JAL-3376 capture VCF POS, ID, QUAL, FILTER as feature attributes

[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 808fe86..1e88665 100644 (file)
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -71,10 +71,10 @@ public class VCFLoaderTest
       // 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\t.\tA\tT,C\t1666.64\tRF\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",
       // 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\tRF\tAC=15;AF=3.0e-03,2.0e-03",
+      "17\t45051613\t.\tG\tGA,C\t1666.65\t.\tAC=15;AF=3.0e-03,2.0e-03",
       // '.' in INFO field should be ignored
       "17\t45051615\t.\tG\tC\t1666.66\tRF\tAC=16;AF=." };
 
@@ -130,6 +130,10 @@ public class VCFLoaderTest
     assertEquals(sf.getValue("AF_AFR"), "2.3e-4");
     assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,C");
     assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getValue("POS"), "45051611");
+    assertEquals(sf.getValue("ID"), "rs384765");
+    assertEquals(sf.getValue("QUAL"), "1666.64");
+    assertEquals(sf.getValue("FILTER"), "RF;XYZ");
     // malformed integer for AC_Female is ignored (JAL-3375)
     assertNull(sf.getValue("AC_Female"));
 
@@ -165,6 +169,8 @@ public class VCFLoaderTest
     assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
             DELTA);
     assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
+    assertNull(sf.getValue("ID")); // '.' is ignored
+    assertNull(sf.getValue("FILTER")); // '.' is ignored
 
     sf = geneFeatures.get(4);
     assertEquals(sf.getFeatureGroup(), "VCF");