feat: Add 80 new unit tests for extended coverage across all modules

SHARED_TASK_NOTES.md

@@ -1,60 +1,104 @@
 # Unit Test Coverage Task Notes
 
 ## Current Status
-Unit tests increased from 119 to 168 tests (49 new tests added this iteration).
+Unit tests increased from 168 to 248 tests (80 new tests added this iteration).
+Total tests: 303 (248 unit tests + 55 library tests)
 
-## Tests Added This Iteration (Iteration 6)
+## Tests Added This Iteration (Iteration 7)
 
-### parser/bed.rs Tests (14 tests)
-- `test_get_bed_headers_zero/partial/full/exceeds_max`: Header generation tests
-- `test_bed_reader_multiple_chroms`: Multi-chromosome parsing
-- `test_bed_reader_max_metadata_columns`: Full 12-column BED support
-- `test_bed_reader_skip_malformed_lines`: Invalid line handling
-- `test_bed_reader_empty_file`: Empty file handling
-- `test_bed_reader_only_empty_lines`: Whitespace-only files
-- `test_bed_reader_varying_metadata`: Variable column count tracking
-- `test_bed_reader_scientific_notation_rejected`: Invalid number formats
-- `test_bed_reader_negative_coords_accepted`: Edge coordinate values
-- `test_bed_reader_large_coordinates`: Large genome coordinate support
-- `test_bed_reader_chunk_boundary`: Chunked reading behavior
+### Extended TSS Tests (8 tests)
+- `test_tss_very_small_region`: 1bp region handling
+- `test_tss_boundary_at_exactly_tss_distance`: Boundary at exact TSS distance
+- `test_tss_region_spans_all_zones`: Region spanning TSS/Promoter/Upstream
+- `test_tss_negative_strand_all_zones`: Negative strand multi-zone tests
+- `test_tss_zero_tss_and_promoter`: Zero-distance edge case
+- `test_tss_percentage_calculations_accuracy`: Percentage calculation validation
+- `test_tss_exactly_at_exon_start`: Boundary at exon start
 
-### parser/gtf.rs Tests (14 tests)
-- `test_parse_gtf_skip_comments`: Comment line handling
-- `test_parse_gtf_multiple_chromosomes`: Multi-chrom annotation
-- `test_parse_gtf_custom_id_tags`: Custom gene_id/transcript_id tags
-- `test_parse_gtf_exon_only_no_gene_entry`: Exon-only GTF files
-- `test_parse_gtf_with_gene_and_transcript_entries`: Full GTF format
-- `test_parse_gtf_multiple_transcripts_per_gene`: Isoform handling
-- `test_parse_gtf_skip_invalid_strand`: Invalid strand filtering
-- `test_parse_gtf_negative_strand_exon_numbering`: Exon numbering logic
-- `test_parse_gtf_max_lengths`: Max gene length tracking
-- `test_parse_gtf_empty_file`: Empty file handling
-- `test_parse_gtf_only_comments`: Comment-only files
-- `test_parse_gtf_multiple_genes_same_chrom`: Gene ordering
-- `test_parse_gtf_gene_strand_preserved`: Strand preservation
+### Extended TTS Tests (7 tests)
+- `test_tts_very_small_region`: 1bp region handling
+- `test_tts_boundary_at_exactly_tts_distance`: Boundary at exact TTS distance
+- `test_tts_negative_strand_downstream`: Negative strand downstream
+- `test_tts_large_tts_region`: Large TTS distance handling
+- `test_tts_percentage_calculations_accuracy`: Percentage calculation validation
+- `test_tts_region_exactly_at_exon_end`: Boundary at exon end
+- `test_tts_negative_strand_exactly_at_start`: Negative strand at start
 
-### Error Type Display Tests (9 tests)
-- `test_parse_strand_error_display/debug/is_error_trait`
-- `test_parse_area_error_display/debug/is_error_trait`
-- `test_parse_report_level_error_display/debug/is_error_trait`
+### Extended Rules Tests (9 tests)
+- `test_apply_rules_empty_candidates`: Empty input handling
+- `test_apply_rules_no_rules`: No rules edge case
+- `test_apply_rules_area_threshold_filter`: Area threshold filtering
+- `test_apply_rules_multiple_groups`: Multiple groups processing
+- `test_select_transcript_empty_candidates`: Empty select_transcript input
+- `test_select_transcript_no_matching_rules`: No matching rules fallback
+- `test_select_transcript_merge_with_different_exon_numbers`: Merge logic
+- `test_apply_rules_all_same_area_different_pctg`: Same area tie-breaking
 
