From 34024cc5dff54ce40583d17b9e517686dc815d27 Mon Sep 17 00:00:00 2001
From: sajvanderzeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Fri, 16 Oct 2015 16:55:59 +0200
Subject: [PATCH] add bcf merge to shiva and create wrapper

---
 .../extensions/bcftools/BcftoolsCall.scala    |  4 +-
 .../extensions/bcftools/BcftoolsMerge.scala   | 49 +++++++++++++++++++
 .../shiva/ShivaVariantcallingTrait.scala      | 13 ++---
 3 files changed, 58 insertions(+), 8 deletions(-)
 create mode 100644 public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala

diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
index 8b721d36a..329ea4a65 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsCall.scala
@@ -34,13 +34,13 @@ class BcftoolsCall(val root: Configurable) extends Bcftools {
   var m: Boolean = config("m", default = false)
   var r: Option[String] = config("r")
   @Input(required = false)
-  var R: Option[String] = config("R")
+  var R: Option[File] = config("R")
   var s: Option[String] = config("s")
   @Input(required = false)
   var S: Option[File] = config("S")
   var t: Option[String] = config("t")
   @Input(required = false)
-  var T: Option[String] = config("T")
+  var T: Option[File] = config("T")
   var A: Boolean = config("A", default = false)
   var f: List[String] = config("f", default = Nil)
   var g: Option[Int] = config("g")
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
new file mode 100644
index 000000000..3a6fb6978
--- /dev/null
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bcftools/BcftoolsMerge.scala
@@ -0,0 +1,49 @@
+package nl.lumc.sasc.biopet.extensions.bcftools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
+/**
+ * Created by sajvanderzeeuw on 16-10-15.
+ */
+class BcftoolsMerge(val root: Configurable) extends Bcftools {
+  @Input(doc = "Input File", required = true)
+  var input: List[File] = Nil
+
+  @Output(doc = "output File", required = false)
+  var output: File = _
+
+  @Input(required = false)
+  var R: Option[File] = config("R")
+
+  @Input(required = false)
+  var useheader: Option[File] = config("useheader")
+
+  @Input(required = false)
+  var l: Option[File] = config("l")
+
+  var forcesamples: Boolean = config("forcesamples", default = false)
+  var printheader: Boolean = config("printheader", default = false)
+  var f: List[String] = config("f", default = Nil)
+  var i: List[String] = config("i", default = Nil)
+  var m: Option[String] = config("m")
+  var O: Option[String] = config("O")
+  var r: List[String] = config("r", default = Nil)
+
+  def cmdLine = required(executable) +
+    required("merge") +
+    (if (outputAsStsout) "" else required("-o", output)) +
+    conditional(forcesamples, "--force-samples") +
+    conditional(printheader, "--print-header") +
+    optional("--use-header", useheader) +
+    optional("-f", f) +
+    optional("-i", i) +
+    optional("-l", l) +
+    optional("-m", m) +
+    optional("-O", O) +
+    optional("-r", r) +
+    optional("-R", R) +
+    repeat(input)
+}
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 365d4e638..1e49e4c38 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
@@ -19,7 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.extensions.bcftools.BcftoolsCall
+import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsMerge, BcftoolsCall }
 import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
 import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
@@ -201,11 +201,12 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag with
         bt.output
       }
 
-      val cv = new CombineVariants(qscript)
-      cv.inputFiles = sampleVcfs
-      cv.outputFile = outputFile
-      cv.setKey = "null"
-      add(cv)
+      val bcfmerge = new BcftoolsMerge(qscript)
+      bcfmerge.input = sampleVcfs
+      bcfmerge.output = outputFile
+      bcfmerge.O = Some("z")
+      add(bcfmerge)
+      add(Tabix(qscript, outputFile))
     }
   }
 
-- 
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