├── .github ├── CONTRIBUTING.md ├── faq.yml ├── faq │ ├── FAQ.md │ └── suggest.md └── workflows │ ├── CI.yml │ ├── faqtory.yml │ └── stale.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CITATION.cff ├── LICENSE ├── README.md ├── _static ├── docs ├── FAQ.md ├── Makefile ├── _static │ ├── example_tomls │ │ ├── COSMIC_cancer_panel.bed │ │ ├── COSMIC_cancer_panel.csv │ │ ├── barcoded_human.toml │ │ ├── human_bed_file_selection.toml │ │ ├── human_chr_depletion.toml │ │ ├── human_chr_selection.toml │ │ ├── human_chr_selection_two_regions.toml │ │ ├── human_chr_selection_with_control.toml │ │ ├── human_csv_file_selection.toml │ │ ├── human_minimap2_extra_params.toml │ │ └── human_regions_barcoded.toml │ ├── images │ │ ├── PlaybackControlRun30Minutes.png │ │ ├── PlaybackRunTargeted.png │ │ ├── PlaybackRunTargetedPeak.png │ │ ├── PlaybackRunTargetedUnblockPeak.png │ │ ├── PlaybackRunUnblock.png │ │ ├── PlaybackRunUnblockCloseUp.png │ │ ├── PlaybackUnblockAll30minutes.png │ │ ├── PlaybackUnblockAllCloseUp.png │ │ ├── Unblock.png │ │ ├── UnblockAllMessages.png │ │ ├── Unblock_closeup.png │ │ ├── control.png │ │ ├── data_model.png │ │ ├── data_model.svg │ │ ├── data_model_no_bg.svg │ │ ├── message.png │ │ ├── minknow_messages.png │ │ └── simulated_playback_run_options.png │ ├── readfish.jpg │ ├── readfish_dark.png │ ├── readfish_light.png │ ├── readfish_light.svg │ ├── readfish_logo.jpg │ └── readfish_small.jpg ├── basecalling-params.md ├── changelog.md ├── conf.py ├── developers-guide.md ├── development.yml ├── getting-started.md ├── images │ ├── PlaybackRunUnblock.png │ ├── PlaybackRunUnblockCloseUp.png │ ├── Unblock.png │ ├── Unblock_closeup.png │ ├── control.png │ ├── message.png │ ├── minknow_messages.png │ ├── readfish.jpg │ ├── readfish.png │ ├── readfish_dark.png │ ├── readfish_logo.jpg │ └── readfish_small.jpg ├── index.md ├── make.bat ├── post-analysis.md ├── questions │ ├── batch-times.question.md │ ├── creating_readfish-environment.question.md │ ├── key_error_adapter.md │ ├── py-guppy-client-error.question.md │ ├── py-guppy-client-version.question.md │ ├── readfish-branches.question.md │ └── split-flongle.md ├── readfish.console.rst ├── readfish.plugins.rst ├── readfish.rst └── toml.md ├── pyproject.toml ├── src └── readfish │ ├── __about__.py │ ├── __init__.py │ ├── __main__.py │ ├── _channels.py │ ├── _cli_args.py │ ├── _cli_base.py │ ├── _compatibility.py │ ├── _config.py │ ├── _loggers.py │ ├── _read_until_client.py │ ├── _statistics.py │ ├── _utils.py │ ├── entry_points │ ├── __init__.py │ ├── demultiplex.py │ ├── stats.py │ ├── targets.py │ ├── unblock_all.py │ └── validate.py │ ├── plugins │ ├── __init__.py │ ├── _filter.py │ ├── _mappy.py │ ├── _no_op.py │ ├── abc.py │ ├── deepnano_blitz.py │ ├── dorado.py │ ├── mappy.py │ ├── mappy_rs.py │ └── utils.py │ └── read_until │ ├── LICENSE.md │ ├── __init__.py │ ├── _version.py │ ├── base.py │ └── read_cache.py └── tests ├── conftest.py ├── describe_test.py ├── static ├── describe_test │ ├── describe.toml │ ├── describe_aligner_barcoded_expected.txt │ ├── describe_aligner_barcoded_regions_expected.txt │ ├── describe_aligner_regions_expected.txt │ ├── describe_barcoded.toml │ ├── describe_barcoded_experiment_expected.txt │ ├── describe_barcoded_missing.toml │ ├── describe_barcoded_regions_experiment_expected.txt │ ├── describe_experiment_regions_expected.txt │ ├── describe_region_and_barcode.toml │ ├── describe_region_and_barcode_missing.toml │ └── yeast_8kb_contigs_test.mmi ├── dorado_validation_test │ ├── README.md │ ├── fail │ │ ├── 001_no_write_socket.txt │ │ ├── 002_missing_socket.txt │ │ ├── 003_no_read_socket.txt │ │ ├── 5555_fail_nr │ │ └── 5555_fail_nw │ └── pass │ │ ├── 001_correct_debug.txt │ │ ├── 002_correct_no_debug.txt │ │ └── 5555_pass ├── mappy_validation_test │ ├── README.md │ ├── fail │ │ ├── 001_wrong_reference_type.toml │ │ ├── 001_wrong_reference_type.txt │ │ ├── 002_reference_not_exist.toml │ │ ├── 002_reference_not_exist.txt │ │ ├── 003_wrong_reference_type_mmi_gz.toml │ │ ├── 003_wrong_reference_type_mmi_gz.txt │ │ ├── 004_bad_reference_file_extension.toml │ │ ├── 004_bad_reference_file_extension.txt │ │ ├── bad_extension.mmi.cabbage │ │ ├── i_am_a_fail_reference.mmi.gz │ │ └── i_am_a_fail_reference.txt │ └── pass │ │ ├── 001_correct_reference_mmi.toml │ │ ├── 001_correct_reference_mmi.txt │ │ ├── 002_correct_reference_fasta.toml │ │ ├── 002_correct_reference_fasta.txt │ │ ├── 003_correct_reference_fastq.toml │ │ ├── 003_correct_reference_fastq.txt │ │ ├── 004_correct_reference_fasta_gz.toml │ │ ├── 004_correct_reference_fasta_gz.txt │ │ ├── 005_correct_reference_fastq_gz.toml │ │ ├── 005_correct_reference_fastq_gz.txt │ │ ├── 006_passing_fna_mmi.toml │ │ ├── 006_passing_fna_mmi.txt │ │ ├── GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.mmi │ │ ├── hello.fasta │ │ ├── hello.fasta.gz │ │ ├── hello.fastq │ │ ├── hello.fastq.gz │ │ └── hello.mmi ├── stats_test │ ├── expected_summary.txt │ ├── simulated_reads.fastq │ ├── stats.tsv │ ├── yeast_8kb_contigs_test.mmi │ ├── yeast_summary_test.toml │ └── yeast_summary_test_mappyrs.toml └── toml_validation_test │ ├── README.md │ ├── fail │ ├── 001_missing_keys.toml │ ├── 001_missing_keys.txt │ ├── 002_wrong_types.toml │ ├── 002_wrong_types.txt │ ├── 003_plugin_fail.toml │ ├── 003_plugin_fail_0.txt │ ├── 003_plugin_fail_1.txt │ ├── 004_target_interval_check.toml │ ├── 004_target_interval_check.txt │ └── COSMIC_cancer_panel_errors.bed │ └── pass │ ├── 001_simple_toml.toml │ └── 001_simple_toml.txt ├── stats_test.py ├── utils_test.py └── validation_test.py /.github/CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/.github/CONTRIBUTING.md -------------------------------------------------------------------------------- /.github/faq.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/.github/faq.yml -------------------------------------------------------------------------------- /.github/faq/FAQ.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/.github/faq/FAQ.md -------------------------------------------------------------------------------- /.github/faq/suggest.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/.github/faq/suggest.md -------------------------------------------------------------------------------- /.github/workflows/CI.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/.github/workflows/CI.yml -------------------------------------------------------------------------------- /.github/workflows/faqtory.