From ff6840c5ba295be678aeeec4e1dcbc9b4d36b035 Mon Sep 17 00:00:00 2001
From: Wai Yi Leung <w.y.leung@lumc.nl>
Date: Tue, 26 Apr 2016 09:51:25 +0200
Subject: [PATCH] Fix clever vcf header and add sorting step
---
.../biopet/extensions/clever/CleverFixVCF.scala | 1 +
.../biopet/pipelines/shiva/svcallers/Clever.scala | 13 ++++++++++---
2 files changed, 11 insertions(+), 3 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
index f89d4f299..407c172ec 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
@@ -81,6 +81,7 @@ object CleverFixVCF extends ToolCommand {
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
##INFO=<ID=PARID,Number=1,Type=String,Description="ID of partner breakend">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
+##INFO=<ID=BPWINDOW,Number=2,Type=Integer,Description="Window of breakpoints">
##INFO=<ID=CILEN,Number=2,Type=Integer,Description="Confidence interval around the inserted material between breakends">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth of segment containing breakend">
##INFO=<ID=DPADJ,Number=.,Type=Integer,Description="Read Depth of adjacency">
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
index eefeb30f4..0baba5e63 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
@@ -15,7 +15,8 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
-import nl.lumc.sasc.biopet.extensions.clever.{ CleverCaller, CleverFixVCF }
+import nl.lumc.sasc.biopet.extensions.clever.{CleverCaller, CleverFixVCF}
+import nl.lumc.sasc.biopet.extensions.picard.SortVcf
import nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caler Clever */
@@ -31,11 +32,17 @@ class Clever(val root: Configurable) extends SvCaller {
val cleverVCF = new CleverFixVCF(this)
cleverVCF.input = clever.outputvcf
- cleverVCF.output = new File(cleverDir, s"${sample}.clever.vcf")
+ cleverVCF.output = new File(cleverDir, s".${sample}.clever.vcf")
cleverVCF.sampleName = sample
+ cleverVCF.isIntermediate = true
add(cleverVCF)
- addVCF(sample, cleverVCF.output)
+ val sortvcf = new SortVcf(this)
+ sortvcf.input = cleverVCF.output
+ sortvcf.output = new File(cleverDir, s"${sample}.clever.vcf")
+ add(sortvcf)
+
+ addVCF(sample, sortvcf.output)
}
}
}
--
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