From 9f604dce317ee6dde415d875304ded9f7941813a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 4 Mar 2015 15:05:10 +0100
Subject: [PATCH] Added todo
---
.../sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala | 1 +
1 file changed, 1 insertion(+)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index e0edf52ce..ea46e04b9 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
@@ -101,6 +101,7 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
fb.isIntermediate = true
add(fb)
+ //TODO: need piping for this
val bz = new Bgzip(qscript)
bz.input = List(fb.outputVcf)
bz.output = outputFile
--
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