From 9cf522d5cf766ef7943226e8d4807643ee93721d Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 10 Nov 2022 16:00:25 +0100
Subject: [PATCH] fix typing issue in AnnotateSvTypes R code

---
 gridss.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gridss.wdl b/gridss.wdl
index 9a09bdd..8e1474c 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -120,7 +120,7 @@ task AnnotateSvTypes {
         svtype <- simpleEventType(gr)
         info(vcf[gr$sourceId])$SVTYPE <- svtype
         # GRIDSS doesn't supply a GT, simply set it to 0/1
-        geno(vcf)$GT <- "0/1"
+        geno(vcf)$GT <- as.matrix(sapply(row.names(vcf), function(x) {"0/1"}))
         # Select only one breakend per event (also removes single breakends):
         # sourceId ends with o or h for paired breakends, the first in the pair
         # end with o the second with h. Single breakend end with b, these will
-- 
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