From 8ad1aa41c186fb02466e8bc29827c9a927a71a10 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 8 Apr 2016 15:22:51 +0200
Subject: [PATCH] Fixed ; in values
---
.../src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala
index 470c95096..481de58f5 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala
@@ -110,7 +110,7 @@ object SnptestToVcf extends ToolCommand {
.stop(end)
.noGenotypes()
- val infoBuilder = infoKeys.foldLeft(builder) { case (a, b) => a.attribute("ST_" + b, values(headerMap(b))) }
+ val infoBuilder = infoKeys.foldLeft(builder) { case (a, b) => a.attribute("ST_" + b, values(headerMap(b)).replaceAll(";", ",")) }
writer.add(builder.id(rsid.replaceAll(";", ",")).make())
--
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