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/.github/workflows/faqtory.yml -------------------------------------------------------------------------------- /.github/workflows/stale.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/.github/workflows/stale.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/CITATION.cff -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/README.md -------------------------------------------------------------------------------- /_static: -------------------------------------------------------------------------------- 1 | docs/_static/ -------------------------------------------------------------------------------- /docs/FAQ.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/FAQ.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/_static/example_tomls/COSMIC_cancer_panel.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/COSMIC_cancer_panel.bed -------------------------------------------------------------------------------- /docs/_static/example_tomls/COSMIC_cancer_panel.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/COSMIC_cancer_panel.csv -------------------------------------------------------------------------------- /docs/_static/example_tomls/barcoded_human.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/barcoded_human.toml -------------------------------------------------------------------------------- /docs/_static/example_tomls/human_bed_file_selection.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/human_bed_file_selection.toml -------------------------------------------------------------------------------- /docs/_static/example_tomls/human_chr_depletion.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/human_chr_depletion.toml -------------------------------------------------------------------------------- /docs/_static/example_tomls/human_chr_selection.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/human_chr_selection.toml -------------------------------------------------------------------------------- /docs/_static/example_tomls/human_chr_selection_two_regions.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/human_chr_selection_two_regions.toml -------------------------------------------------------------------------------- /docs/_static/example_tomls/human_chr_selection_with_control.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/human_chr_selection_with_control.toml -------------------------------------------------------------------------------- /docs/_static/example_tomls/human_csv_file_selection.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/human_csv_file_selection.toml -------------------------------------------------------------------------------- /docs/_static/example_tomls/human_minimap2_extra_params.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/human_minimap2_extra_params.toml -------------------------------------------------------------------------------- /docs/_static/example_tomls/human_regions_barcoded.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/example_tomls/human_regions_barcoded.toml -------------------------------------------------------------------------------- /docs/_static/images/PlaybackControlRun30Minutes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/PlaybackControlRun30Minutes.png -------------------------------------------------------------------------------- /docs/_static/images/PlaybackRunTargeted.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/PlaybackRunTargeted.png -------------------------------------------------------------------------------- /docs/_static/images/PlaybackRunTargetedPeak.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/PlaybackRunTargetedPeak.png -------------------------------------------------------------------------------- /docs/_static/images/PlaybackRunTargetedUnblockPeak.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/PlaybackRunTargetedUnblockPeak.png -------------------------------------------------------------------------------- /docs/_static/images/PlaybackRunUnblock.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/PlaybackRunUnblock.png -------------------------------------------------------------------------------- /docs/_static/images/PlaybackRunUnblockCloseUp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/PlaybackRunUnblockCloseUp.png -------------------------------------------------------------------------------- /docs/_static/images/PlaybackUnblockAll30minutes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/PlaybackUnblockAll30minutes.png -------------------------------------------------------------------------------- /docs/_static/images/PlaybackUnblockAllCloseUp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/PlaybackUnblockAllCloseUp.png -------------------------------------------------------------------------------- /docs/_static/images/Unblock.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/Unblock.png -------------------------------------------------------------------------------- /docs/_static/images/UnblockAllMessages.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/UnblockAllMessages.png -------------------------------------------------------------------------------- /docs/_static/images/Unblock_closeup.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/Unblock_closeup.png -------------------------------------------------------------------------------- /docs/_static/images/control.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/control.png -------------------------------------------------------------------------------- /docs/_static/images/data_model.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/data_model.png -------------------------------------------------------------------------------- /docs/_static/images/data_model.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/data_model.svg -------------------------------------------------------------------------------- /docs/_static/images/data_model_no_bg.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/data_model_no_bg.svg -------------------------------------------------------------------------------- /docs/_static/images/message.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/message.png -------------------------------------------------------------------------------- /docs/_static/images/minknow_messages.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/minknow_messages.png -------------------------------------------------------------------------------- /docs/_static/images/simulated_playback_run_options.