From bb46c23925ce9e4d3f35f755058c9156424fb005 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Mon, 18 Jan 2016 17:06:44 +0100
Subject: [PATCH] changes to get rid of reference calls
---
.../variantcallers/VarscanCnsSingleSample.scala | 15 ++++++---------
1 file changed, 6 insertions(+), 9 deletions(-)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
index 1f13a37c9..896bdffd7 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
@@ -60,14 +60,11 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
sampleVcf
}
- if (sampleVcfs.size > 1) {
- val cv = new CombineVariants(this)
- cv.inputFiles = sampleVcfs
- cv.outputFile = outputFile
- cv.setKey = "null"
- cv.excludeNonVariants = true
- add(cv)
- } else add(Ln.apply(this, sampleVcfs.head, outputFile))
- add(Tabix(this, outputFile))
+ val cv = new CombineVariants(this)
+ cv.inputFiles = sampleVcfs
+ cv.outputFile = outputFile
+ cv.setKey = "null"
+ cv.excludeNonVariants = true
+ add(cv)
}
}
--
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