Hubs 3 (#1722)

* fix problem with genome name aliasing * refinements to hub loading -- as "genome" => only sequence, cytoband, and tracks in group "genes" -- as "session" => all tracks in hubs.txt not marked "visibility=hide".
igvteam · Oct 26, 2023 · 7209cd6 · 7209cd6
1 parent e318ae7
commit 7209cd6
Show file tree

Hide file tree

Showing 13 changed files with 194 additions and 454 deletions.
diff --git a/dev/tnt/chm13v2.0.html b/dev/tnt/chm13v2.0.html
diff --git a/dev/twobit/twobit_aliasBB.html b/dev/twobit/twobit_aliasBB.html
diff --git a/dev/twobit/twobit_basic.html b/dev/twobit/twobit_basic.html
diff --git a/dev/twobit/twobit_chromSizes.html b/dev/twobit/twobit_chromSizes.html
diff --git a/dev/twobit/twobit_t2t.html b/dev/twobit/twobit_t2t.html
diff --git a/dev/ucsc/hub.html b/dev/ucsc/hub.html
@@ -38,21 +38,29 @@
         includeTracks: true
     }
 
-    const hub = await Hub.loadHub("https://hgdownload.soe.ucsc.edu/hubs/GCA/018/471/515/GCA_018471515.1/hub.txt", hubOptions)
+    const hub = await Hub.loadHub("https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt", hubOptions)
     const ref = hub.getGenomeConfig()
 
     const igvConfig = {
-        locus: hub.getDefaultPosition(),
-        showChromosomeWidget: false,
         reference: ref
     }
 
+    // for(let tc of hub.getTrackConfigurations()) {
+    //     for(let t of tc.tracks) {
+    //         if(t.url.endsWith("undefined")) console.log(`${tc.label}  ${t.name}  ${t.url}`)
+    //     }
+    // }
+
     const browser = await igv.createBrowser(document.getElementById('igvDiv'), igvConfig)
 
     const selector = document.getElementById("select")
     selector.addEventListener("change", () => document.getElementById("hub-input").value = selector.value)
+
+    document.getElementById("hub-input").value = "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt"
+
     document.getElementById("load-genome").addEventListener("click", () =>
         browser.loadGenome({url: document.getElementById("hub-input").value}))
+
     document.getElementById("load-session").addEventListener("click", () =>
         browser.loadSession({url: document.getElementById("hub-input").value}))
 

diff --git a/dev/twobit/twobit.html → dev/ucsc/twobit.html b/dev/twobit/twobit.html → dev/ucsc/twobit.html