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{ bionix
, nixpkgs
, dictIndexAttrs ? {}
, faidxAttrs ? {}
, flags ? null
, unmappedReads ? false
, minClipLength ? 5
, config ? null
}:
with nixpkgs;
with lib;
with bionix.types;
input:
let
ref = matchFiletype "gridss-extractSVReads" { bam = x: x.ref; } input;
in
stdenv.mkDerivation rec {
name = "gridss-extractSVReads";
buildInputs = [ jre R ];
buildCommand = ''
ln -s ${ref} ref.fa
ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai
ln -s ${bionix.samtools.dict dictIndexAttrs ref} ref.fa.dict
ln -s ${input} input.bam
mkdir $out
java -Dsamjdk.create_index=true \
-cp ${bionix.gridss.jar} gridss.ExtractSVReads \
REFERENCE_SEQUENCE=ref.fa \
I=input.bam \
O=$out/input.sv.bam \
METRICS_OUTPUT=$out/input.sv_metrics \
INSERT_SIZE_METRICS=$out/input.insert_size_metrics \
UNMAPPED_READS=${if unmappedReads then "true" else "false"} \
${optionalString config ("CONFIGURATION_FILE=" + gridssConfig config)} \
MIN_CLIP_LENGTH=${toString minClipLength}
'';
}
|
