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{ bionix
, nixpkgs
, flags ? null
, outfmt ? null
}:
inputs:
with nixpkgs;
with lib;
let
inherit (bionix.types) matchFiletype matchSorting;
inputIsHomogenous = length (unique (map (matchFiletype "samtools-merge" {bam = x: x // {sorting = matchSorting "samtools-merge" {coord = _: "coord";} x;};}) inputs)) == 1;
in
assert inputIsHomogenous;
stdenv.mkDerivation {
name = "samtools-merge";
buildInputs = [ samtools ];
buildCommand = ''
samtools merge ${optionalString (flags != null) flags} $out ${concatStringsSep " " inputs}
'';
passthru.filetype = (builtins.elemAt inputs 0).filetype;
}
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