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GMOD · Dec 20, 2023 · 305e7d0 · 305e7d0
1 parent ce5b1c2
commit 305e7d0
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Showing 4 changed files with 26 additions and 15 deletions.
diff --git a/packages/core/assemblyManager/assembly.ts b/packages/core/assemblyManager/assembly.ts
@@ -60,10 +60,20 @@ async function loadRefNameMap(
   signal?: AbortSignal,
 ) {
   const { sessionId } = options
-  await when(() => !!(assembly.regions && assembly.refNameAliases), {
-    signal,
-    name: 'when assembly ready',
-  })
+
+  console.log('wpw', adapterConfig)
+  await when(
+    () =>
+      !!(
+        assembly.regions &&
+        assembly.refNameAliases &&
+        adapterConfig.sequenceAdapter
+      ),
+    {
+      signal,
+      name: 'when assembly ready',
+    },
+  )
 
   const refNames = (await assembly.rpcManager.call(
     sessionId || 'assemblyRpc',
@@ -82,10 +92,9 @@ async function loadRefNameMap(
   }
 
   const refNameMap = Object.fromEntries(
-    refNames.map(name => {
-      checkRefName(name)
-      return [assembly.getCanonicalRefName(name), name]
-    }),
+    refNames
+      .map(name => checkRefName(name))
+      .map(name => [assembly.getCanonicalRefName(name), name]),
   )
 
   // make the reversed map too
@@ -107,6 +116,7 @@ function checkRefName(refName: string) {
   if (!refNameRegex.test(refName)) {
     throw new Error(`Encountered invalid refName: "${refName}"`)
   }
+  return refName
 }
 
 type RefNameAliases = Record<string, string | undefined>

diff --git a/packages/core/pluggableElementTypes/models/baseTrackConfig.ts b/packages/core/pluggableElementTypes/models/baseTrackConfig.ts
@@ -234,9 +234,10 @@ export function createBaseTrackConfig(pluginManager: PluginManager) {
                   .filter(notEmpty),
               )
               const c = assemblyManager.get(assemblyNames[0])?.configuration
-              console.log({ c })
               if (c) {
-                self.adapter.setSequenceAdapter?.(readConfObject(c))
+                self.adapter.setSequenceAdapter?.(
+                  readConfObject(c.sequence.adapter),
+                )
               }
             }),
           )

diff --git a/plugins/alignments/src/CramAdapter/configSchema.ts b/plugins/alignments/src/CramAdapter/configSchema.ts
@@ -46,7 +46,7 @@ const configSchema = ConfigurationSchema(
      * generally refers to the reference genome assembly's sequence adapter
      * currently needs to be manually added
      */
-    sequenceAdapters: {
+    sequenceAdapter: {
       type: 'frozen',
       description: 'sequence data adapter',
       defaultValue: null,

diff --git a/plugins/alignments/src/LinearPileupDisplay/model.ts b/plugins/alignments/src/LinearPileupDisplay/model.ts
@@ -207,7 +207,9 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
          */
         renderReady() {
           const view = getContainingView(self) as LGV
+          console.log(self.adapterConfig.sequenceAdapter)
           return (
+            self.adapterConfig.sequenceAdapter &&
             self.modificationsReady &&
             self.currSortBpPerPx === view.bpPerPx &&
             superRenderReady()
@@ -338,10 +340,7 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
             if (!self.autorunReady) {
               return
             }
-
-            const { bpPerPx } = view
-
-            self.setCurrSortBpPerPx(bpPerPx)
+            self.setCurrSortBpPerPx(view.bpPerPx)
           },
           { delay: 1000 },
         )
@@ -362,6 +361,7 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
               (!sortReady || self.currSortBpPerPx === view.bpPerPx)
             ) {
               const { pos, refName, assemblyName } = sortedBy
+              console.log(adapterConfig)
               // render just the sorted region first
               // @ts-expect-error
               await self.rendererType.renderInClient(rpcManager, {