From e8b95688f79187a484d5b8f5c02720ba04970519 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Wed, 13 Jul 2016 17:08:11 +0200
Subject: [PATCH] fix for #372
---
.../variantcallers/HaplotypeCallerGvcf.scala | 4 +--
.../HaploTypeCallerGvcfTest.scala | 33 +++++++++++++++++++
2 files changed, 35 insertions(+), 2 deletions(-)
create mode 100644 shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
index 1228520fc..2e4d5c822 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
@@ -42,13 +42,13 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
)
def biopetScript() {
- val gvcfFiles = for ((sample, inputBam) <- inputBams) yield {
+ gVcfFiles = for ((sample, inputBam) <- inputBams) yield {
val hc = gatk.HaplotypeCaller(this, List(inputBam), new File(outputDir, sample + ".gvcf.vcf.gz"))
add(hc)
sample -> hc.out
}
- val genotypeGVCFs = gatk.GenotypeGVCFs(this, gvcfFiles.values.toList, outputFile)
+ val genotypeGVCFs = gatk.GenotypeGVCFs(this, gVcfFiles.values.toList, outputFile)
add(genotypeGVCFs)
}
}
diff --git a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
new file mode 100644
index 000000000..820efe247
--- /dev/null
+++ b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaploTypeCallerGvcfTest.scala
@@ -0,0 +1,33 @@
+package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
+
+import java.io.File
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by Sander Bollen on 13-7-16.
+ */
+class HaploTypeCallerGvcfTest extends TestNGSuite with Matchers {
+
+ @Test
+ def testGvcfFiles = {
+ val samples = List("sample01", "sample02", "sample03")
+ val hc = new HaplotypeCallerGvcf(null)
+ hc.inputBams = createInputMap(samples)
+ hc.biopetScript()
+
+ hc.getGvcfs.size shouldBe 3
+ hc.getGvcfs.keys.toList shouldEqual samples
+ }
+
+ def createInputMap(samples: List[String]): Map[String, File] = {
+ samples map { x =>
+ val file = File.createTempFile(x, ".bam")
+ file.deleteOnExit()
+ x -> file
+ } toMap
+ }
+
+}
--
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