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{ bionix
, nixpkgs
, bwaIndexAttrs ? {}
, faidxAttrs ? {}
, alignerStreaming ? false
, flags ? null
, config ? null
}:
with nixpkgs;
with lib;
with bionix.types;
input:
let
ref = matchFiletype "gridss-softClipsToSplitReads" { bam = x: x.ref; } input;
in
stdenv.mkDerivation rec {
name = "gridss-softClipsToSplitReads";
buildInputs = [ jre bwa ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
for f in ${bionix.bwa.index bwaIndexAttrs ref}/*; do
ln -s $f
done
java -Xmx2G -Dsamjdk.create_index=false \
-cp ${bionix.gridss.jar} gridss.SoftClipsToSplitReads \
REFERENCE_SEQUENCE=ref.fa \
I=${input} \
O=$out \
${optionalString alignerStreaming "ALIGNER_STREAMING=true"} \
${optionalString (config != null) ("CONFIGURATION_FILE=" + bionix.gridss.gridssConfig config)} \
WORKER_THREADS=$NIX_BUILD_CORES
'';
passthru.filetype = filetype.bam { ref = ref; sorting = matchFileSorting "grids-softClipsToSplitReads" { coord = _: input.sorting; name = _: sort.none {}; none = _: input.sorting;} input;};
}
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