From 65a8df76e891616bcb6be09ca67fe3df80503a96 Mon Sep 17 00:00:00 2001
From: smehringer <svenja.mehringer@gmail.com>
Date: Mon, 19 Aug 2024 14:00:07 +0200
Subject: [PATCH] Add config validation.

---
 src/chopper_layout.cpp | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/src/chopper_layout.cpp b/src/chopper_layout.cpp
index aef768fa..08903684 100644
--- a/src/chopper_layout.cpp
+++ b/src/chopper_layout.cpp
@@ -28,6 +28,24 @@
 namespace chopper
 {
 
+void validate_configuration(sharg::parser & parser,
+                            chopper::configuration & config,
+                            chopper::configuration const & sketch_config)
+{
+    if (parser.is_option_set("sketch-bits"))
+        throw sharg::parser_error{"You cannot set --sketch-bits when using a sketch file as input."};
+
+    if (parser.is_option_set("kmer") && config.k != sketch_config.k)
+    {
+        std::cerr << sharg::detail::to_string(
+            "[WARNING] Given k-mer size (",
+            config.k,
+            ") differs from k-mer size in the sketch file (",
+            config.k,
+            "). The results may be suboptimal. If this was a conscious decision, you can ignore this warning.\n");
+    }
+}
+
 int chopper_layout(chopper::configuration & config, sharg::parser & parser)
 {
     parser.parse();
@@ -55,6 +73,7 @@ int chopper_layout(chopper::configuration & config, sharg::parser & parser)
 
         filenames = std::move(sin.filenames);
         sketches = std::move(sin.hll_sketches);
+        validate_configuration(parser, config, sin.chopper_config);
     }
     else
     {