feat: Add 58 new unit tests for TSS, TTS, rules, overlap, output, and parsers

SHARED_TASK_NOTES.md

@@ -1,65 +1,85 @@
 # 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 226 tests (58 new tests added this iteration).
 
-## 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
+### TSS Extended Tests (10 tests)
+- Spanning all zones (TSS, PROMOTER, UPSTREAM)
+- Exact boundary tests (positive and negative strand)
+- Very small region (1bp)
+- Zero TSS/promoter distance handling
+- Percentage calculation accuracy
 
-### 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
+### TTS Extended Tests (8 tests)
+- Entirely within TTS zone
+- Spanning TTS and DOWNSTREAM
+- Negative strand downstream handling
+- Exact boundary tests
+- Very large TTS zone
+- Percentage accuracy
 
-### 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`
+### Rules Extended Tests (9 tests)
+- Empty candidates handling
+- All fail thresholds fallback
+- pctg_area filter behavior
+- Multiple groups independence
+- Three-candidate merging
+- No rules match fallback
+- Exact threshold boundary
 
-### 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
+### Overlap Extended Tests (9 tests)
+- find_search_start_index edge cases
+- Region completely within exon
+- Region spanning multiple exons
+- Single exon gene handling
+- Beyond distance threshold
+- Transcript/gene level processing
+- Negative strand first exon
+
+### Output Extended Tests (6 tests)
+- Metadata with newlines/whitespace
+- Special characters handling
+- Exact header output
+- Negative coordinates
+- Merged transcripts format
+- All strands handling
+
+### Parser BED Extended Tests (5 tests)
+- Whitespace handling
+- Very long lines
+- Mixed valid/invalid lines
+- Tab-only lines
+- Coordinate ordering edge cases
+
+### Parser GTF Extended Tests (7 tests)
+- Overlapping genes
+- Malformed attributes
+- CDS/UTR entries (non-exon)
+- Quoted values with spaces
+- No exon entries
+- Different sources
+- Max length multiple chroms
+
+### Config Comprehensive Tests (6 tests)
+- Whitespace in rules parsing
+- All area combinations
+- Extreme values
+- Percentage value ranges
+- Report level default
+- Distance overflow prevention
 
 ## Running Tests
 ```bash
-cargo test --test unit_tests  # Unit tests (168 tests)
+cargo test --test unit_tests  # Unit tests (226 tests)
 cargo test --lib              # Library tests (55 tests)
-cargo test                    # All tests (223 total)
+cargo test                    # All tests (~281 total)
 ```
 
 ## Next Steps for Coverage
 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
+4. Add property-based tests for coordinate calculations
+5. Consider code coverage analysis with cargo-tarpaulin