From 0ea57ce23ff978061243b2bbc3f6985ff64fcd54 Mon Sep 17 00:00:00 2001
From: Jim Robinson <933148+jrobinso@users.noreply.github.com>
Date: Thu, 30 Nov 2023 20:30:00 -0800
Subject: [PATCH] Hub2 (#1738)

* misc bug fixes

* hub updates

* fix unit test
---
 dev/ucsc/genomes.html           |  49 ++++++++++++
 dev/ucsc/hub.html               |   4 +-
 js/bigwig/bwReader.js           |  19 +----
 js/bigwig/bwSource.js           |  11 +--
 js/bigwig/trix.js               |   3 +-
 js/browser.js                   |   4 +-
 js/genome/chromAliasBB.js       |  17 ++--
 js/genome/chromAliasDefaults.js | 138 ++++++++++++++++++++++++++++++++
 js/genome/chromAliasFile.js     |  19 ++++-
 js/genome/fasta.js              |  11 ++-
 js/genome/genome.js             |  60 +++++++-------
 js/sequenceTrack.js             |   4 +-
 test/testChromAlias.js          |  61 +++++++++++++-
 test/testCytobands.js           |  10 ---
 test/testFasta.js               |  10 +--
 test/testGenome.js              |   2 +-
 test/testUCSC.js                |   4 +
 17 files changed, 335 insertions(+), 91 deletions(-)
 create mode 100644 dev/ucsc/genomes.html
 create mode 100644 js/genome/chromAliasDefaults.js
diff --git a/dev/ucsc/genomes.html b/dev/ucsc/genomes.html
new file mode 100644
index 000000000..53c99d0ce
--- /dev/null
+++ b/dev/ucsc/genomes.html
@@ -0,0 +1,49 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <title>twobit</title>
+</head>
+
+<body>
+
+<select id="select">
+    <option value=""></option>
+    <option value="gorGor4">gorGor4</option>
+    <option value="gorGor6">gorGor6</option>
+</select>
+<button id="load-genome">Load  genome</button>
+<br>
+
+
+<div id="igvDiv" style="padding-top: 50px;padding-bottom: 20px; height: auto"></div>
+
+<script type="module">
+
+    import igv from "../../js/index.js"
+    import Hub from "../../js/ucsc/ucscHub.js"
+
+
+    const igvConfig = {
+        genome: "gorGor4",
+        listeners: {
+            'genomechange': ({genome, trackConfigurations}) => {
+                console.log('genomechange')
+                console.log(genome)
+                console.log(trackConfigurations)
+            }
+        }
+    }
+
+
+    const browser = await igv.createBrowser(document.getElementById('igvDiv'), igvConfig)
+
+    document.getElementById("load-genome").addEventListener("click", async () => {
+        await browser.loadGenome(document.getElementById("select").value)
+    })
+
+
+</script>
+
+</body>
+
+</html>
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/bwReader.js b/js/bigwig/bwReader.js
index edba6dd67..ebd6117b5 100644
--- a/js/bigwig/bwReader.js
+++ b/js/bigwig/bwReader.js
@@ -345,6 +345,7 @@ class BWReader {
             const nZooms = header.nZoomLevels
             binaryParser = new BinaryParser(new DataView(data), this.littleEndian)
 
+            // Load zoom headers, store in order of decreasing reduction level (increasing resolution)
             this.zoomLevelHeaders = []
             this.firstZoomDataOffset = Number.MAX_SAFE_INTEGER
             for (let i = 1; i <= nZooms; i++) {
@@ -393,11 +394,7 @@ class BWReader {
             if (header.extensionOffset > 0) {
                 await this.loadExtendedHeader(header.extensionOffset)
             }
-
-            this.setDefaultVisibilityWindow(header)
-
-
-            return this.header
+          return this.header
         }
     }
 
