feat: Add 49 new unit tests for BED/GTF parsers, error types, and config

SHARED_TASK_NOTES.md

@@ -1,62 +1,65 @@
 # Unit Test Coverage Task Notes
 
 ## Current Status
-Unit tests increased from 82 to 119 tests (37 new tests added this iteration).
-
-## Tests Added This Iteration (Iteration 4)
-
-### overlap.rs Edge Cases
-- `match_region_to_genes_intron_overlap`: Region in intron gap
-- `match_region_to_genes_negative_strand`: Negative strand exon numbering
-- `match_region_to_genes_upstream_proximity`: Upstream region detection
-- `match_region_to_genes_downstream_proximity`: Downstream region detection
-- `match_region_to_genes_multiple_genes`: Region overlapping multiple genes
-- `match_region_to_genes_gene_body`: Region in gene body (not exons)
-
-### tss.rs Edge Cases
-- `tss_exon_info_creation`: Struct creation
-- `entirely_in_tss_zone`: 100% TSS overlap
-- `entirely_in_promoter_zone`: Promoter-only overlap
-- `spans_promoter_and_upstream`: Multi-zone spanning
-- `entirely_in_upstream_zone`: Upstream-only
-- `neg_strand_entirely_in_tss`: Negative strand TSS
-- `neg_strand_upstream`: Negative strand upstream
-
-### tts.rs Edge Cases
-- `tts_exon_info_creation`: Struct creation
-- `entirely_in_tts_zone`: 100% TTS overlap
-- `entirely_in_downstream_zone`: Downstream-only
-- `neg_strand_entirely_in_tts`: Negative strand TTS
-- `neg_strand_entirely_in_downstream`: Negative strand downstream
-- `tts_zero_distance`: Zero TTS distance
-- `tts_pctg_calculations`: Percentage verification
-
-### rules.rs Additional Tests
-- `empty_grouped_by`: Empty input handling
-- `pctg_area_threshold_filter`: pctg_area filtering
-- `multiple_groups`: Multiple transcript groups
-- `rules_no_matching_area`: No rule matches fallback
-- `select_transcript_empty`: Empty input
-- `select_transcript_no_rules_match`: Rule fallback
-- `select_transcript_multiple_genes`: Multi-gene selection
-
-### output.rs Tests
-- Basic output formatting
-- Metadata handling (empty, multiple columns)
-- Header generation (0, 6, 9 columns)
-- Precision verification (2 decimal places)
-- Edge cases (zero values, large values, all areas)
+Unit tests increased from 119 to 168 tests (49 new tests added this iteration).
+
+## Tests Added This Iteration (Iteration 6)
+
+### 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
+
+### 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
+
+### 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`
+
+### 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
 
 ## Running Tests
 ```bash
-cargo test --test unit_tests  # Unit tests (119 tests)
+cargo test --test unit_tests  # Unit tests (168 tests)
 cargo test --lib              # Library tests (55 tests)
-cargo test                    # All tests (174 total)
+cargo test                    # All tests (223 total)
 ```
 
 ## Next Steps for Coverage
-1. Add tests for `parser/bed.rs` BedReader with gzip files
-2. Add tests for `parser/gtf.rs` edge cases (custom ID tags)
-3. Add integration tests with real BED/GTF sample files
-4. Test Config with various parameter combinations
-5. Increase coverage of error paths in parsers
+1. Add integration tests with real BED/GTF sample files
+2. Test gzip-compressed file reading (requires test fixtures)
+3. Add tests for main.rs CLI argument parsing
+4. Test error recovery paths in parsers
+5. Add property-based tests for coordinate calculations