Merge branch 'optimize-display'

src/lib.rs

@@ -160,7 +160,10 @@ pub fn back_to_multiple_sequences(
         .unwrap();
 
     if input_files.len() != output_files.len() {
-        anyhow::bail!("Error: the number of input files and output files must be the same");
+        // anyhow::bail!("The number of input files and output files must be the same");
+        eprintln!("Error: the number of input files and output files must be the same");
+        // exit the program
+        std::process::exit(1);
     }
 
     let (kmer_set, kmer_size) = kmer_hash::index_kmers::<RelaxedCounter>(

src/main.rs

@@ -24,7 +24,8 @@ fn main() -> anyhow::Result<()> {
 
     // If out_sequences and out_kmers are not provided, we do nothing, we can quit
     if args.out_sequences.is_empty() && args.out_filelist.is_empty() && args.out_kmers.is_empty() {
-        anyhow::bail!("no output file provided, nothing to do");
+        eprintln!("Error: no output file provided, nothing to do");
+        std::process::exit(1);
     }
 
     // If out_kmers is not provided but output_kmer_positions is true, warn that it has no effect
@@ -42,18 +43,21 @@ fn main() -> anyhow::Result<()> {
     }
 
     if args.min_threshold > args.max_threshold {
-        anyhow::bail!("--min-threshold must be <= --max-threshold");
+        eprintln!("Error: --min-threshold must be <= --max-threshold");
+        std::process::exit(1);
     }
 
     if args.in_sequences.is_empty() && !args.in_filelist.is_empty() {
         if args.out_filelist.is_empty() {
-            anyhow::bail!("--in-filelist requires --out-filelist");
+            eprintln!("Error: --in-filelist requires --out-filelist");
+            std::process::exit(1);
         }
 
         if args.output_kmer_positions {
-            anyhow::bail!(
-                "--in-filelist and --output-kmer-positions are mutually exclusive (for now)"
+            eprintln!(
+                "Error: --in-filelist and --output-kmer-positions are mutually exclusive (for now)"
             );
+            std::process::exit(1);
         }
         back_to_multiple_sequences(
             args.in_filelist,

tests/functional.rs

@@ -213,7 +213,7 @@ kmers with their number of occurrences in the original sequences are in file {}
         kmers_out_path.display(),
     );
 
-    let assert = cmd.assert().stdout(out);
+    let assert = cmd.assert().stderr(out);
 
     assert.success();
 
@@ -273,7 +273,7 @@ kmers with their number of occurrences in the original sequences are in file {}
         kmers_out_path.display(),
     );
 
-    let assert = cmd.assert().stdout(out);
+    let assert = cmd.assert().stderr(out);
 
     assert.success();
 
@@ -330,7 +330,7 @@ kmers with their number of occurrences in the original sequences are in file {}
         kmers_out_path.display(),
     );
 
-    let assert = cmd.assert().stdout(out);
+    let assert = cmd.assert().stderr(out);
 
     assert.success();
 
@@ -396,7 +396,7 @@ kmers with their number of occurrences in the original sequences are in file {}
         kmers_out_path.display(),
     );
 
-    let assert = cmd.assert().stdout(out);
+    let assert = cmd.assert().stderr(out);
 
     assert.success();
 
@@ -446,7 +446,7 @@ fn multi_inout_not_same_length() -> std::result::Result<(), anyhow::Error> {
 
     let assert = cmd
         .assert()
-        .stderr("Error: Error: the number of input files and output files must be the same\n");
+        .stderr("Error: the number of input files and output files must be the same\n");
 
     assert.failure();
 
@@ -513,7 +513,7 @@ kmers with their number of occurrences in the original sequences are in file {}
         kmers_out_path.display(),
     );
 
-    let assert = cmd.assert().stdout(out);
+    let assert = cmd.assert().stderr(out);
 
     assert.success();
 
@@ -601,7 +601,7 @@ kmers with their number of occurrences in the original sequences are in file {}
         kmers_out_path.display(),
     );
 
-    let assert = cmd.assert().stdout(out);
+    let assert = cmd.assert().stderr(out);
 
     assert.success();