← Về thư mục
tests/pysam/test_scripts.py
- ArgumentValidatorTests · class · L38-L62 — class ArgumentValidatorTests(unittest.TestCase)
- test_positive_int_accepts_only_values_above_zero · method · L39-L44 — def test_positive_int_accepts_only_values_above_zero(self) -> None
- test_nonnegative_int_admits_zero · method · L46-L49 — def test_nonnegative_int_admits_zero(self) -> None
- test_non_numeric_input_raises · method · L51-L55 — def test_non_numeric_input_raises(self) -> None
- test_the_validators_are_shared_across_the_scripts · method · L57-L62 — def test_the_validators_are_shared_across_the_scripts(self) -> None: # Three scripts define the same pair; they must agree.
- FileModeTests · class · L65-L88 — class FileModeTests(unittest.TestCase)
- test_the_htslib_mode_follows_the_suffix · method · L66-L70 — def test_the_htslib_mode_follows_the_suffix(self) -> None
- test_the_suffix_check_is_case_insensitive · method · L72-L73 — def test_the_suffix_check_is_case_insensitive(self) -> None
- test_an_unrecognised_suffix_is_refused · method · L75-L79 — def test_an_unrecognised_suffix_is_refused(self) -> None
- test_the_writing_mode_differs_from_the_reading_mode · method · L81-L88 — def test_the_writing_mode_differs_from_the_reading_mode(self) -> None: # htslib needs "wb" to write a BAM; reusing "rb" silently produces SAM.
- RatioTests · class · L91-L102 — class RatioTests(unittest.TestCase)
- test_a_ratio_over_zero_is_none_rather_than_an_error · method · L92-L95 — def test_a_ratio_over_zero_is_none_rather_than_an_error(self) -> None: # An empty BAM must report "no reads", not divide by zero.
- test_ordinary_ratios_and_averages · method · L97-L99 — def test_ordinary_ratios_and_averages(self) -> None
- test_a_zero_numerator_is_zero_not_none · method · L101-L102 — def test_a_zero_numerator_is_zero_not_none(self) -> None
- LocalFileTests · class · L105-L122 — class LocalFileTests(unittest.TestCase)
- setUp · method · L106-L109 — def setUp(self) -> None
- test_an_existing_file_is_returned · method · L111-L114 — def test_an_existing_file_is_returned(self) -> None
- test_a_missing_path_is_reported_with_its_label · method · L116-L118 — def test_a_missing_path_is_reported_with_its_label(self) -> None
- test_a_directory_is_not_a_regular_file · method · L120-L122 — def test_a_directory_is_not_a_regular_file(self) -> None
- DestinationTests · class · L125-L161 — class DestinationTests(unittest.TestCase)
- setUp · method · L126-L131 — def setUp(self) -> None
- test_a_fresh_destination_is_accepted · method · L133-L136 — def test_a_fresh_destination_is_accepted(self) -> None
- test_an_existing_output_is_never_overwritten · method · L138-L142 — def test_an_existing_output_is_never_overwritten(self) -> None
- test_writing_over_the_input_is_refused · method · L144-L149 — def test_writing_over_the_input_is_refused(self) -> None: # Truncating the input mid-filter would destroy the only copy. The # exists-check happens to fire first, so accept either refusal -- # what matters is that the call does not go through.
- test_a_differently_spelled_path_to_the_input_is_also_refused · method · L151-L155 — def test_a_differently_spelled_path_to_the_input_is_also_refused(self) -> None
- test_a_missing_output_directory_is_refused · method · L157-L161 — def test_a_missing_output_directory_is_refused(self) -> None
- ExclusionTests · class · L164-L252 — class ExclusionTests(unittest.TestCase)
- flags · method · L168-L179 — def flags(**overrides) -> argparse.Namespace
- read · method · L182-L195 — def read(**attributes)
- Read · class · L183-L190 — class Read
- test_a_clean_read_has_no_exclusion_reasons · method · L197-L200 — def test_a_clean_read_has_no_exclusion_reasons(self) -> None
- test_each_flag_excludes_only_its_own_category · method · L202-L221 — def test_each_flag_excludes_only_its_own_category(self) -> None
- test_a_read_below_the_mapq_threshold_is_dropped · method · L223-L232 — def test_a_read_below_the_mapq_threshold_is_dropped(self) -> None
- test_improper_pairs_are_dropped_only_when_asked · method · L234-L242 — def test_improper_pairs_are_dropped_only_when_asked(self) -> None
- test_every_applicable_reason_is_reported_not_just_the_first · method · L244-L252 — def test_every_applicable_reason_is_reported_not_just_the_first(self) -> None
- KindDetectionTests · class · L255-L282 — class KindDetectionTests(unittest.TestCase)
- test_the_documented_kinds_are_the_advertised_set · method · L256-L260 — def test_the_documented_kinds_are_the_advertised_set(self) -> None
- test_alignment_suffixes_are_detected · method · L262-L265 — def test_alignment_suffixes_are_detected(self) -> None
- test_variant_suffixes_are_detected · method · L267-L270 — def test_variant_suffixes_are_detected(self) -> None
- test_detection_is_case_insensitive · method · L272-L273 — def test_detection_is_case_insensitive(self) -> None
- test_every_detected_kind_is_one_the_script_handles · method · L275-L282 — def test_every_detected_kind_is_one_the_script_handles(self) -> None