From 3b0bbaf7c93e9324b0f36d260d85a7c3bf2c2734 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 17 Nov 2014 07:00:22 +0100
Subject: [PATCH] Added collect consensus
---
.../scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
index 9e73788f7..abd41b5dd 100644
--- a/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+++ b/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
@@ -47,6 +47,11 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
val catVariantsSnps = Cat(this, refVariantSnps.variants :: samplesOutput.map(_._2.outputSnps.variants).toList, outputDir + "fastas/variant.snps_only.fasta")
add(catVariantsSnps)
+ val catConsensus = Cat(this, refVariants.consensus :: samplesOutput.map(_._2.output.consensus).toList, outputDir + "fastas/consensus.fasta")
+ add(catConsensus)
+ val catConsensusSnps = Cat(this, refVariantSnps.consensus :: samplesOutput.map(_._2.outputSnps.consensus).toList, outputDir + "fastas/consensus.snps_only.fasta")
+ add(catConsensusSnps)
+
val catConsensusVariants = Cat(this, refVariants.consensusVariants :: samplesOutput.map(_._2.output.consensusVariants).toList, outputDir + "fastas/consensus.variant.fasta")
add(catConsensusVariants)
val catConsensusVariantsSnps = Cat(this, refVariantSnps.consensusVariants :: samplesOutput.map(_._2.outputSnps.consensusVariants).toList, outputDir + "fastas/consensus.variant.snps_only.fasta")
--
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