tools: Fix VariantContextConverterTest. #TASK-4682

opencb · Nov 7, 2024 · 2520821 · 2520821
1 parent 2187ae8
commit 2520821
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/...ls/src/main/java/org/opencb/biodata/tools/variant/converters/VariantContextConverter.java b/...ls/src/main/java/org/opencb/biodata/tools/variant/converters/VariantContextConverter.java
@@ -445,7 +445,7 @@ protected static String allelesToString(Collection<String> alleles) {
     }
 
     private static String alleleToString(String a) {
-        return a.length() > 10 ? (a.substring(0, 10) + "...[" + a.length() + "]") : a;
+        return a.length() > 20 ? (a.substring(0, 10) + "...[" + a.length() + "]") : a;
     }
 
 }
diff --git a/...rc/test/java/org/opencb/biodata/tools/variant/converters/VariantContextConverterTest.java b/...rc/test/java/org/opencb/biodata/tools/variant/converters/VariantContextConverterTest.java
@@ -37,6 +37,11 @@ public class VariantContextConverterTest {
 
     @Test
     public void testDuplicatedAllele() throws NonStandardCompliantSampleField {
+        // REF :                         AGTATATTGTGT      AGTATATTGTG
+        // V1  :  1000:AGTATATTGT/A      A---------GT  ->  A---------G  ->  AG
+        // V2  :  1002:TATATTGTGT/TT     AGT--------T  ->  AGT--------  ->  AGT
+        // V3  :  1002:TATATTGTGT/T      AG---------T  ->  AG---------  ->  AG
+
         String studyId = "s";
         Variant variant = Variant.newBuilder("1", 1000, null, "AGTATATTGT", "A")
                 .setStudyId(studyId)
@@ -51,9 +56,9 @@ public void testDuplicatedAllele() throws NonStandardCompliantSampleField {
                 .addSample("s4", "1/1", "1,10,1")
                 .build();
 
-        checkVcf("1 1000 . AGTATATTGT A,AGT . . . GT:AD  1/1:10,10,0,0 0/1:0,10,0,0   ./.:.        2/2:1,0,1,10", merge(norm(variant), norm(variant2)));
-        checkVcf("1 1001 . GTATATTGTG G,GT  . . . GT:AD  ./.:.         ./.:.          0/1:1,10,1,0 2/2:1,1,10,0", merge(norm(variant2), norm(variant)));
-        checkVcf("1 1000 . AGTATATTGT A,AGT . . . GT:AD  1/1:10,10,0,0 0/1:0,10,0,0   ./.:.        2/2:1,0,1,10", merge(norm(variant), norm(variant2, 1)));
+        checkVcf("1 1000 . AGTATATTGTG  AG,AGT . . . GT:AD  1/1:10,10,0,0 0/1:0,10,0,0   ./.:.        2/2:1,0,1,10", merge(norm(variant), norm(variant2)));
+        checkVcf("1 1001 . GTATATTGTG   G,GT   . . . GT:AD  ./.:.         ./.:.          0/1:1,10,1,0 2/2:1,1,10,0", merge(norm(variant2), norm(variant)));
+        checkVcf("1 1000 . AGTATATTGTG  AG,AGT . . . GT:AD  1/1:10,10,0,0 0/1:0,10,0,0   ./.:.        2/2:1,0,1,10", merge(norm(variant), norm(variant2, 1)));
     }
 
     @Test