JAL-3469 add "Number=." fields (all values) to all alleles in VCF record

[jalview.git] / test / jalview / io / vcf / VCFLoaderTest.java

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index 87cf727..c050029 100644 (file)
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -61,16 +61,17 @@ public class VCFLoaderTest
           + ">transcript4/1-18\n-----TGG-GGACGAGAGTGTGA-A\n";
 
   private static final String[] VCF = { "##fileformat=VCFv4.2",
-      // fields other than AF are ignored when parsing as they have no INFO definition
+      // note fields with no INFO definition are ignored when parsing
       "##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">",
       "##INFO=<ID=AC_Female,Number=A,Type=Integer,Description=\"Allele count in Female genotypes\"",
       "##INFO=<ID=AF_AFR,Number=A,Type=Float,Description=\"Allele Frequency among African/African American genotypes\"",
+      "##INFO=<ID=CLNSIG,Number=.,Type=String,Description=\"Clinical significance for this single variant\"",
       "##reference=Homo_sapiens/GRCh38",
       "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
       // A/T,C variants in position 2 of gene sequence (precedes transcript)
       // should create 2 variant features with respective AF values
       // malformed values for AC_Female and AF_AFR should be ignored
-      "17\t45051611\trs384765\tA\tT,C\t1666.64\tRF;XYZ\tAC=15;AF=5.0e-03,4.0e-03;AC_Female=12,3d;AF_AFR=low,2.3e-4",
+      "17\t45051611\trs384765\tA\tT,C\t1666.64\tRF;XYZ\tAC=15;AF=5.0e-03,4.0e-03;AC_Female=12,3d;AF_AFR=low,2.3e-4;CLNSIG=benign,probably_benign",
       // SNP G/C in position 4 of gene sequence, position 2 of transcript
       // insertion G/GA is transferred to nucleotide but not to peptide
       "17\t45051613\t.\tG\tGA,C\t1666.65\t.\tAC=15;AF=3.0e-03,2.0e-03",
@@ -133,6 +134,10 @@ public class VCFLoaderTest
     assertEquals(sf.getValue("ID"), "rs384765");
     assertEquals(sf.getValue("QUAL"), "1666.64");
     assertEquals(sf.getValue("FILTER"), "RF;XYZ");
+    /*
+     * if INFO declares Number=1, all values are attached to each allele
+     */
+    assertEquals(sf.getValue("CLNSIG"), "benign,probably_benign");
     // malformed integer for AC_Female is ignored (JAL-3375)
     assertNull(sf.getValue("AC_Female"));
 
@@ -148,6 +153,7 @@ public class VCFLoaderTest
     // malformed float for AF_AFR is ignored (JAL-3375)
     assertNull(sf.getValue("AC_AFR"));
     assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,T");
+    assertEquals(sf.getValue("CLNSIG"), "benign,probably_benign");
 
     sf = geneFeatures.get(2);
     assertEquals(sf.getFeatureGroup(), "VCF");