From b7bf9221c5666eb3ad97857dea7010e3fac94e48 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 8 Apr 2016 15:15:36 +0200
Subject: [PATCH] Fixed rsid
---
.../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 2473c7bfe..470c95096 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
@@ -112,7 +112,7 @@ object SnptestToVcf extends ToolCommand {
val infoBuilder = infoKeys.foldLeft(builder) { case (a, b) => a.attribute("ST_" + b, values(headerMap(b))) }
- writer.add(builder.id(rsid).make())
+ writer.add(builder.id(rsid.replaceAll(";", ",")).make())
counter += 1
if (counter % 10000 == 0) logger.info(s"$counter lines processed")
--
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