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GMOD · Feb 4, 2025 · 6f53fbd · 6f53fbd
1 parent 2b057d3
commit 6f53fbd
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Showing 2 changed files with 68 additions and 52 deletions.
diff --git a/plugins/alignments/src/BamAdapter/BamAdapter.ts b/plugins/alignments/src/BamAdapter/BamAdapter.ts
@@ -83,35 +83,40 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
   private async setupPre(opts?: BaseOptions) {
     const { statusCallback = () => {} } = opts || {}
     const { bam } = await this.configure()
+    console.log('wow')
     this.samHeader = await updateStatus(
       'Downloading index',
       statusCallback,
       async () => {
-        const samHeader = await bam.getHeader()
-
-        // use the @SQ lines in the header to figure out the
-        // mapping between ref ref ID numbers and names
-        const idToName: string[] = []
-        const nameToId: Record<string, number> = {}
-        samHeader
-          ?.filter(l => l.tag === 'SQ')
-          .forEach((sqLine, refId) => {
-            const SN = sqLine.data.find(item => item.tag === 'SN')
-            if (SN) {
-              // this is the ref name
-              const refName = SN.value
-              nameToId[refName] = refId
-              idToName[refId] = refName
-            }
-          })
-
-        return { idToName, nameToId }
+        return new Promise(res =>
+          setTimeout(async () => {
+            const samHeader = await bam.getHeader()
+
+            // use the @SQ lines in the header to figure out the
+            // mapping between ref ref ID numbers and names
+            const idToName: string[] = []
+            const nameToId: Record<string, number> = {}
+            samHeader
+              ?.filter(l => l.tag === 'SQ')
+              .forEach((sqLine, refId) => {
+                const SN = sqLine.data.find(item => item.tag === 'SN')
+                if (SN) {
+                  // this is the ref name
+                  const refName = SN.value
+                  nameToId[refName] = refId
+                  idToName[refId] = refName
+                }
+              })
+
+            res({ idToName, nameToId })
+          }, 4000),
+        )
       },
     )
     return this.samHeader
   }
 
-  async setup(opts?: BaseOptions) {
+  async setupPre2(opts?: BaseOptions) {
     if (!this.setupP) {
       this.setupP = this.setupPre(opts).catch((e: unknown) => {
         this.setupP = undefined
@@ -121,6 +126,13 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     return this.setupP
   }
 
+  async setup(opts?: BaseOptions) {
+    const { statusCallback = () => {} } = opts || {}
+    return updateStatus('Downloading index', statusCallback, () =>
+      this.setupPre2(opts),
+    )
+  }
+
   async getRefNames(opts?: BaseOptions) {
     const { idToName } = await this.setup(opts)
     return idToName

diff --git a/plugins/alignments/src/CramAdapter/CramAdapter.ts b/plugins/alignments/src/CramAdapter/CramAdapter.ts
@@ -148,42 +148,39 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     return sequence
   }
 
-  private async setupPre(opts?: BaseOptions) {
-    const { statusCallback = () => {} } = opts || {}
-    return updateStatus('Downloading index', statusCallback, async () => {
-      const conf = await this.configure()
-      const { cram } = conf
-      const samHeader = await cram.cram.getSamHeader()
-
-      // use the @SQ lines in the header to figure out the mapping between ref
-      // ID numbers and names
-      const idToName: string[] = []
-      const nameToId: Record<string, number> = {}
-      samHeader
-        .filter(l => l.tag === 'SQ')
-        .forEach((sqLine, refId) => {
-          const SN = sqLine.data.find(item => item.tag === 'SN')
-          if (SN) {
-            const refName = SN.value
-            nameToId[refName] = refId
-            idToName[refId] = refName
-          }
-        })
+  private async setupPre(_opts?: BaseOptions) {
+    const conf = await this.configure()
+    const { cram } = conf
+    const samHeader = await cram.cram.getSamHeader()
+
+    // use the @SQ lines in the header to figure out the mapping between ref
+    // ID numbers and names
+    const idToName: string[] = []
+    const nameToId: Record<string, number> = {}
+    samHeader
+      .filter(l => l.tag === 'SQ')
+      .forEach((sqLine, refId) => {
+        const SN = sqLine.data.find(item => item.tag === 'SN')
+        if (SN) {
+          const refName = SN.value
+          nameToId[refName] = refId
+          idToName[refId] = refName
+        }
+      })
 
-      const readGroups = samHeader
-        .filter(l => l.tag === 'RG')
-        .map(rgLine => rgLine.data.find(item => item.tag === 'ID')?.value)
+    const readGroups = samHeader
+      .filter(l => l.tag === 'RG')
+      .map(rgLine => rgLine.data.find(item => item.tag === 'ID')?.value)
 
-      const data = { idToName, nameToId, readGroups }
-      this.samHeader = data
-      return {
-        samHeader: data,
-        ...conf,
-      }
-    })
+    const data = { idToName, nameToId, readGroups }
+    this.samHeader = data
+    return {
+      samHeader: data,
+      ...conf,
+    }
   }
 
-  private async setup(opts?: BaseOptions) {
+  private async setupPre2(opts?: BaseOptions) {
     if (!this.setupP) {
       this.setupP = this.setupPre(opts).catch((e: unknown) => {
         this.setupP = undefined
@@ -193,6 +190,13 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     return this.setupP
   }
 
+  async setup(opts?: BaseOptions) {
+    const { statusCallback = () => {} } = opts || {}
+    return updateStatus('Downloading index', statusCallback, () =>
+      this.setupPre2(opts),
+    )
+  }
+
   async getRefNames(opts?: BaseOptions) {
     const { samHeader } = await this.setup(opts)
     if (!samHeader.idToName) {