Feature/claude assisted tests#263
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Rewrites/expands test coverage for split_inputs, bed_func, read, and vcf_func modules — raising coverage from <50% to 88–100% across all four. - test_split_inputs.py: rewrite from 1 → 25 tests covering chunk_record, write_fasta, disk_bytes_free, print_stderr, and main() in both contig and block modes (100% coverage) - test_bed_func.py: new file with 37 tests covering intersect_regions, fill_out_mut_regions, recalibrate_mutation_regions, parse_single_bed, fill_out_bed_dict, and parse_beds (98% coverage) - test_read.py: new file with 47 tests covering Read construction, comparisons, apply_mutations, calculate_flags, make_cigar, finalize_read_and_write, and all helper methods (98% coverage) - test_vcf_func.py: new file with 28 tests covering retrieve_genotype, variant_genotype, and parse_input_vcf for all variant types and genotype formats (88% coverage; remaining 12% is the unreachable WP legacy genotype branches due to a known bug fixed separately) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
25 tests covering find_random_non_n, map_non_n_regions, and generate_variants — including input variant range filtering, offset ref_start handling, mutation count bounds, variant type validation, qual score assignment, reproducibility, and high-vs-low mutation rate comparison. Also surfaces a pre-existing bug: when mutation_rate_regions has multiple entries, probability_rates (len N) may not match the length of local_mut_regions returned by intersect_regions, causing a numpy ValueError. Documented by replacing the multi-region test with a single-region variant that avoids the mismatch. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Add coverage artifacts (.coverage, htmlcov/), pytest cache, NEAT log files (*.log), compiled bytecode (__pycache__, *.pyc/pyo/pyd), common virtual environment directories, and build/packaging output. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
20 tests covering concat, merge_vcfs, merge_bam, and main: - concat: single file, multiple files, empty list, content preservation, ordering - merge_vcfs: comment/header line filtering, multi-file merge, empty input, data line ordering - merge_bam: pysam merge+sort call verification, output path, temp file cleanup, >500-file chunking behaviour - main: fq1-only, fq1+fq2, vcf, all-None entries, multi-chunk concatenation, BAM delegation to merge_bam Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
16 unit tests cover filter_thread_variants and filter_bed_regions: range boundaries (inclusive lower, exclusive upper), partial overlap, empty inputs, multi-region spanning, and return types. 6 integration tests exercise read_simulator_runner end-to-end against a 400 bp single-contig reference with low coverage: - FASTQ output created and contains valid records - Paired-end mode produces two FASTQ files - Missing output directory is created automatically - Output files carry the supplied prefix - Identical seeds produce identical output - VCF output mode creates a vcf.gz file Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
24 tests covering: - reg2bin: same-bin, large-span fallback, adjacent coordinates - Constructor: fq1/fq2/vcf/bam file handle creation, no-files ValueError, None paths when output type not requested - VCF header: fileformat line, contig entries, #CHROM column header - write_fastq_record: content written to gzip, unknown-file ValueError, multiple records - write_vcf_record: data appended, unknown-file ValueError - flush_and_close_files: handle closed, idempotent double-close - write_bam_record: forward strand, reverse strand, odd-length padding Also includes minor whitespace fix in test_generate_reads.py. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