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/images/simulated_playback_run_options.png -------------------------------------------------------------------------------- /docs/_static/readfish.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/readfish.jpg -------------------------------------------------------------------------------- /docs/_static/readfish_dark.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/readfish_dark.png -------------------------------------------------------------------------------- /docs/_static/readfish_light.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/readfish_light.png -------------------------------------------------------------------------------- /docs/_static/readfish_light.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/readfish_light.svg -------------------------------------------------------------------------------- /docs/_static/readfish_logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/readfish_logo.jpg -------------------------------------------------------------------------------- /docs/_static/readfish_small.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/_static/readfish_small.jpg -------------------------------------------------------------------------------- /docs/basecalling-params.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/basecalling-params.md -------------------------------------------------------------------------------- /docs/changelog.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/changelog.md -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/developers-guide.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/developers-guide.md -------------------------------------------------------------------------------- /docs/development.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/development.yml -------------------------------------------------------------------------------- /docs/getting-started.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/getting-started.md -------------------------------------------------------------------------------- /docs/images/PlaybackRunUnblock.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/PlaybackRunUnblock.png -------------------------------------------------------------------------------- /docs/images/PlaybackRunUnblockCloseUp.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/PlaybackRunUnblockCloseUp.png -------------------------------------------------------------------------------- /docs/images/Unblock.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/Unblock.png -------------------------------------------------------------------------------- /docs/images/Unblock_closeup.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/Unblock_closeup.png -------------------------------------------------------------------------------- /docs/images/control.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/control.png -------------------------------------------------------------------------------- /docs/images/message.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/message.png -------------------------------------------------------------------------------- /docs/images/minknow_messages.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/minknow_messages.png -------------------------------------------------------------------------------- /docs/images/readfish.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/readfish.jpg -------------------------------------------------------------------------------- /docs/images/readfish.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/readfish.png -------------------------------------------------------------------------------- /docs/images/readfish_dark.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/readfish_dark.png -------------------------------------------------------------------------------- /docs/images/readfish_logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/readfish_logo.jpg -------------------------------------------------------------------------------- /docs/images/readfish_small.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/images/readfish_small.jpg -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/index.md -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/post-analysis.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/post-analysis.md -------------------------------------------------------------------------------- /docs/questions/batch-times.question.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/questions/batch-times.question.md -------------------------------------------------------------------------------- /docs/questions/creating_readfish-environment.question.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/questions/creating_readfish-environment.question.md -------------------------------------------------------------------------------- /docs/questions/key_error_adapter.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/questions/key_error_adapter.md -------------------------------------------------------------------------------- /docs/questions/py-guppy-client-error.question.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/questions/py-guppy-client-error.question.md -------------------------------------------------------------------------------- /docs/questions/py-guppy-client-version.question.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/questions/py-guppy-client-version.question.md -------------------------------------------------------------------------------- /docs/questions/readfish-branches.question.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/questions/readfish-branches.question.md -------------------------------------------------------------------------------- /docs/questions/split-flongle.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/questions/split-flongle.md -------------------------------------------------------------------------------- /docs/readfish.console.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/readfish.console.rst -------------------------------------------------------------------------------- /docs/readfish.plugins.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/readfish.plugins.rst -------------------------------------------------------------------------------- /docs/readfish.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/readfish.rst -------------------------------------------------------------------------------- /docs/toml.