Fix usage of aliases for isValidRefName

[cmdcolin]

Currently on master searching chr5:1-100 does not work since chr5 is an alias

This fixes that.. This is a knock on from #1369

Note that having an integration test for this would be great. Have tried to do this here recently but didn't get it completed https://github.com/GMOD/jbrowse-components/compare/search_test

[garrettjstevens]

Agreed, would good to get an integration test for this as it was definitely working at one point. This fixes isValidRefName, but I'd also like to fix allRefNames, which appears to be why isValidRefName stopped working. Something like this, maybe:

diff --git a/packages/core/assemblyManager/assembly.ts b/packages/core/assemblyManager/assembly.ts
--- a/packages/core/assemblyManager/assembly.ts
+++ b/packages/core/assemblyManager/assembly.ts
@@ -155,9 +155,11 @@ export default function assemblyFactory(assemblyConfigType: IAnyType) {
         if (!(this.refNames && self.refNameAliases)) {
           return undefined
         }
-        let aliases: string[] = []
-        self.refNameAliases.forEach(aliasList => {
-          aliases = aliases.concat(aliasList)
+        const aliases: string[] = []
+        self.refNameAliases.forEach((_canonicalName, alias) => {
+          if (!this.refNames?.includes(alias)) {
+            aliases.push(alias)
+          }
         })
         return [...this.refNames, ...aliases]
       },

[garrettjstevens]

Oh wait, didn't realize this was already merged. I'll open a separate PR.