{ lib , fetchFromGitHub , python3Packages }: python3Packages.buildPythonApplication rec { pname = "truvari"; version = "1.3.4"; src = fetchFromGitHub { owner = "spiralgenetics"; repo = "truvari"; rev = "v${version}"; sha256 = "1bph7v48s7pyfagz8a2fzl5fycjliqzn5lcbv3m2bp2ih1f1gd1v"; }; propagatedBuildInputs = with python3Packages; [ pyvcf python-Levenshtein progressbar2 pysam pyfaidx intervaltree ]; prePatch = '' substituteInPlace ./setup.py \ --replace '"progressbar2==3.41.0",' '"progressbar2",' \ --replace '"pysam==0.15.2",' '"pysam",' \ --replace '"pyfaidx==0.5.5.2",' '"pyfaidx",' \ --replace '"intervaltree==3.0.2",' '"intervaltree",' ''; meta = with lib; { description = "Structural variant comparison tool for VCFs"; homepage = "https://github.com/spiralgenetics/truvari"; license = licenses.mit; maintainers = with maintainers; [ scalavision ]; longDescription = '' Truvari is a benchmarking tool for comparison sets of SVs. It can calculate the recall, precision, and f-measure of a vcf from a given structural variant caller. The tool is created by Spiral Genetics. ''; }; }