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/docs/toml.md -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/pyproject.toml -------------------------------------------------------------------------------- /src/readfish/__about__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/__about__.py -------------------------------------------------------------------------------- /src/readfish/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/__init__.py -------------------------------------------------------------------------------- /src/readfish/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/__main__.py -------------------------------------------------------------------------------- /src/readfish/_channels.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/_channels.py -------------------------------------------------------------------------------- /src/readfish/_cli_args.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/_cli_args.py -------------------------------------------------------------------------------- /src/readfish/_cli_base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/_cli_base.py -------------------------------------------------------------------------------- /src/readfish/_compatibility.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/_compatibility.py -------------------------------------------------------------------------------- /src/readfish/_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/_config.py -------------------------------------------------------------------------------- /src/readfish/_loggers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/_loggers.py -------------------------------------------------------------------------------- /src/readfish/_read_until_client.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/_read_until_client.py -------------------------------------------------------------------------------- /src/readfish/_statistics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/_statistics.py -------------------------------------------------------------------------------- /src/readfish/_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/_utils.py -------------------------------------------------------------------------------- /src/readfish/entry_points/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/readfish/entry_points/demultiplex.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/readfish/entry_points/stats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/entry_points/stats.py -------------------------------------------------------------------------------- /src/readfish/entry_points/targets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/entry_points/targets.py -------------------------------------------------------------------------------- /src/readfish/entry_points/unblock_all.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/entry_points/unblock_all.py -------------------------------------------------------------------------------- /src/readfish/entry_points/validate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/entry_points/validate.py -------------------------------------------------------------------------------- /src/readfish/plugins/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/readfish/plugins/_filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/plugins/_filter.py -------------------------------------------------------------------------------- /src/readfish/plugins/_mappy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/plugins/_mappy.py -------------------------------------------------------------------------------- /src/readfish/plugins/_no_op.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/plugins/_no_op.py -------------------------------------------------------------------------------- /src/readfish/plugins/abc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/plugins/abc.py -------------------------------------------------------------------------------- /src/readfish/plugins/deepnano_blitz.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/readfish/plugins/dorado.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/plugins/dorado.py -------------------------------------------------------------------------------- /src/readfish/plugins/mappy.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/plugins/mappy.py -------------------------------------------------------------------------------- /src/readfish/plugins/mappy_rs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/plugins/mappy_rs.py -------------------------------------------------------------------------------- /src/readfish/plugins/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/plugins/utils.py -------------------------------------------------------------------------------- /src/readfish/read_until/LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/read_until/LICENSE.md -------------------------------------------------------------------------------- /src/readfish/read_until/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/read_until/__init__.py -------------------------------------------------------------------------------- /src/readfish/read_until/_version.py: -------------------------------------------------------------------------------- 1 | __version__ = "3.5.2" 2 | -------------------------------------------------------------------------------- /src/readfish/read_until/base.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/read_until/base.py -------------------------------------------------------------------------------- /src/readfish/read_until/read_cache.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/src/readfish/read_until/read_cache.py -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/describe_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/describe_test.py -------------------------------------------------------------------------------- /tests/static/describe_test/describe.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe.toml -------------------------------------------------------------------------------- /tests/static/describe_test/describe_aligner_barcoded_expected.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe_aligner_barcoded_expected.txt -------------------------------------------------------------------------------- /tests/static/describe_test/describe_aligner_barcoded_regions_expected.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe_aligner_barcoded_regions_expected.txt -------------------------------------------------------------------------------- /tests/static/describe_test/describe_aligner_regions_expected.