From d79fc6785f2b8714fa2762bd07a9a9f937bf4513 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 11 Dec 2018 14:11:21 +1100
Subject: gridss: fix softClipsToSplitReads after assembly

---
 tools/gridss-annotateVariants.nix | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

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

diff --git a/tools/gridss-annotateVariants.nix b/tools/gridss-annotateVariants.nix
index 655b268..3560f77 100644
--- a/tools/gridss-annotateVariants.nix
+++ b/tools/gridss-annotateVariants.nix
@@ -5,7 +5,7 @@
 , indexAttrs ? {}
 , assemblyAttrs ? {}
 , collectMetricsAttrs ? {}
-, softClipsToSplitReadsAttrs ? {}
+, softClipsToSplitReadsAttrs ? { flags = "REALIGN_ENTIRE_READ=true"; }
 , identifyVariantsAttrs ? {}
 , flags ? null
 , config ? null
@@ -45,7 +45,7 @@ let
     ln -s ${bionix.samtools.index indexAttrs input} $WRKDIR/$BASENAME.sv.bai
   '';
 
-  assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.samtools.sort { nameSort = true;} (bionix.gridss.assemble assemblyAttrs inputs)));
+  assembly = bionix.samtools.sort {} (softClipsToSplitReads softClipsToSplitReadsAttrs (bionix.gridss.assemble assemblyAttrs inputs));
 in
 
 assert (all sorted inputs);
-- 
cgit v1.2.3