From 85f345d5850e76d805238d9dea53178ce2a066fe Mon Sep 17 00:00:00 2001
From: kpjonsson <philip.jonsson@gmail.com>
Date: Tue, 29 Oct 2019 13:47:36 -0400
Subject: [PATCH] add legacy object conversion

---
 convert-legacy-rdata.R | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100755 convert-legacy-rdata.R

diff --git a/convert-legacy-rdata.R b/convert-legacy-rdata.R
new file mode 100755
index 0000000..c03c426
--- /dev/null
+++ b/convert-legacy-rdata.R
@@ -0,0 +1,39 @@
+#!/usr/bin/env Rscript
+suppressPackageStartupMessages({
+    library(argparse)
+})
+
+args = commandArgs(TRUE)
+if (length(args) == 0) {
+    message('Run convert-legacy-rdata.R --help for list of input arguments.')
+    quit()
+}
+
+parser = ArgumentParser(description = 'Convert .Rdata file from older versions of facets-suite to the new .rds format.')
+parser$add_argument('-i', '--input-file', required = TRUE,
+                    help = 'Input file')
+parser$add_argument('-o', '--output-prefix', required = FALSE,
+                    help = 'Name of output file [default input basename]')
+args = parser$parse_args()
+
+output = ifelse(is.null(args$output_prefix),
+                paste0(gsub('.Rdata', '', basename(args$input_file)), '.rds'),
+                paste0(args$output_prefix, '.rds'))
+
+# Convert input to new format -------------------------------------------------------------------------------------
+
+load(args$input_file)
+
+new_format = list(
+    snps = out$jointseg,
+    segs = fit$cncf,
+    purity = fit$purity,
+    ploidy = fit$ploidy,
+    diplogr = fit$dipLogR,
+    alballogr = out$alBalLogR,
+    flags = out$flags,
+    em_flags = fit$emflags,
+    loglik = fit$loglik
+)
+
+saveRDS(new_format, output)