diff --git a/public/biopet-framework/src/test/resources/unvep_online.vcf.gz b/public/biopet-framework/src/test/resources/unvep_online.vcf.gz
new file mode 100644
index 0000000000000000000000000000000000000000..f102295f99d0bc62e25de296b84dc6610930a683
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diff --git a/public/biopet-framework/src/test/resources/unvep_online.vcf.gz.tbi b/public/biopet-framework/src/test/resources/unvep_online.vcf.gz.tbi
new file mode 100644
index 0000000000000000000000000000000000000000..bb43ff545f591dd276973e7158919e6d14c78f23
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diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
index b3c77eb416ad5d98c61289c3147a9e0adeef287e..f8116db2bd2e0c0a4ca41c068997a456188f9c52 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
@@ -17,13 +17,16 @@ package nl.lumc.sasc.biopet.tools
import java.io.File
import java.nio.file.Paths
+import java.util
+import htsjdk.variant.vcf.VCFFileReader
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
import scala.util.Random
+import scala.collection.JavaConversions._
/**
* Test class for [[VcfWithVcfTest]]
@@ -38,7 +41,7 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
}
val veppedPath = resourcePath("/VEP_oneline.vcf.gz")
- val unveppedPath = resourcePath("/unvepped.vcf.gz")
+ val unveppedPath = resourcePath("/unvep_online.vcf.gz")
val rand = new Random()
@Test def testOutputTypeVcf() = {
@@ -91,4 +94,70 @@ class VcfWithVcfTest extends TestNGSuite with MockitoSugar with Matchers {
thrown.getMessage should equal("Type of field CSQ is not numeric")
}
+ @Test
+ def testFieldMap = {
+ val unvep_record = new VCFFileReader(new File(unveppedPath)).iterator().next()
+
+ var fields = List(new Fields("FG", "FG"))
+ fields :::= List(new Fields("FD", "FD"))
+ fields :::= List(new Fields("GM", "GM"))
+ fields :::= List(new Fields("GL", "GL"))
+ fields :::= List(new Fields("CP", "CP"))
+ fields :::= List(new Fields("CG", "CG"))
+ fields :::= List(new Fields("CN", "CN"))
+ fields :::= List(new Fields("DSP", "DSP"))
+ fields :::= List(new Fields("AC", "AC"))
+ fields :::= List(new Fields("AF", "AF"))
+ fields :::= List(new Fields("AN", "AN"))
+ fields :::= List(new Fields("BaseQRankSum", "BaseQRankSum"))
+ fields :::= List(new Fields("DP", "DP"))
+ fields :::= List(new Fields("FS", "FS"))
+ fields :::= List(new Fields("MLEAC", "MLEAC"))
+ fields :::= List(new Fields("MLEAF", "MLEAF"))
+ fields :::= List(new Fields("MQ", "MQ"))
+ fields :::= List(new Fields("MQ0", "MQ0"))
+ fields :::= List(new Fields("MQRankSum", "MQRankSum"))
+ fields :::= List(new Fields("QD", "QD"))
+ fields :::= List(new Fields("RPA", "RPA"))
+ fields :::= List(new Fields("RU", "RU"))
+ fields :::= List(new Fields("ReadPosRankSum", "ReadPosRankSum"))
+ fields :::= List(new Fields("VQSLOD", "VQSLOD"))
+ fields :::= List(new Fields("culprit", "culprit"))
+
+
+ val fieldMap = createFieldMap(fields, List(unvep_record))
+
+ fieldMap("FG") shouldBe List("intron")
+ fieldMap("FD") shouldBe List("unknown")
+ fieldMap("GM") shouldBe List("NM_152486.2")
+ fieldMap("GL") shouldBe List("SAMD11")
+ fieldMap("CP") shouldBe List("0.000")
+ fieldMap("CG") shouldBe List("-1.630")
+ val cn = new util.ArrayList[String]
+ cn.addAll(List("2294", "3274", "30362", "112930"))
+ fieldMap("CN") shouldBe List(cn)
+ fieldMap("DSP") shouldBe List("107")
+ fieldMap("AC") shouldBe List("2")
+ fieldMap("AF") shouldBe List("0.333")
+ fieldMap("AN") shouldBe List("6")
+ fieldMap("DP") shouldBe List("124")
+ fieldMap("FS") shouldBe List("1.322")
+ fieldMap("MLEAC") shouldBe List("2")
+ fieldMap("MLEAF") shouldBe List("0.333")
+ fieldMap("MQ") shouldBe List("60.0")
+ fieldMap("MQ0") shouldBe List("0")
+ fieldMap("MQRankSum") shouldBe List("-0.197")
+ fieldMap("QD") shouldBe List("19.03")
+ val rpa = new util.ArrayList[String]
+ rpa.addAll(List("1", "2"))
+ fieldMap("RPA") shouldBe List(rpa)
+ fieldMap("RU") shouldBe List("A")
+ fieldMap("ReadPosRankSum") shouldBe List("-0.424")
+ fieldMap("VQSLOD") shouldBe List("0.079")
+ fieldMap("culprit") shouldBe List("FS")
+
+
+
+ }
+
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
index b2a063f9853c07ceb23f623b174e5d7980dc275f..5a12e9b579296b58a2764fdaa0b5b916717e384f 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
@@ -47,37 +47,37 @@ class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
val rand = new Random()
@Test def testGzOutputExplode(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf.gz"
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
+ val tmpPath = File.createTempFile("VepNormalizer_", ".vcf.gz").getAbsolutePath
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpPath, "-m", "explode")
main(arguments)
}
@Test def testVcfOutputExplode(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf"
- val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
+ val tmpPath = File.createTempFile("VepNormalizer_", ".vcf").getAbsolutePath
+ val arguments: Array[String] = Array("-I", vepped_path, "-O", tmpPath, "-m", "explode")
main(arguments)
}
@Test def testBcfOutputExplode(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".bcf"
+ val tmp_path = File.createTempFile("VepNormalizer_", ".bcf").getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "explode")
main(arguments)
}
@Test def testGzOutputStandard(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf.gz"
+ val tmp_path = File.createTempFile("VepNormalizer_", ".vcf.gz").getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
main(arguments)
}
@Test def testVcfOutputStandard(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".vcf"
+ val tmp_path = File.createTempFile("VepNormalizer_", ".vcf").getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
main(arguments)
}
@Test def testBcfOutputStandard(): Unit = {
- val tmp_path = "/tmp/VepNorm_" + rand.nextString(10) + ".bcf"
+ val tmp_path = File.createTempFile("VepNormalizer_", ".bcf").getAbsolutePath
val arguments: Array[String] = Array("-I", vepped_path, "-O", tmp_path, "-m", "standard")
main(arguments)
}