@@ -478,16 +475,6 @@ class BWReader {
         }
     }
 
-    setDefaultVisibilityWindow(header) {
-        if (this.type === "bigwig") {
-            this.visibilityWindow = -1
-        } else {
-            this.visibilityWindow = -1
-            // bigbed -- todo
-
-        }
-    }
-
     /**
      * Directly load features given a file offset and size.  Added to support search index.
      * @param offset
@@ -660,7 +647,6 @@ function decodeZoomData(data, chrIdx1, bpStart, chrIdx2, bpEnd, featureArray, ch
 
     while (binaryParser.remLength() >= minSize) {
         const chromId = binaryParser.getInt()
-        const chr = chrDict[chromId]
         const chromStart = binaryParser.getInt()
         const chromEnd = binaryParser.getInt()
         const validCount = binaryParser.getInt()
@@ -685,6 +671,7 @@ function decodeZoomData(data, chrIdx1, bpStart, chrIdx2, bpEnd, featureArray, ch
 
 
         if (Number.isFinite(value)) {
+            const chr = chrDict[chromId]
             featureArray.push({chr: chr, start: chromStart, end: chromEnd, value: value})
 
 
diff --git a/js/bigwig/bwSource.js b/js/bigwig/bwSource.js
index 8c8577c75..7b153374f 100755
--- a/js/bigwig/bwSource.js
+++ b/js/bigwig/bwSource.js
@@ -56,16 +56,13 @@ class BWSource {
         return this.reader.loadHeader()
     }
 
-    getDefaultRange() {
-        if (this.reader.totalSummary !== undefined) {
-            return this.reader.totalSummary.defaultRange
+    async defaultVisibilityWindow() {
+        if (this.reader.type === "bigwig") {
+            return -1
         } else {
-            return undefined
+            return this.reader.featureDensity ?  Math.floor(10000 / this.reader.featureDensity) : -1
         }
-    }
 
-    async defaultVisibilityWindow() {
-        return Math.floor(10000 / this.reader.featureDensity)
     }
 
     async getWGValues(windowFunction) {
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/browser.js b/js/browser.js
index 88b23d65f..b130a0036 100755
--- a/js/browser.js
+++ b/js/browser.js
@@ -764,8 +764,10 @@ class Browser {
         if (idOrConfig.url && StringUtils.isString(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt")) {
             const hub = await Hub.loadHub(idOrConfig.url, idOrConfig)
             genomeConfig = hub.getGenomeConfig("genes")
+        } else if (StringUtils.isString(idOrConfig)) {
+            genomeConfig = await GenomeUtils.expandReference(this.alert, idOrConfig)
         } else {
-            genomeConfig = idOrConfig //await GenomeUtils.expandReference(this.alert, idOrConfig)
+            genomeConfig = idOrConfig
         }
 
         await this.loadReference(genomeConfig)
diff --git a/js/genome/chromAliasBB.js b/js/genome/chromAliasBB.js
index d3ff4cce6..dfa14442f 100644
--- a/js/genome/chromAliasBB.js
+++ b/js/genome/chromAliasBB.js
@@ -1,15 +1,13 @@
+import BWReader from "../bigwig/bwReader.js"
+
 /**
- * Represenets a UCSC bigbed alias file
+ * Chromosome alias source backed by a UCSC bigbed file
  *
  *
  * @param aliasURL
  * @param config
  * @returns {Promise<*[]>}
  */
-import {isNumber, buildOptions} from "../util/igvUtils.js"
-import {igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
-import BWSource from "../bigwig/bwSource.js"
-import BWReader from "../bigwig/bwReader.js"
 
 class ChromAliasBB {
 
@@ -22,7 +20,9 @@ class ChromAliasBB {
     }
 
     /**
-     * Return the canonical chromosome name for the alias.  If none found return the alias
+     * Return the canonical chromosome name for the alias.  If none found return the alias.
+     *
+     * Note this will only work if a "search" for ths chromosome has been performed previously.
      *
      * @param alias
      * @returns {*}
@@ -33,6 +33,9 @@ class ChromAliasBB {
 
