diff --git a/biopet-tools/src/test/resources/star_genotype.vcf.gz b/biopet-tools/src/test/resources/star_genotype.vcf.gz new file mode 100644 index 0000000000000000000000000000000000000000..719fa80d143fa157fe229e5cdfabe129e2d3a9e7 Binary files /dev/null and b/biopet-tools/src/test/resources/star_genotype.vcf.gz differ diff --git a/biopet-tools/src/test/resources/star_genotype.vcf.gz.tbi b/biopet-tools/src/test/resources/star_genotype.vcf.gz.tbi new file mode 100644 index 0000000000000000000000000000000000000000..52b6c13ae020debc91807d496f20d596cdf72299 Binary files /dev/null and b/biopet-tools/src/test/resources/star_genotype.vcf.gz.tbi differ diff --git a/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala b/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala index 9cc0d60d27439cc4c06065db7716ccf9cf95b6f8..6ff7a170bc9d41fba0e0ebead1f382d72365a55f 100644 --- a/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala +++ b/biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala @@ -39,7 +39,9 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers { } val veppedPath = resourcePath("/VEP_oneline.vcf") + val starPath = resourcePath("/star_genotype.vcf.gz") val vepped = new File(veppedPath) + val star = new File(starPath) val rand = new Random() @Test def testOutputTypeVcf() = { @@ -183,6 +185,9 @@ class VcfFilterTest extends TestNGSuite with MockitoSugar with Matchers { mustHaveVariant(record, List("Sample_101")) shouldBe true mustHaveVariant(record, List("Sample_101", "Sample_102")) shouldBe true mustHaveVariant(record, List("Sample_101", "Sample_102", "Sample_103")) shouldBe false + + val starReader = new VCFFileReader(star, false) + starReader.iterator().foreach(x => mustHaveVariant(x, List("Sample_101")) shouldBe false) } @Test def testSameGenotype() = {