From 54673e3d23b2d14501525a35c046b1e33cfa3b19 Mon Sep 17 00:00:00 2001
From: Sander Bollen <a.h.b.bollen@lumc.nl>
Date: Thu, 13 Aug 2015 18:30:07 +0200
Subject: [PATCH] basty generate fasta test stub
---
.../biopet/tools/BastyGenerateFasta.scala | 9 ++--
.../biopet/tools/BastyGenerateFastaTest.scala | 41 +++++++++++++++++++
2 files changed, 47 insertions(+), 3 deletions(-)
create mode 100644 public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index 33c26353d..66f5ba800 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
@@ -155,7 +155,7 @@ object BastyGenerateFasta extends ToolCommand {
}
}
- protected var cmdArgs: Args = _
+ protected implicit var cmdArgs: Args = _
private val chunkSize = 100000
/**
@@ -253,7 +253,7 @@ object BastyGenerateFasta extends ToolCommand {
}
}
- protected def writeVariantsOnly() {
+ protected[tools] def writeVariantsOnly() {
val writer = new PrintWriter(cmdArgs.outputVariants)
writer.println(">" + cmdArgs.outputName)
val vcfReader = new VCFFileReader(cmdArgs.inputVcf, false)
@@ -265,7 +265,10 @@ object BastyGenerateFasta extends ToolCommand {
vcfReader.close()
}
- protected def getMaxAllele(vcfRecord: VariantContext): String = {
+ // TODO: what does this do?
+ // Seems to me it finds the allele in a sample with the highest AD value
+ // if this allele is shorter than the largest allele, it will append '-' to the string
+ protected[tools] def getMaxAllele(vcfRecord: VariantContext)(implicit cmdArgs: Args): String = {
val maxSize = getLongestAllele(vcfRecord).getBases.length
if (cmdArgs.sampleName == null) return fillAllele(vcfRecord.getReference.getBaseString, maxSize)
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
new file mode 100644
index 000000000..48ff9cfe2
--- /dev/null
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFastaTest.scala
@@ -0,0 +1,41 @@
+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.nio.file.Paths
+
+import htsjdk.variant.vcf.VCFFileReader
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+import org.scalatest.mock.MockitoSugar
+import org.mockito.Mockito._
+
+/**
+ * Created by ahbbollen on 13-8-15.
+ */
+class BastyGenerateFastaTest extends TestNGSuite with MockitoSugar with Matchers {
+
+ import BastyGenerateFasta._
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ val vepped_path = resourcePath("/VEP_oneline.vcf")
+ val vepped = new File(vepped_path)
+
+ @Test def testGetMaxAllele = {
+ val reader = new VCFFileReader(vepped, false)
+ val record = reader.iterator().next()
+
+ val child = mock[Args]
+ when(child.sampleName) thenReturn "Child_7006504"
+ val father = mock[Args]
+ when(father.sampleName) thenReturn "Father_7006506"
+
+
+ getMaxAllele(record)(child) shouldBe "C-"
+ getMaxAllele(record)(father) shouldBe "CA"
+
+ }
+
+}
--
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