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe_aligner_regions_expected.txt -------------------------------------------------------------------------------- /tests/static/describe_test/describe_barcoded.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe_barcoded.toml -------------------------------------------------------------------------------- /tests/static/describe_test/describe_barcoded_experiment_expected.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe_barcoded_experiment_expected.txt -------------------------------------------------------------------------------- /tests/static/describe_test/describe_barcoded_missing.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe_barcoded_missing.toml -------------------------------------------------------------------------------- /tests/static/describe_test/describe_barcoded_regions_experiment_expected.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe_barcoded_regions_experiment_expected.txt -------------------------------------------------------------------------------- /tests/static/describe_test/describe_experiment_regions_expected.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe_experiment_regions_expected.txt -------------------------------------------------------------------------------- /tests/static/describe_test/describe_region_and_barcode.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe_region_and_barcode.toml -------------------------------------------------------------------------------- /tests/static/describe_test/describe_region_and_barcode_missing.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/describe_region_and_barcode_missing.toml -------------------------------------------------------------------------------- /tests/static/describe_test/yeast_8kb_contigs_test.mmi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/describe_test/yeast_8kb_contigs_test.mmi -------------------------------------------------------------------------------- /tests/static/dorado_validation_test/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/dorado_validation_test/README.md -------------------------------------------------------------------------------- /tests/static/dorado_validation_test/fail/001_no_write_socket.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/dorado_validation_test/fail/001_no_write_socket.txt -------------------------------------------------------------------------------- /tests/static/dorado_validation_test/fail/002_missing_socket.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/dorado_validation_test/fail/002_missing_socket.txt -------------------------------------------------------------------------------- /tests/static/dorado_validation_test/fail/003_no_read_socket.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/dorado_validation_test/fail/003_no_read_socket.txt -------------------------------------------------------------------------------- /tests/static/dorado_validation_test/fail/5555_fail_nr: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/dorado_validation_test/fail/5555_fail_nw: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/dorado_validation_test/pass/001_correct_debug.txt: -------------------------------------------------------------------------------- 1 | Caller initialised 2 | -------------------------------------------------------------------------------- /tests/static/dorado_validation_test/pass/002_correct_no_debug.txt: -------------------------------------------------------------------------------- 1 | Caller initialised 2 | -------------------------------------------------------------------------------- /tests/static/dorado_validation_test/pass/5555_pass: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/README.md -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/001_wrong_reference_type.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/fail/001_wrong_reference_type.toml -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/001_wrong_reference_type.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/fail/001_wrong_reference_type.txt -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/002_reference_not_exist.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/fail/002_reference_not_exist.toml -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/002_reference_not_exist.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/fail/002_reference_not_exist.txt -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/003_wrong_reference_type_mmi_gz.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/fail/003_wrong_reference_type_mmi_gz.toml -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/003_wrong_reference_type_mmi_gz.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/fail/003_wrong_reference_type_mmi_gz.txt -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/004_bad_reference_file_extension.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/fail/004_bad_reference_file_extension.toml -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/004_bad_reference_file_extension.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/fail/004_bad_reference_file_extension.txt -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/bad_extension.mmi.cabbage: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/i_am_a_fail_reference.mmi.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/fail/i_am_a_fail_reference.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/001_correct_reference_mmi.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/pass/001_correct_reference_mmi.toml -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/001_correct_reference_mmi.txt: -------------------------------------------------------------------------------- 1 | Aligner initialised 2 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/002_correct_reference_fasta.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/pass/002_correct_reference_fasta.toml -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/002_correct_reference_fasta.txt: -------------------------------------------------------------------------------- 1 | Aligner initialised 2 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/003_correct_reference_fastq.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/pass/003_correct_reference_fastq.toml -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/003_correct_reference_fastq.txt: -------------------------------------------------------------------------------- 1 | Aligner initialised 2 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/004_correct_reference_fasta_gz.