Merge branch 'release/0.1.2'

msk-access · Feb 28, 2023 · 1e8aa88 · 1e8aa88
2 parents ba09ad4 + ad2ea07
commit 1e8aa88
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/R/compile_reads.R b/R/compile_reads.R
@@ -32,7 +32,7 @@ compile_reads <- function(
   }
 
   # data from DMP -----------------------------------------------------------
-  DMP.key <- fread(dmp.key.path)
+  DMP.key <- as.data.table(read.csv(dmp.key.path, header = FALSE, sep = ","))
   if (any(!master.ref[grepl("^P-", dmp_patient_id)]$dmp_patient_id %in% gsub("-T..-IH.|-T..-IM.|-T..-XS", "", DMP.key[grepl("IH|IM|XS", V1)]$V1))) {
     stop(paste0(
       "These DMP IDs are not found in DMP key file: ",

diff --git a/R/compile_reads_all.R b/R/compile_reads_all.R
@@ -39,7 +39,7 @@ compile_reads_all <- function(master.ref,
   }
 
   # data from DMP -----------------------------------------------------------
-  DMP.key <- fread(dmp.key.path)
+  DMP.key <- as.data.table(read.csv(dmp.key.path, header = FALSE, sep = ","))
   if (any(!master.ref[grepl("^P-", dmp_patient_id)]$dmp_patient_id %in% gsub("-T..-IH.|-T..-IM.", "", DMP.key[grepl("IH|IM", V1)]$V1))) {
     message(paste0(
       "These DMP IDs are not found in DMP key file: ",