Merge pull request #199 from BimberLab/discvr-22.11

Merge 22.11 to 23.3

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/ChainFileValidator.java

@@ -295,7 +295,18 @@ private String resolveSequenceId(String refName, int genomeId)
                 @Override
                 public void exec(ResultSet rs) throws SQLException
                 {
-                    cachedReferences.put(rs.getString("name"), rs.getString("name"));
+                    String name = rs.getString("name");
+                    cachedReferences.put(name, name);
+
+                    // Always store the numeric version, if present:
+                    if (name.startsWith("chr0"))
+                    {
+                        cachedReferences.put(name.replaceAll("chr0", ""), name);
+                    }
+                    else if (name.startsWith("chr"))
+                    {
+                        cachedReferences.put(name.replaceAll("chr", ""), name);
+                    }
 
                     if (StringUtils.trimToNull(rs.getString("genbank")) != null)
                     {
@@ -346,6 +357,12 @@ public void exec(Results rs) throws SQLException
             {
                 return cachedReferences.get(toTest);
             }
+
+            toTest = refName.replaceFirst("chr0", "chr");
+            if (cachedReferences.containsKey(toTest))
+            {
+                return cachedReferences.get(toTest);
+            }
         }
 
         if (refName.startsWith("chr"))