From bc5709e934bbe1d477764fe153a198ccc669e6bb Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 2 Aug 2021 21:54:37 +1000
Subject: gridss: drop softclip to split read conversion

Unnecessary if aligner supports split reads. Best to leave to user
to manage.
---
 tools/gridss.nix | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tools/gridss.nix b/tools/gridss.nix
index 0e32366..6bfd495 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -60,7 +60,7 @@ rec {
   /* 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
+  /* Preprocess BAM files to extract SV reads and compute required stats
   Type: preprocessBam :: bam -> bam
   */
   preprocessBam = with samtools;
@@ -68,7 +68,6 @@ rec {
       (gridss.extractSVReads {})
       (sort {nameSort = true;})
       (gridss.computeSamTags {})
-      (gridss.softClipsToSplitReads {})
       (sort {})
     ];
 
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