Merge pull request #2317 from opencb/TASK-4816

TASK-4816 - Error fetching original call for INDELs export step from exomiser from complex contigs
opencb · Jul 31, 2023 · 41b33a1 · 41b33a1
2 parents d69eb73 + 45fd837
commit 41b33a1
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Showing 2 changed files with 20 additions and 5 deletions.
diff --git a/...e-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryUtils.java b/...e-core/src/main/java/org/opencb/opencga/storage/core/variant/query/VariantQueryUtils.java
@@ -25,6 +25,7 @@
 import org.opencb.biodata.models.core.Region;
 import org.opencb.biodata.models.variant.StudyEntry;
 import org.opencb.biodata.models.variant.Variant;
+import org.opencb.biodata.models.variant.VariantBuilder;
 import org.opencb.biodata.models.variant.annotation.ConsequenceTypeMappings;
 import org.opencb.biodata.models.variant.avro.*;
 import org.opencb.commons.datastore.core.*;
@@ -515,9 +516,18 @@ public static boolean isHpo(String value) {
      */
     public static boolean isVariantId(String value) {
         int count = StringUtils.countMatches(value, ':');
-        return count == 3
-                // It may have more colons if is a symbolic alternate like <DUP:TANDEM>, or a breakend 4:100:C:]15:300]A
-                || count > 3 && StringUtils.containsAny(value, '<', '[', ']');
+        if (count == 3) {
+            return true;
+        }
+        if (count > 3) {
+            try {
+                new VariantBuilder(value);
+            } catch (RuntimeException e) {
+                return false;
+            }
+            return true;
+        }
+        return false;
     }
 
     /**

diff --git a/...src/test/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQueryUtilsTest.java b/...src/test/java/org/opencb/opencga/storage/core/variant/adaptors/VariantQueryUtilsTest.java
@@ -435,22 +435,27 @@ public void isVariantId() {
         checkIsVariantId("1:1000:A:T");
         checkIsVariantId("1:1000-2000:A:T");
         checkIsVariantId("1:1000-2000:A:<DUP:TANDEM>");
+        checkIsVariantId("HLA-DRB1*04:03:01:3349:GAGACAGAG:-", true);
+        checkIsVariantId("HLA-DRB1*04:03:01:3349:GAGACAGAG:-:2", false);
         checkIsVariantId("11:14525312:-:]11:14521700].");
         checkIsVariantId("4:100:C:[15:300[A");
         checkIsVariantId("4:100:C:]15:300]A");
         checkIsVariantId("rs123");
     }
 
     public void checkIsVariantId(String v) {
-
-        boolean actual = VariantQueryUtils.isVariantId(v);
         boolean expected;
         try {
             new Variant(v);
             expected = true;
         } catch (Exception e) {
             expected = false;
         }
+        checkIsVariantId(v, expected);
+    }
+
+    public void checkIsVariantId(String v, boolean expected) {
+        boolean actual = VariantQueryUtils.isVariantId(v);
         assertEquals(v, expected, actual);
     }