     /**
      * Return an alternate chromosome name (alias).  If not exists, return chr
+     *
+     * Note this will only work if a "search" for ths chromosome has been performed previously.
+     *
      * @param chr
      * @param nameSet -- The name set, e.g. "ucsc"
      * @returns {*|undefined}
@@ -44,7 +47,7 @@ class ChromAliasBB {
     }
 
     /**
-     * Search for chromosome alias bed record.  If found, catch results in the alias -> chr map
+     * Search for chromosome alias bed record.  If found, cache results in the alias -> chr map
      * @param alias
      * @returns {Promise<any>}
      */
diff --git a/js/genome/chromAliasDefaults.js b/js/genome/chromAliasDefaults.js
new file mode 100644
index 000000000..b6294df71
--- /dev/null
+++ b/js/genome/chromAliasDefaults.js
@@ -0,0 +1,138 @@
+/**
+ * Default chromosome aliases, mostly 1<->chr1 etc.  Used if chrom alias file is not supplied.
+ *
+ */
+import {isNumber, buildOptions} from "../util/igvUtils.js"
+import {igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
+
+class ChromAliasDefaults {
+
+    aliasRecordCache = new Map()
+
+    constructor(id, chromosomeNames) {
+        this.init(id, chromosomeNames)
+    }
+
+    /**
+     * Return the canonical chromosome name for the alias.  If none found return the alias
+     *
+     * @param alias
+     * @returns {*}
+     */
+    getChromosomeName(alias) {
+        return this.aliasRecordCache.has(alias) ? this.aliasRecordCache.get(alias).chr : alias
+    }
+
+    /**
+     * Return an alternate chromosome name (alias).
+     *
+     * @param chr
+     * @param nameSet -- The name set, e.g. "ucsc"
+     * @returns {*|undefined}
+     */
+    getChromosomeAlias(chr, nameSet)
+    {
+        const aliasRecord =  this.aliasRecordCache.get(chr)
+        return aliasRecord ? aliasRecord[nameSet] || chr : chr
+    }
+
+    init(id, chromosomeNames) {
+
+        const aliasRecords = []
+        for (let name of chromosomeNames) {
+
+            let skipRest = false
+            const record = {chr: name}
+            aliasRecords.push(record)
+
+            if (name.startsWith("gi|")) {
+                // NCBI
+                const alias = ChromAliasDefaults.getNCBIName(name)
+                record["ncbi-gi-versioned"] = alias
+
+                // Also strip version number out, if present
+                const dotIndex = alias.lastIndexOf('.')
+                if (dotIndex > 0) {
+                    const alias = alias.substring(0, dotIndex)
+                    record["ncbi-gi"] = alias
+                }
+            } else {
+                // Special cases for human and mouse
+                if (id.startsWith("hg") || id.startsWith("GRCh") || id === "1kg_ref" || id === "b37") {
+                    switch (name) {
+                        case "23":
+                            record["ucsc"] = "chrX"
+                            skipRest = true
+                            break
+                        case "24":
+                            record["ucsc"] = "chrY"
+                            skipRest = true
+                            break
+                        case "chrX":
+                            record["ncbi"] = "23"
+                            skipRest = true
+                            break
+                        case "chrY":
+                            record["ncbi"] = "24"
+                            skipRest = true
+                            break
+                    }
+                } else if (id.startsWith("mm") || id.startsWith("GRCm") || id.startsWith("rheMac")) {
+                    switch (name) {
+                        case "21":
+                            record["ucsc"] = "chrX"
+                            skipRest = true
+                            break
+                        case "22":
+                            record["ucsc"] = "chrY"
+                            skipRest = true
+                            break
+                        case "chrX":
+                            record["ncbi"] = "21"
+                            skipRest = true
+                            break
+                        case "chrY":
+                            record["ncbi"] = "22"
+                            skipRest = true
+                            break
+                    }
+                }
+                if (skipRest) continue
+
+                //
+                if (name === "chrM") {
+                    record["ncbi"] = "MT"
+                } else if (name === "MT") {
+                    record["ucsc"] = "chrM"
+                } else if (name.toLowerCase().startsWith("chr")) {
+                    record["ncbi"] = name.substring(3)
+                } else if (Number.isInteger(Number(name))) {
+                    record["ucsc"] = "chr" + name
+                }
+            }
+        }
+
+        for (let rec of aliasRecords) {
+            for (let a of Object.values(rec)) {
+                this.aliasRecordCache.set(a, rec)
+            }
+        }
+    }
+
+    search(alias) {
+        return this.aliasRecordCache.get(alias)
+
+    }
+
+    /**
+     * Extract the user friendly name from an NCBI accession
+     * example: gi|125745044|ref|NC_002229.3|  =>  NC_002229.3
+     */
+    static getNCBIName(name) {
+        const tokens = name.split("\\|")
+        return tokens[tokens.length - 1]
+    }
+
+}
+
+export default ChromAliasDefaults
diff --git a/js/genome/chromAliasFile.js b/js/genome/chromAliasFile.js
index fdb7ef49b..4a80ada14 100644
--- a/js/genome/chromAliasFile.js
+++ b/js/genome/chromAliasFile.js
@@ -32,6 +32,18 @@ class ChromAliasFile {
         return this.aliasRecordCache.has(alias) ? this.aliasRecordCache.get(alias).chr : alias
     }
 
