From 886af7beaaa98ac32db88a7453d917409cf11ae8 Mon Sep 17 00:00:00 2001
From: l-d-s <distefano.l@wehi.edu.au>
Date: Wed, 7 Nov 2018 16:39:47 +1100
Subject: Fix to gridss.

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

(limited to 'tools')

diff --git a/tools/gridss.nix b/tools/gridss.nix
index d46a8ce..792d279 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -16,6 +16,6 @@ rec {
   assemble = callBionix ./gridss-assemble.nix;
   identifyVariants = callBionix ./gridss-identifyVariants.nix;
   annotateVariants = callBionix ./gridss-annotateVariants.nix;
-  preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (softClipsToSplitReads {} (computeSamTags {} (sort {nameSort = true;} input)))));
-  call = inputs: annotateVariants {} (map preprocessBam inputs);
+  preprocessBam = input: with samtools; markdup {} (sort {} (fixmate {mateScore = true;} (bionix.gridss.softClipsToSplitReads {} (bionix.gridss.computeSamTags {} (sort {nameSort = true;} input)))));
+  call = inputs: bionix.gridss.annotateVariants {} (map bionix.gridss.preprocessBam inputs);
 }
-- 
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