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/pass/004_correct_reference_fasta_gz.toml -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/004_correct_reference_fasta_gz.txt: -------------------------------------------------------------------------------- 1 | Aligner initialised 2 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/005_correct_reference_fastq_gz.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/pass/005_correct_reference_fastq_gz.toml -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/005_correct_reference_fastq_gz.txt: -------------------------------------------------------------------------------- 1 | Aligner initialised 2 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/006_passing_fna_mmi.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/mappy_validation_test/pass/006_passing_fna_mmi.toml -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/006_passing_fna_mmi.txt: -------------------------------------------------------------------------------- 1 | Aligner initialised 2 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.mmi: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/hello.fasta: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/hello.fasta.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/hello.fastq: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/hello.fastq.gz: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/mappy_validation_test/pass/hello.mmi: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/static/stats_test/expected_summary.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/stats_test/expected_summary.txt -------------------------------------------------------------------------------- /tests/static/stats_test/simulated_reads.fastq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/stats_test/simulated_reads.fastq -------------------------------------------------------------------------------- /tests/static/stats_test/stats.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/stats_test/stats.tsv -------------------------------------------------------------------------------- /tests/static/stats_test/yeast_8kb_contigs_test.mmi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/stats_test/yeast_8kb_contigs_test.mmi -------------------------------------------------------------------------------- /tests/static/stats_test/yeast_summary_test.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/stats_test/yeast_summary_test.toml -------------------------------------------------------------------------------- /tests/static/stats_test/yeast_summary_test_mappyrs.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/stats_test/yeast_summary_test_mappyrs.toml -------------------------------------------------------------------------------- /tests/static/toml_validation_test/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/toml_validation_test/README.md -------------------------------------------------------------------------------- /tests/static/toml_validation_test/fail/001_missing_keys.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/toml_validation_test/fail/001_missing_keys.toml -------------------------------------------------------------------------------- /tests/static/toml_validation_test/fail/001_missing_keys.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/toml_validation_test/fail/001_missing_keys.txt -------------------------------------------------------------------------------- /tests/static/toml_validation_test/fail/002_wrong_types.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/toml_validation_test/fail/002_wrong_types.toml -------------------------------------------------------------------------------- /tests/static/toml_validation_test/fail/002_wrong_types.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/toml_validation_test/fail/002_wrong_types.txt -------------------------------------------------------------------------------- /tests/static/toml_validation_test/fail/003_plugin_fail.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/toml_validation_test/fail/003_plugin_fail.toml -------------------------------------------------------------------------------- /tests/static/toml_validation_test/fail/003_plugin_fail_0.txt: -------------------------------------------------------------------------------- 1 | No module named 'caller_that_does_not_exist' 2 | -------------------------------------------------------------------------------- /tests/static/toml_validation_test/fail/003_plugin_fail_1.txt: -------------------------------------------------------------------------------- 1 | No module named 'mapper_that_does_not_exist' 2 | -------------------------------------------------------------------------------- /tests/static/toml_validation_test/fail/004_target_interval_check.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/toml_validation_test/fail/004_target_interval_check.toml -------------------------------------------------------------------------------- /tests/static/toml_validation_test/fail/004_target_interval_check.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/toml_validation_test/fail/004_target_interval_check.txt -------------------------------------------------------------------------------- /tests/static/toml_validation_test/fail/COSMIC_cancer_panel_errors.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/toml_validation_test/fail/COSMIC_cancer_panel_errors.bed -------------------------------------------------------------------------------- /tests/static/toml_validation_test/pass/001_simple_toml.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/static/toml_validation_test/pass/001_simple_toml.toml -------------------------------------------------------------------------------- /tests/static/toml_validation_test/pass/001_simple_toml.txt: -------------------------------------------------------------------------------- 1 | Loaded TOML config without error 2 | -------------------------------------------------------------------------------- /tests/stats_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/stats_test.py -------------------------------------------------------------------------------- /tests/utils_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/utils_test.py -------------------------------------------------------------------------------- /tests/validation_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/LooseLab/readfish/HEAD/tests/validation_test.py --------------------------------------------------------------------------------