From 0e6e9427d863db138d70fbb3b2d14f1787d7546e Mon Sep 17 00:00:00 2001 From: Louis Bergelson Date: Mon, 30 Jan 2023 16:17:50 -0500 Subject: [PATCH] add test --- .../htsjdk/variant/vcf/VCFEncoderTest.java | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/src/test/java/htsjdk/variant/vcf/VCFEncoderTest.java b/src/test/java/htsjdk/variant/vcf/VCFEncoderTest.java index b0c88cd02a..89537eaf51 100644 --- a/src/test/java/htsjdk/variant/vcf/VCFEncoderTest.java +++ b/src/test/java/htsjdk/variant/vcf/VCFEncoderTest.java @@ -11,6 +11,7 @@ import org.testng.annotations.DataProvider; import org.testng.annotations.Test; +import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; @@ -150,6 +151,26 @@ public void testEncodeGT(){ Assert.assertEquals(VCFEncoder.encodeGtField(vc, g2), "1/2"); } + @Test + public void testsWriteGtField() throws IOException { + final VariantContextBuilder vcb = new VariantContextBuilder("test", + "chr?", 100, 100, + Arrays.asList(Allele.REF_A, Allele.ALT_T, Allele.create("TC"))); + final Genotype g1 = new GenotypeBuilder("s1", Arrays.asList(Allele.REF_A, Allele.REF_A)).make(); + final Genotype g2 = new GenotypeBuilder("s2", Arrays.asList(Allele.ALT_T, Allele.create("TC"))).make(); + vcb.genotypes(g1, g2); + final VariantContext vc = vcb.make(); + final Map alleleStringMap = VCFEncoder.buildAlleleStrings(vc); + + final StringBuilder b1 = new StringBuilder(); + VCFEncoder.writeGtField(alleleStringMap, b1, g1 ); + Assert.assertEquals(b1.toString(), "0/0"); + + final StringBuilder b2 = new StringBuilder(); + VCFEncoder.writeGtField(alleleStringMap, b2, g2); + Assert.assertEquals(b2.toString(), "1/2"); + } + @Test(dataProvider = "MissingFormatTestData") public void testMissingFormatFields(final VCFEncoder encoder, final VariantContext vc, final String expectedLastColumn, final Map alleleMap, final List genotypeFormatKeys) { final StringBuilder sb = new StringBuilder();