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|
{ stdenv
, callPackage
, lib
, bwa
, samtools ? null
, ref
, bamOutput ? true
, flags ? null
}:
{ input1
, input2 ? null
}:
assert bamOutput -> samtools != null;
with lib;
let index = callPackage ./bwa-index.nix { inherit bwa stdenv lib; } ref;
in stdenv.mkDerivation {
name = "bwa-mem";
buildInputs = [ bwa ] ++ optional bamOutput samtools;
buildCommand = ''
ln -s ${ref} ref.fa
for f in ${index}/* ; do
ln -s $f
done
bwa mem ${optionalString (flags != null) flags} -t $NIX_BUILD_CORES ref.fa ${input1} \
${optionalString (input2 != null) input2} \
${optionalString bamOutput "| samtools view -b"} \
> $out
'';
}
|