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        "author": "Wouter De Coster",
        "author_email": "decosterwouter@gmail.com",
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            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
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        "description": "# surpyvor\nA python wrapper around [SURVIVOR](https://github.com/fritzsedlazeck/SURVIVOR), with additional convenience functions.\n\n## Installation and dependencies\nsurpyvor requires bcftools, bgzip, tabix and SURVIVOR to be installed and in the $PATH.\nRequired python modules are cyvcf2, matplotlib, numpy, matplotlib-venn and upsetplot\n\nsurpyvor and its dependencies can be installed from [bioconda](https://anaconda.org/bioconda/surpyvor):\n\n`conda install -c bioconda surpyvor`\n\n## USAGE\n### sub-commands:\n    merge               merging vcf files of SVs\n    highsens            get union of SV vcfs\n    highconf            get intersection of SV vcfs\n    prf                 calculate precision, recall and F-measure\n    upset               Make upset plot for multiple SV vcf files\n    venn                Make venn diagram for 2 or 3 SV vcf files\n\nEach sub-command has its own help information, accessible by running `surpyvor <command> -h/--help`\n\n### General and common arguments for most sub-commands:\n```\n-o/--output: output variant file to write. Default: stdout\n--plotout: name ouf output plot to write. Default names depending on plot type.\n-d/--distance: maximal pairwise distance between coordinates of SVs to be considered concordant. Default: 500\n-l/--minlength: minimal SV length to include. Default: 50\n--variants: vcf files to combine\n```\n\n### Specific arguments\n\n#### surpyvor prf\n```\n--ignore_chroms: ignore some chromosomes for calculations. Default: chrEBV\n--bar: create a stacked bar chart colored by validation status [not created by default]\n--matrix: create a confusion matrix [not created by default]\n```\n\n## Citation\nIf you use this tool, please consider citing our [publication](https://genome.cshlp.org/content/early/2019/06/11/gr.244939.118.abstract) and the [citation for SURVIVOR](https://www.nature.com/articles/ncomms14061).",
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