From b07e613546c3c1fd6534070ac4558581cb4213f7 Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Thu, 30 Nov 2023 20:19:13 -0800
Subject: [PATCH] hub updates

---
 dev/ucsc/hub.html   | 4 ++--
 js/bigwig/trix.js   | 3 ++-
 js/genome/fasta.js  | 7 +++++++
 js/genome/genome.js | 9 ++++-----
 test/testUCSC.js    | 4 ++++
 5 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/dev/ucsc/hub.html b/dev/ucsc/hub.html
index d6f96a44f..c0acd6238 100644
--- a/dev/ucsc/hub.html
+++ b/dev/ucsc/hub.html
@@ -17,7 +17,7 @@
     </option>
     <option value="https://hgdownload.soe.ucsc.edu/hubs/GCF/013/103/735/GCF_013103735.1/hub.txt">24 large chromosomes
     </option>
-    <option value="https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt">T2T</option>
+    <option value="">T2T</option>
 </select>
 
 <label>
@@ -43,7 +43,7 @@
         includeTracks: true
     }
 
-    const hub = await Hub.loadHub("https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt", hubOptions)
+    const hub = await Hub.loadHub("", hubOptions)
 
     const igvConfig = {
         reference: hub.getGenomeConfig(),
diff --git a/js/bigwig/trix.js b/js/bigwig/trix.js
index 533e0016a..1e841d85b 100644
--- a/js/bigwig/trix.js
+++ b/js/bigwig/trix.js
@@ -100,7 +100,8 @@ export default class Trix {
         const indexes = await this.getIndex(opts)
         for (let i = 0; i < indexes.length; i++) {
             const [key, value] = indexes[i]
-            const trimmedKey = key.slice(0, searchWord.length)
+            const trimmedEnd = Math.min(key.length, searchWord.length)
+            const trimmedKey = key.slice(0, trimmedEnd)
             if (trimmedKey < searchWord) {
                 start = value
                 end = value + 65536
diff --git a/js/genome/fasta.js b/js/genome/fasta.js
index df8f589af..6fd5b7bbc 100644
--- a/js/genome/fasta.js
+++ b/js/genome/fasta.js
@@ -5,6 +5,13 @@ import ChromSizes from "./chromSizes.js"
 import Twobit from "./twobit.js"
 import CachedSequence from "./cachedSequence.js"
 
+/**
+ * Create a sequence object.  The referenced object can include multiple sequence references, in particular
+ * fasta and 2bit URLs.  This is for backward compatibility, the 2bit URL has preference.
+ *
+ * @param reference
+ * @returns {Promise<CachedSequence|ChromSizes|NonIndexedFasta>}
+ */
 async function loadSequence(reference) {
 
     let fasta
diff --git a/js/genome/genome.js b/js/genome/genome.js
index 8f52e9af9..54587b483 100644
--- a/js/genome/genome.js
+++ b/js/genome/genome.js
@@ -42,12 +42,12 @@ class Genome {
 
         this.sequence = await loadSequence(config)
 
-        if (config.chromSizes) {
+        if (config.chromSizesURL) {
             // a chromSizes file is neccessary for 2bit sequences for whole-genome view or chromosome pulldown
-            this.chromosomes = await loadChromSizes(config.chromSizes)
+            this.chromosomes = await loadChromSizes(config.chromSizesURL)
         } else {
             // if the sequence defines chromosomes use them (fasta does, 2bit does not)
-            this.chromosomes = this.sequence.chromosomes || new Map() // This might be undefined, depending on sequence type
+            this.chromosomes = this.sequence.chromosomes || new Map()
         }
 
         if (this.chromosomes.size > 0) {
@@ -144,9 +144,8 @@ class Genome {
 
     async loadChromosome(chr) {
 
-        let chromAliasRecord
         if (this.chromAlias) {
-            chromAliasRecord = await this.chromAlias.search(chr)
+           const chromAliasRecord = await this.chromAlias.search(chr)
             if(chromAliasRecord) {
                 chr = chromAliasRecord.chr
             }
diff --git a/test/testUCSC.js b/test/testUCSC.js
index cc27a396d..c70cfbe35 100644
--- a/test/testUCSC.js
+++ b/test/testUCSC.js
@@ -14,10 +14,14 @@ suite("ucsc utilities", function () {
         const trix = new Trix(ixxFile, ixFile)
         const results = await trix.search("ykoX")
         assert.ok(results)
+
         const exactMatches = results.get('ykox')
         assert.ok(exactMatches)
         assert.ok(exactMatches[0].startsWith('NP_389226.1'))
         console.log(results)
+
+        const nomatches = await trix.search("zzzz");
+        assert.isUndefined(nomatches);
     })
 
     test("test gene bb extra index search", async function () {