test_error_models.py (21 tests): - TraditionalQualityModel: default construction, quality score range, error rate dict, uniform mode init and score bounds, get_quality_scores for uniform/non-uniform/exact-length/shorter-than-model cases, ndarray return, reproducibility - SequencingErrorModel: default construction, variant prob sum, custom error rate, zero-error returns empty list, high-error produces ErrorContainers with valid locations and alt bases, padding returned - ErrorContainer: field storage for SNV, Deletion, Insertion types test_single_runner.py (37 tests, 3 classes): - TestInitializeAllModels: returns 4-tuple of correct types, rng attached, mutation_rate override, fragment_mean path, default mean=read_len*2 - TestWriteBlockVcf: single SNV written, ref/alt/qual correct, empty input produces no output, multiple SNVs in sorted order, 10 VCF columns - TestReadSimulatorSingle: return tuple structure, thread_idx/contig_name passthrough, ContigVariants return, all file_dict keys present, FASTQ file created and valid, content has FASTQ records, seed reproducibility, vcf=None when produce_vcf=False Note: quality_score_model.py is a standalone Markov analysis script with hardcoded BAM paths — not a library module and not tested here. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- test_error_models.py: 4 new indel error tests (deletion, insertion, blacklist deduplication); fix monkeypatch approach for numpy Generator - test_single_runner.py: 2 new tests covering produce_bam=True path (lines 127-152) and bam=None when not requested - test_runner.py: 8 new integration tests covering discard_bed, mutation_bed, ploidy=1, ploidy=4, min_mutations, and produce_bam=True; also input VCF, target_bed, and mutation_rate override - tests/test_variants/: new test_variant_types.py (73 tests for all comparison operators, __repr__, contains(), get_alt()) and test_contig_variants.py (24 tests documenting known bugs in remove_variant and check_if_ins) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
generate_variants.py:
- N in mutation region (lines 139-157 avoidance logic)
- N-heavy subsequence skip (line 204)
- Trinucleotide with N triggers disallowed_chars path (lines 246-249)
- High-rate deletion overlap handling (lines 291-302)
error_models.py:
- MarkovQualityModel stub coverage (lines 112-118)
- Score clamped to min 1 and max 42 via extreme qual_score_probs (lines 102-104)
- Documents unreachable indel branches (lines 209-235, 252) caused by
the total_indel_length > read_length//4 circular gate; includes
TODO comment with proposed assertions for after the bug fix
vcf_func.py:
- Three WP-genotype tests document that the WP condition is always False
(string "WP" never equals a list); each includes a TODO comment with
exact updated assertions to apply once the condition is corrected to
any(x.split('=')[0] == "WP" for x in ...)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Duplicates removed: - test_error_and_mut_models.py: test_sequencing_error_model_zero_error_returns_none_or_empty (covered by test_error_models.py::test_sem_zero_error_rate_returns_empty) - test_error_and_mut_models.py: test_traditional_quality_model_reproducible_with_seed (covered by test_error_models.py::test_tqm_get_quality_scores_reproducible) - test_seq_error.py: test_no_errors_when_avg_zero (same as above) - test_models/test_stitch_outputs.py: test_concat_joins_files_in_order (covered by test_read_simulator/test_stitch_outputs.py) Vacuous assertions fixed: - test_error_models.py: rename indel dead-code tests and assert == 0 (not >= 0) - test_output_file_writer.py: replace `assert True` with bam_handle.tell() > pos_before - test_output_file_writer.py: strengthen test_reg2bin_same_16kb_bin to check determinism - test_runner.py: test_filter_bed_regions_returns_list now checks content - test_single_runner.py: test_returns_four_element_tuple now checks element types - test_vcf_func.py: test_variant_genotype_returns_correct_ploidy_length checks values - test_generate_variants.py: test_generate_variants_variant_types_are_valid checks attributes - test_contig_variants.py: test_remove_variant_method_exists adds TODO comment for post-fix update Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- generate_reads.py lines 234-236: paired-end discard check for read2 (test_generate_reads_paired_discard_region_removes_all) - generate_reads.py: paired no-discard regression guard (test_generate_reads_paired_no_discard_produces_read_pairs) - single_runner.py line 85: "Record too small" debug log path, with generate_reads/generate_variants patched to avoid infinite loop (test_record_too_small_logs_and_continues) - bed_func.py line 209: mutation rate > 0.3 warning log (test_parse_single_bed_mutation_high_rate_logs_warning) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
2. Change version to 4.3.6 in pyproject.toml 3. Fixed channel order in environment.ylm which cause crash due to not satisfied requirements of bcftools
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Tests written to cover gaps in test coverage with Claude help.