Fix test compilation errors by adding frequency field

All test files needed the new `frequency: None,` field added to their
Args struct initializations after the field was added to support the
--frequency command-line option.

Fixed files:
- tests/bidirected_inversion_test.rs
- tests/bidirected_tests.rs
- tests/integration_tests.rs
- tests/mathematical_bidirected_tests.rs
- tests/test_complex_structural_variations.rs
- tests/test_edge_traversal.rs
- tests/test_inversion_detection.rs
- tests/test_programmatic_variations.rs
- tests/test_real_inversion.rs
- tests/test_topological_sort.rs

All tests now compile and run successfully.

Author: ekg

tests/bidirected_inversion_test.rs

@@ -55,6 +55,7 @@ fn test_simple_inversion() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -142,6 +143,7 @@ fn test_complex_rearrangement() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -237,6 +239,7 @@ fn test_self_inverse_palindrome() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();

tests/bidirected_tests.rs

@@ -128,6 +128,7 @@ fn test_reverse_complement_alignment() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -186,6 +187,7 @@ fn test_palindromic_sequence() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -238,6 +240,7 @@ fn test_inversion_between_sequences() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -300,6 +303,7 @@ fn test_complex_rearrangement() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -350,6 +354,7 @@ fn test_self_alignment_with_repeats() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -437,6 +442,7 @@ fn test_multiple_sequence_alignment() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();

tests/integration_tests.rs

@@ -66,6 +66,7 @@ fn test_performance_scaling() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+            frequency: None,
         };
 
         let start = Instant::now();
@@ -166,6 +167,7 @@ fn test_real_world_example() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush(args).unwrap();
@@ -219,6 +221,7 @@ fn test_command_line_interface() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush(args).unwrap();
@@ -284,6 +287,7 @@ fn test_parallel_consistency() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+            frequency: None,
         };
 
         run_seqrush(args).unwrap();

tests/mathematical_bidirected_tests.rs

@@ -105,6 +105,7 @@ fn test_base_case_empty() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -168,6 +169,7 @@ fn test_base_case_single_base() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -278,6 +280,7 @@ fn test_identical_sequences_share_nodes() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -342,6 +345,7 @@ fn test_inductive_sequence_extension() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+            frequency: None,
         };
 
         run_seqrush_bidirected_simple(args).unwrap();
@@ -450,6 +454,7 @@ fn test_path_reconstruction_correctness() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -519,6 +524,7 @@ fn test_edge_connectivity() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -587,6 +593,7 @@ fn test_palindromic_sequences() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -642,6 +649,7 @@ fn test_union_find_with_matches() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -709,6 +717,7 @@ fn test_large_sequences() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -765,6 +774,7 @@ fn test_transitivity_of_matches() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();

tests/test_complex_structural_variations.rs

@@ -181,6 +181,7 @@ fn test_complex_cnv_repeats() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -247,6 +248,7 @@ fn test_y_shaped_breakpoint() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -307,6 +309,7 @@ fn test_nested_inversions() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -378,6 +381,7 @@ fn test_random_rearrangements() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -450,6 +454,7 @@ fn test_tandem_repeat_polymorphism() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -517,6 +522,7 @@ fn test_complex_nested_variations() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -588,6 +594,7 @@ fn test_interspersed_repeats_with_inversions() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -666,6 +673,7 @@ fn test_breakpoint_resolution() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();

tests/test_edge_traversal.rs

@@ -140,6 +140,7 @@ fn test_self_loops_in_gfa() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush(args).unwrap();
@@ -213,6 +214,7 @@ fn test_complex_graph_produces_valid_gfa() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush(args).unwrap();

tests/test_inversion_detection.rs

@@ -55,6 +55,7 @@ fn test_inversion_detection_simple() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     println!("Running inversion-aware alignment...");
@@ -132,6 +133,7 @@ fn test_inversion_detection_with_context() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     println!("\nRunning inversion detection with context...");
@@ -189,6 +191,7 @@ fn test_no_inversion() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -244,6 +247,7 @@ fn test_multiple_inversions() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     println!("\nRunning multiple inversion detection...");

tests/test_programmatic_variations.rs

@@ -202,6 +202,7 @@ fn test_programmatic_inversions_scale() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -279,6 +280,7 @@ fn test_gc_content_variation() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush_bidirected_simple(args).unwrap();
@@ -372,6 +374,7 @@ fn test_motif_based_variations() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -456,6 +459,7 @@ fn test_microsatellite_instability() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -542,6 +546,7 @@ fn test_complex_structural_variation_patterns() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();
@@ -639,6 +644,7 @@ fn test_nested_tandem_inversions() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_inversion_aware_seqrush(args).unwrap();

tests/test_real_inversion.rs

@@ -56,6 +56,7 @@ fn test_real_inversion_case() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     println!("Testing real inversion case...");
@@ -113,6 +114,7 @@ fn test_larger_inversion_with_unique_content() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     println!("\nTesting larger inversion with unique content...");
@@ -169,6 +171,7 @@ fn test_inversion_with_snps() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     println!("\nTesting inversion detection with SNPs...");

tests/test_topological_sort.rs

@@ -84,6 +84,7 @@ fn test_sorting_creates_sequential_node_ids() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush(args_unsorted).unwrap();
@@ -197,6 +198,7 @@ fn test_sorting_preserves_graph_structure() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush(args_sorted).unwrap();
@@ -233,6 +235,7 @@ fn test_sorting_preserves_graph_structure() {
             sgd_sort: false,
             groom: false,
         aligner: "allwave".to_string(),
+        frequency: None,
     };
 
     run_seqrush(args_unsorted).unwrap();