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 ++--
 tools/gridss-assemble.nix              | 2 +-
 tools/gridss-softClipsToSplitReads.nix | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

(limited to 'tools')

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);
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index 847830a..a8124e0 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -55,5 +55,5 @@ stdenv.mkDerivation rec {
       WORKING_DIR=$TMPDIR/ \
       TMP_DIR=$TMPDIR/
   '';
-  passthru.filetype = filetype.bam { ref = ref; sorting = sort.coord {}; };
+  passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; };
 }
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index 9bce063..c23168f 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -35,5 +35,5 @@ stdenv.mkDerivation rec {
       ${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
 			WORKER_THREADS=$NIX_BUILD_CORES
     '';
-  passthru.filetype = filetype.bam { ref = ref; sorting = matchFileSorting "grids-softClipsToSplitReads" { coord = _: input.sorting; name = _: sort.none {}; none = _: input.sorting;} input;};
+  passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; };
 }
-- 
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