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|
{ bionix
, nixpkgs
, flags ? null
}:
ref:
with nixpkgs;
with lib;
with bionix.types;
assert (matchFiletype "bwa-index" { fa = _: true; } ref);
stdenv.mkDerivation {
name = "bwa-index";
buildInputs = [ bwa ];
buildCommand = ''
ln -s ${ref} ref.fa
bwa index ${optionalString (flags != null) flags} ref.fa
mkdir $out
mv ref.fa.* $out
grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true
'';
}
|