├── .github └── workflows │ └── build_docs.yml ├── .gitignore ├── MANIFEST.in ├── README.rst ├── docs ├── Makefile ├── make.bat └── source │ ├── _static │ └── flowchart.png │ ├── cmds │ ├── annotate_ase.rst │ ├── calc_ase.rst │ ├── calc_asts.rst │ ├── fetch_haplotype.rst │ ├── hap_aligner.sh.rst │ ├── index.rst │ ├── make_new_vcf.sh.rst │ ├── process_asts.rst │ └── process_vcf.sh.rst │ ├── conf.py │ ├── index.rst │ ├── lorals.rst │ └── modules.rst ├── images ├── logo.png ├── logo.svg ├── lorals_pipeline.png ├── lorals_pipeline.svg ├── pipeline_analysis.png └── pipeline_analysis.svg ├── lorals ├── __init__.py ├── annotate.py ├── ase.py ├── asts.py ├── blacklists │ ├── hg38-blacklist.v2.bed │ └── wgEncodeCrgMapabilityAlign100mer.hg38.mappingover5.bed.gz ├── cigar.py ├── fancy_logging.py ├── features.py ├── maths.py ├── process.py ├── py.typed ├── scripts.py └── utils.py ├── scripts ├── hap_aligner.sh ├── make_new_vcf.sh └── process_vcf.sh └── setup.py /.github/workflows/build_docs.yml: 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