From 001e834a4b8e660be8797690a2b0eb418b01fbbb Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 8 Apr 2019 09:33:33 +1000
Subject: grids: add function to include assemblies with annotated VCF

---
 test-tnpair.nix           |  1 +
 tools/gridss-variants.nix | 10 ++++++++++
 tools/gridss.nix          |  6 ++++++
 3 files changed, 17 insertions(+)

diff --git a/test-tnpair.nix b/test-tnpair.nix
index da37068..c88b68a 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -51,6 +51,7 @@ let
     (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam")
     (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss")
     (ln (gridss.call (with tnpairResult.alignments; [normal tumour])) "gridss2")
+    (ln (gridss.callAndAssemble (with tnpairResult.alignments; [normal tumour])) "gridss3")
     (ln (samtools.merge {} [tnpairResult.alignments.tumour tnpairResult.alignments.normal]) "alignments/merged.bam")
     (ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.tumour)) "alignments/${tnpair.tumour.name}.cram")
     #(ln (samtools.view { outfmt = types.toCram; } (tnpairResult.alignments.normal)) "alignments/${tnpair.normal.name}.cram")
diff --git a/tools/gridss-variants.nix b/tools/gridss-variants.nix
index b564725..4f39b1e 100644
--- a/tools/gridss-variants.nix
+++ b/tools/gridss-variants.nix
@@ -111,4 +111,14 @@ rec {
       gridss.assembly = assembly;
     };
   };
+
+  annotateAndAssemble = stage rec {
+    name = "gridss-annotateVariants-assemble";
+    buildCommand = ''
+      mkdir $out
+      ln -s ${annotate} $out/gridss.vcf
+      ln -s ${assembly} $out/gridss.bam
+      ln -s ${bionix.samtools.index indexAttrs assembly} $out/gridss.bam.bai
+    '';
+  };
 }
diff --git a/tools/gridss.nix b/tools/gridss.nix
index 050a628..176bd34 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -53,6 +53,9 @@ rec {
   */
   annotateVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate);
 
+  /* As annotateVariants except include assembly in output */
+  annotateAndAssemble = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotateAndAssemble);
+
   /* Preprocess BAM files to extract SV reads and convert soft clips to split reads
   Type: preprocessBam :: bam -> bam
   */
@@ -69,4 +72,7 @@ rec {
   Type: [bam] -> GRIDSS result
   */
   call = inputs: gridss.annotateVariants {} (map gridss.preprocessBam inputs);
+
+  /* As call but include assemblies in output */
+  callAndAssemble = inputs: gridss.annotateAndAssemble {} (map gridss.preprocessBam inputs);
 }
-- 
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