├── .github └── workflows │ └── main.yml ├── .gitignore ├── .isort.cfg ├── .pre-commit-config.yaml ├── LICENSE ├── MANIFEST.in ├── README.md ├── covviz ├── __init__.py ├── bed.py ├── covviz.py ├── gff.py ├── ped.py ├── templates │ └── covviz.html ├── utils.py └── vcf.py ├── data ├── Homo_sapiens.GRCh37.82.gff3.gz ├── g1k_v37_decoy.fa.fai ├── img │ ├── covviz_tracks.gif │ ├── min_samples.png │ ├── proportional_coverage.png │ └── significant_regions.png ├── indexcov.bed.gz ├── indexcov.ped ├── indexcov.wchr.bed.gz └── indexes │ ├── S-101.cram.crai │ ├── S-1041.cram.crai │ ├── S-1042.cram.crai │ ├── S-1078.cram.crai │ ├── S-11.cram.crai │ ├── S-1117.cram.crai │ ├── S-1119.cram.crai │ ├── S-1123.cram.crai │ ├── S-1174.cram.crai │ ├── S-1184.cram.crai │ ├── S-1185.cram.crai │ ├── S-1207.cram.crai │ ├── S-128.cram.crai │ ├── S-150.cram.crai │ ├── S-151.cram.crai │ ├── S-152.cram.crai │ ├── S-184.cram.crai │ ├── S-185.cram.crai │ ├── S-218.cram.crai │ ├── S-22.cram.crai │ ├── S-220.cram.crai │ ├── S-225.cram.crai │ ├── S-251.cram.crai │ ├── S-26.cram.crai │ ├── S-276.cram.crai │ ├── S-307.cram.crai │ ├── S-324.cram.crai │ ├── S-383.cram.crai │ ├── S-386.cram.crai │ ├── S-39.cram.crai │ ├── S-413.cram.crai │ ├── S-428.cram.crai │ ├── S-446.cram.crai │ ├── S-498.cram.crai │ ├── S-594.cram.crai │ ├── S-635.cram.crai │ ├── S-642.cram.crai │ ├── S-72.cram.crai │ ├── S-746.cram.crai │ ├── S-765.cram.crai │ ├── S-774.cram.crai │ ├── S-775.cram.crai │ ├── S-819.cram.crai │ ├── S-839.cram.crai │ ├── S-861.cram.crai │ ├── S-863.cram.crai │ ├── S-871.cram.crai │ ├── S-974.cram.crai │ └── S-986.cram.crai ├── docker └── Dockerfile ├── index.html ├── main.nf ├── nextflow.config ├── setup.py ├── templates └── merge_peds.py └── wdl ├── covviz.wdl ├── inputs.json ├── manifest.tsv └── options.json /.github/workflows/main.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/brwnj/covviz/HEAD/.github/workflows/main.yml 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