From 979bf4c65ad668b668750b58eefa9996f51b1242 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 12 Dec 2018 10:23:11 +1100
Subject: gridss: refactor identify & annotate variants

---
 tools/gridss-annotateVariants.nix | 85 ---------------------------------------
 1 file changed, 85 deletions(-)
 delete mode 100644 tools/gridss-annotateVariants.nix

(limited to 'tools/gridss-annotateVariants.nix')

diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
deleted file mode 100644
index 3560f77..0000000
--- a/tools/gridss-annotateVariants.nix
+++ /dev/null
@@ -1,85 +0,0 @@
-{ bionix
-, nixpkgs
-, bwaIndexAttrs ? {}
-, faidxAttrs ? {}
-, indexAttrs ? {}
-, assemblyAttrs ? {}
-, collectMetricsAttrs ? {}
-, softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; }
-, identifyVariantsAttrs ? {}
-, flags ? null
-, config ? null
-}:
-
-with nixpkgs;
-with lib;
-with bionix.types;
-with bionix.gridss;
-
-inputs:
-
-let
-  getref = matchFiletype "gridss-annotateVariants" { bam = x: x.ref; };
-  ref = getref (head inputs);
-  sorted = matchFileSorting "gridss-annotateVariants" { coord = _: true; };
-  homoRef = length (unique (map getref inputs)) == 1;
-
-  linkInput = f: attrs: input: ''
-    BASENAME=$(basename ${input})
-    WRKDIR="''${BASENAME}.gridss.working"
-    if [[ ! -e $WRKDIR ]] ; then
-      mkdir $WRKDIR
-    fi
-    for f in ${f attrs input}/* ; do
-      ln -s $f $WRKDIR/$BASENAME.''${f##*.}
-    done
-  '';
-
-  linkSV = input: ''
-    BASENAME=$(basename ${input})
-    WRKDIR="''${BASENAME}.gridss.working"
-    if [[ ! -e $WRKDIR ]] ; then
-    mkdir $WRKDIR
-    fi
-    ln -s ${input} $WRKDIR/$BASENAME.sv.bam
-    ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai
-  '';
-
-  assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.gridss.assemble assemblyAttrs inputs));
-in
-
-assert (all sorted inputs);
-assert (homoRef);
-
-stdenv.mkDerivation rec {
-  name = "gridss-identifyVariants";
-  buildInputs = [ jre ];
-  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
-    ${concatMapStringsSep "\n" (linkSV) inputs}
-    ${linkSV assembly}
-    ${concatMapStringsSep "\n" (linkInput collectMetrics collectMetricsAttrs) inputs}
-    ${linkInput collectMetrics collectMetricsAttrs assembly}
-    ln -s ${identifyVariants identifyVariantsAttrs inputs} input.vcf
-	  java -Xmx4g -Dsamjdk.create_index=true \
-      -cp ${jar} gridss.AnnotateVariants \
-      REFERENCE_SEQUENCE=ref.fa \
-      ${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
-      ASSEMBLY=${assembly} \
-      INPUT_VCF=input.vcf \
-      OUTPUT_VCF=out.vcf \
-      WORKING_DIR=$TMPDIR/ \
-      ${optionalString (config != null) ("OPTIONS_FILE=" +  bionix.gridss.gridssConfig config)} \
-      TMP_DIR=$TMPDIR/
-
-    mv out.vcf $out
-    '';
-  passthru = {
-    filetype = filetype.vcf { ref = ref; };
-    gridss.assembly = assembly;
-  };
-}
-- 
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