├── .circleci └── config.yml ├── .dockerignore ├── .gitignore ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── _config.yml ├── bin └── pynnotator ├── composer ├── Dockerfile ├── docker-compose-dev.yml ├── docker-compose.yml └── run-pynnotator-with-docker.sh ├── devlog.txt ├── docs ├── Makefile ├── conf.py ├── data.rst ├── getting_started.rst ├── index.rst ├── installation.rst └── make.bat ├── fabfile.py ├── pynnotator ├── __init__.py ├── annotator.py ├── helpers │ ├── __init__.py │ ├── common.py │ ├── dbnsfp.bcftools.py │ ├── dbnsfp.cyvcf2.py │ ├── dbnsfp.new.py │ ├── dbnsfp.old.py │ ├── dbnsfp.py │ ├── dbnsfp.snpsift.py │ ├── decipher.py │ ├── func_pred.py │ ├── gemini.py │ ├── gnomad.py │ ├── hgmd.py │ ├── merge.py │ ├── merge.pysam.py │ ├── merge2.py │ ├── sanity_check.py │ ├── snpeff.py │ ├── snpsift.py │ ├── tests.py │ ├── validator.py │ ├── vcf_annotator.py │ ├── vcfanno.py │ ├── vep.py │ └── vt.py ├── install.py ├── main.py ├── pynnotator.py ├── scripts │ ├── download_data.sh │ ├── header.vcf │ ├── install.sh │ ├── install_libs.py │ ├── install_vep.sh │ ├── test.py │ └── vcf2csv.py ├── settings.py └── tests │ ├── benchmarks │ └── test_dbnfsp.py │ ├── examples │ ├── NA12878.compound_heterozygous.vcf.gz │ ├── NA12878.dominant.vcf.gz │ ├── NA12878.recessive.vcf.gz │ ├── NA12878.xlinked.vcf.gz │ ├── miller.vcf.gz │ └── schinzel_giedion.vcf.gz │ ├── sample.100.vcf.gz │ ├── sample.1000.vcf.gz │ ├── sample.70.hg38.vcf.gz │ ├── sample.70.vcf.gz │ ├── test_cyvcf2.py │ ├── test_htslib.py │ └── test_snpeff.py ├── requirements.txt ├── scripts ├── build_docker.sh ├── download_from_gs.sh └── install.sh ├── setup.cfg └── setup.py /.circleci/config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/raonyguimaraes/pynnotator/HEAD/.circleci/config.yml -------------------------------------------------------------------------------- /.dockerignore: 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