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{bionix, nixpkgs}:
with nixpkgs;
with bionix;
rec {
jar = fetchurl {
url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar";
sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k";
};
callVariants = callBionix ./gridss-callVariants.nix;
computeSamTags = callBionix ./gridss-computeSamTags.nix;
softClipsToSplitReads = callBionix ./gridss-softClipsToSplitReads.nix;
collectMetrics = callBionix ./gridss-collectMetrics.nix;
extractSVReads = callBionix ./gridss-extractSVReads.nix;
assemble = callBionix ./gridss-assemble.nix;
identifyVariants = callBionix ./gridss-identifyVariants.nix;
annotateVariants = callBionix ./gridss-annotateVariants.nix;
preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (softClipsToSplitReads {} (computeSamTags {} (sort {nameSort = true;} input)))));
call = inputs: annotateVariants {} (map preprocessBam inputs);
}
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