Commit bb46c239 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

changes to get rid of reference calls

parent 59923a55
...@@ -60,14 +60,11 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller { ...@@ -60,14 +60,11 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
sampleVcf sampleVcf
} }
if (sampleVcfs.size > 1) { val cv = new CombineVariants(this)
val cv = new CombineVariants(this) cv.inputFiles = sampleVcfs
cv.inputFiles = sampleVcfs cv.outputFile = outputFile
cv.outputFile = outputFile cv.setKey = "null"
cv.setKey = "null" cv.excludeNonVariants = true
cv.excludeNonVariants = true add(cv)
add(cv)
} else add(Ln.apply(this, sampleVcfs.head, outputFile))
add(Tabix(this, outputFile))
} }
} }
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