├── .github └── workflows │ └── test.yml ├── .gitignore ├── CHANGELOG.rst ├── CONTRIBUTING.rst ├── LICENSE.txt ├── README.rst ├── alignparse ├── __init__.py ├── ccs.py ├── consensus.py ├── constants.py ├── cs_tag.py ├── minimap2.py ├── targets.py └── utils.py ├── docs ├── .nojekyll ├── Makefile ├── README.rst ├── _static │ └── BloomLogo.jpg ├── acknowledgements.rst ├── conf.py ├── doc_requirements.txt ├── examples.rst ├── flu_virus_seq_example.nblink ├── index.rst ├── installation.rst ├── lasv_pilot.nblink ├── package_index.rst └── recA_DMS.nblink ├── environment.yml ├── nbval_sanitize.cfg ├── notebooks ├── README.rst ├── flu_virus_seq_example.ipynb ├── input_files │ ├── LASV_Josiah_OPT.gb │ ├── LASV_Josiah_WT.gb │ ├── README.rst │ ├── flu_WSN_amplicons.gb │ ├── flu_WSN_ccs.fastq │ ├── flu_WSN_feature_parse_specs.yaml │ ├── lasv_example_ccs.fastq.gz │ ├── lasv_feature_parse_specs.yaml │ ├── lasv_pilot_report.txt │ ├── recA_amplicon.gb │ ├── recA_feature_parse_specs.yaml │ ├── recA_lib-1_ccs.fastq │ ├── recA_lib-1_report.txt │ ├── recA_lib-2_ccs.fastq │ └── recA_lib-2_report.txt ├── lasv_pilot.ipynb └── recA_DMS.ipynb ├── paper ├── README.rst ├── paper.bib └── paper.md ├── pytest.ini ├── ruff.toml ├── setup.py ├── test_requirements.txt └── tests ├── README.rst ├── check_Targets_align_and_parse.ipynb ├── profile_recA.ipynb ├── test_Targets_objects.ipynb ├── test_Targets_parse_alignment.ipynb ├── test_Targets_parse_alignment_consistency.ipynb ├── test_ccs_summaries.ipynb ├── test_cs_tag_Alignment.ipynb └── test_cs_tag_Alignment_accuracy.ipynb /.github/workflows/test.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jbloomlab/alignparse/HEAD/.github/workflows/test.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 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