From 06a147a3b979a4f7b2310da84a136207a1d528b4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 6 Apr 2017 16:10:43 +0200
Subject: [PATCH] Adding bqsr implementation

---
 .../shiva/variantcallers/HaplotypeCallerAllele.scala     | 9 ++++++++-
 .../shiva/variantcallers/UnifiedGenotyperAllele.scala    | 8 ++++++++
 2 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
index e36f4c758..a2ded8a46 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
@@ -20,7 +20,7 @@
 package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
 
 import nl.lumc.sasc.biopet.extensions.gatk
-import nl.lumc.sasc.biopet.utils.Logging
+import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Allele mode for Haplotypecaller */
@@ -33,6 +33,13 @@ class HaplotypeCallerAllele(val parent: Configurable) extends Variantcaller {
   def biopetScript() {
     val hc = gatk.HaplotypeCaller(this, inputBams.values.toList, outputFile)
     hc.alleles = Some(alleles)
+    hc.BQSR = if (inputBqsrFiles.isEmpty) None else {
+      val gather = new BqsrGather
+      gather.inputBqsrFiles = inputBqsrFiles.values.toList
+      gather.outputBqsrFile = new File(outputDir, "bqsr.merge")
+      add(gather)
+      Some(gather.outputBqsrFile)
+    }
     hc.genotyping_mode = Some("GENOTYPE_GIVEN_ALLELES")
     add(hc)
   }
diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
index 4d2b9501e..61fc86c6b 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
@@ -20,6 +20,7 @@
 package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
 
 import nl.lumc.sasc.biopet.extensions.gatk
+import nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
 import nl.lumc.sasc.biopet.utils.config.Configurable
 
 /** Allele mode for GenotyperAllele */
@@ -33,6 +34,13 @@ class UnifiedGenotyperAllele(val parent: Configurable) extends Variantcaller {
     val ug = gatk.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
     ug.alleles = Some(alleles)
     ug.genotyping_mode = Some("GENOTYPE_GIVEN_ALLELES")
+    ug.BQSR = if (inputBqsrFiles.isEmpty) None else {
+      val gather = new BqsrGather
+      gather.inputBqsrFiles = inputBqsrFiles.values.toList
+      gather.outputBqsrFile = new File(outputDir, "bqsr.merge")
+      add(gather)
+      Some(gather.outputBqsrFile)
+    }
     add(ug)
   }
 }
-- 
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