read and parse the input file cat("Reading and parsing the input file.\n") @@ -115,7 +116,6 @@ generate_cross_object <- function(control_file_path, json_data) { geno_codes = json_data$geno_codes, alleles = json_data$alleles, na.strings = json_data$na.strings, - geno_transposed = json_data$geno_transposed, sex_file = json_data$sex_file, founder_geno_file = json_data$founder_geno_file, covar_file = json_data$covar_file, @@ -125,7 +125,9 @@ generate_cross_object <- function(control_file_path, json_data) { crossinfo_covar = json_data$crossinfo_covar, crossinfo_codes = json_data$crossinfo_codes, xchr = json_data$xchr, - overwrite = TRUE + overwrite = TRUE, + founder_geno_transposed = json_data$founder_geno_transposed, + geno_transposed = json_data$geno_transposed ) } @@ -135,6 +137,7 @@ generate_cross_object(control_file_path, json_data) # Read the cross object cat("Reading the cross object from", control_file_path, "\n") + cross <- read_cross2(control_file_path, quiet = FALSE) # Check the integrity of the cross object |