-### Config Extended Tests (12 tests)
-- `test_config_default_tags`: Default ID tags
-- `test_config_custom_tags`: Custom tag configuration
-- `test_config_all_levels`: ReportLevel variants
-- `test_config_set_distance_kb_large`: Large distance values
-- `test_config_max_lookback_with_large_tss/promoter/tts`: Lookback calculations
-- `test_config_parse_rules_with_extra_duplicates`: Rule deduplication
-- `test_config_parse_rules_preserves_order`: Rule ordering
-- `test_config_debug_output`: Debug trait implementation
-- `test_config_clone_independence`: Clone isolation
-- `test_config_boundary_values`: Zero/edge values
+### Extended Overlap Tests (14 tests)
+- `test_find_search_start_index_single_gene`: Single gene binary search
+- `test_find_search_start_index_multiple_genes`: Multiple gene binary search
+- `test_match_region_no_genes`: No genes edge case
+- `test_match_region_gene_far_away`: Gene beyond distance threshold
+- `test_match_region_within_distance`: Gene within distance threshold
+- `test_match_region_exact_overlap`: Exact region-gene overlap
+- `test_match_region_intron_overlap`: Region in intron
+- `test_match_region_negative_strand_first_exon`: Negative strand first exon
+- `test_process_candidates_exon_level`: Exon level processing
+- `test_process_candidates_transcript_level`: Transcript level processing
+- `test_process_candidates_gene_level`: Gene level processing
+- `test_match_regions_to_genes_multiple_regions`: Multiple regions batch
+- `test_match_region_region_completely_inside_exon`: Region inside gene body
+- `test_match_region_partial_left/right_overlap`: Partial overlap cases
+
+### Extended GTF Parser Tests (9 tests)
+- `test_parse_gtf_file_not_found`: Missing file error handling
+- `test_parse_gtf_all_comment_lines`: Comment-only files
+- `test_parse_gtf_mixed_features`: Gene/transcript/exon/CDS mix
+- `test_parse_gtf_invalid_strand_skipped`: Invalid strand filtering
+- `test_parse_gtf_multiple_transcripts_same_gene`: Multi-transcript genes
+- `test_parse_gtf_max_length_calculation`: Max length tracking
+- `test_parse_gtf_exon_numbering_positive/negative_strand`: Exon numbering
+- `test_parse_gtf_custom_tags`: Custom ID tag handling
+
+### Extended BED Parser Tests (11 tests)
+- `test_parse_bed_file_not_found`: Missing file error handling
+- `test_parse_bed_completely_empty`: Empty file handling
+- `test_parse_bed_only_whitespace`: Whitespace-only files
+- `test_parse_bed_with_browser_track_lines`: Browser/track header handling
+- `test_parse_bed_max_metadata_columns`: BED12 full format
+- `test_parse_bed_exceeds_max_metadata`: >12 columns handling
+- `test_bed_reader_chunked_reading`: Chunk reading verification
+- `test_bed_reader_single_region_per_chunk`: Single region per chunk
+- `test_get_bed_headers_boundary`: Header generation boundaries
+- `test_parse_bed_negative_coordinates`: Negative coordinate support
+- `test_parse_bed_large_coordinates`: Large coordinate support
+
+### Extended Types Tests (13 tests)
+- `test_exon_zero_length`: Zero-length exon
+- `test_exon_single_base`: Single base exon
+- `test_exon_large_coordinates`: Large coordinate handling
+- `test_transcript_calculate_size_single/multiple_exons`: Size calculation
+- `test_transcript_renumber_single_exon`: Single exon numbering
+- `test_transcript_renumber_many_exons`: Many exon numbering
+- `test_gene_calculate_size_single/multiple_transcripts`: Gene size calculation
+- `test_region_zero_length`: Zero-length region
+- `test_region_with_unicode_chrom`: Unicode chromosome names
+- `test_candidate_all_negative_values`: Negative value handling
+
+### Extended Config Tests (12 tests)
+- `test_max_lookback_all_zeros`: Zero lookback calculation
+- `test_max_lookback_tss/tts/promoter/distance_largest`: Max lookback variants
+- `test_set_distance_kb_zero/large`: Distance setting edge cases
+- `test_parse_rules_with_mixed_valid_invalid`: Mixed rules parsing
+- `test_parse_rules_exact_eight_valid`: Exact valid rules
+- `test_config_default_values`: Default value verification
+- `test_config_new_same_as_default`: new() vs default() equality
 
 ## Running Tests
 ```bash
-cargo test --test unit_tests  # Unit tests (168 tests)
+cargo test --test unit_tests  # Unit tests (248 tests)
 cargo test --lib              # Library tests (55 tests)
-cargo test                    # All tests (223 total)
+cargo test                    # All tests (303 total)
 ```
 
 ## Next Steps for Coverage