From 52a98118550e2d4024b8c50538a0f6a968938ef8 Mon Sep 17 00:00:00 2001
From: Andrew D Smith <andrewds@usc.edu>
Date: Sat, 25 Nov 2023 19:08:53 -0800
Subject: [PATCH] roi: ensuring regions file is a regular file because
 otherwise we might not be able to read it multiple times to verify its
 contents; this can be improved later and the restrition removed

---
 src/analysis/roimethstat.cpp | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/analysis/roimethstat.cpp b/src/analysis/roimethstat.cpp
index 08357ed9..ee2e8569 100644
--- a/src/analysis/roimethstat.cpp
+++ b/src/analysis/roimethstat.cpp
@@ -26,6 +26,7 @@
 #include <unordered_map>
 #include <utility>
 #include <vector>
+#include <filesystem>
 
 #include "GenomicRegion.hpp"
 #include "LevelsCounter.hpp"
@@ -49,6 +50,8 @@ using std::vector;
 
 using bamxx::bgzf_file;
 
+namespace fs = std::filesystem;
+
 bool
 cmp_within_chrom(const GenomicRegion &r1, const GenomicRegion &r2) {
   return (r1.get_start() < r2.get_start() ||
@@ -299,6 +302,7 @@ get_bed_columns(const string &regions_file) {
   return n_columns;
 }
 
+
 int
 main_roimethstat(int argc, const char **argv) {
   try {
@@ -391,6 +395,10 @@ Columns (beyond the first 6) in the BED format output:
 
     if (VERBOSE) cerr << "loading regions" << endl;
 
+    if (!fs::is_regular_file(regions_file))
+      // otherwise we could not read the file twice
+      throw runtime_error("regions file must be regular file");
+
     // MAGIC: below allow for ==3 or >=6 columns in the bed format
     const auto n_columns = get_bed_columns(regions_file);
     if (n_columns != 3 && n_columns < 6)