Set number of sequences via a CLI argument

src/repertoire.r

@@ -1,13 +1,31 @@
 library(immuneSIM)
 
-sim_repertoire <- immuneSIM(
-  number_of_seqs = 1000,
-  species = "hs",
-  receptor = "tr",
-  chain = "b",
-  verbose = TRUE
-)
+generate_repertoires <- function(number_of_sequences) {
+  a_chain <- immuneSIM(
+    number_of_seqs = number_of_sequences,
+    species = "hs",
+    receptor = "tr",
+    chain = "a",
+    verbose = TRUE
+  )
+  b_chain <- immuneSIM(
+    number_of_seqs = number_of_sequences,
+    species = "hs",
+    receptor = "tr",
+    chain = "b",
+    verbose = TRUE
+  )
+  return(list("a_chain" = a_chain, "b_chain" = b_chain))
+}
 
-save(sim_repertoire, file = "data/repertoire")
 
-plot_report_repertoire(sim_repertoire, output_dir = "data/reports")
+parse_cli_arguments <- function(args) {
+  if (length(args) != 1) {
+    stop("usage: repertoire.r <number of sequences>")
+  }
+  return(as.integer(args[1]))
+}
+
+args <- commandArgs(trailingOnly = TRUE)
+number_of_sequences <- parse_cli_arguments(args)
+sim_repertoire <- generate_repertoires(number_of_sequences)