+    /**
+     * Return an alternate chromosome name (alias).  If not exists, return chr
+     * @param chr
+     * @param nameSet -- The name set, e.g. "ucsc"
+     * @returns {*|undefined}
+     */
+    getChromosomeAlias(chr, nameSet)
+    {
+        const aliasRecord =  this.aliasRecordCache.get(chr)
+        return aliasRecord ? aliasRecord[nameSet] || chr : chr
+    }
+
 
     async loadAliases() {
 
@@ -39,17 +51,18 @@ class ChromAliasFile {
         const lines = StringUtils.splitLines(data)
         const firstLine = lines[0]
         if (firstLine.startsWith("#")) {
-            this.headings = firstLine.split("\t").map(h => h.trim())
+            this.headings = firstLine.substring(1).split("\t").map(h => h.trim())
             this.altNameSets = this.headings.slice(1)
         }
 
-        const chromosomeNameSet = this.genome.chromosomes ?
-            new Set(this.genome.chromosomes.keys()) : new Set()
+        const chromosomeNameSet = this.genome.chromosomeNames ?
+            new Set(this.genome.chromosomeNames) : new Set()
 
         for (let line of lines) {
             if (!line.startsWith("#") && line.length > 0) {
                 const tokens = line.split("\t")
 
+                // Find the canonical chromosome
                 let chr = tokens.find(t => chromosomeNameSet.has(t))
                 if(!chr) {
                     chr = tokens[0]
diff --git a/js/genome/fasta.js b/js/genome/fasta.js
index 4e4aa6b42..6fd5b7bbc 100644
--- a/js/genome/fasta.js
+++ b/js/genome/fasta.js
@@ -5,7 +5,14 @@ import ChromSizes from "./chromSizes.js"
 import Twobit from "./twobit.js"
 import CachedSequence from "./cachedSequence.js"
 
-async function loadFasta(reference) {
+/**
+ * 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
     if ("chromsizes" === reference.format) {
@@ -21,4 +28,4 @@ async function loadFasta(reference) {
     return fasta
 }
 
-export {loadFasta}
+export {loadSequence}
diff --git a/js/genome/genome.js b/js/genome/genome.js
index 7002766d0..54587b483 100644
--- a/js/genome/genome.js
+++ b/js/genome/genome.js
@@ -1,12 +1,13 @@
 import {StringUtils} from "../../node_modules/igv-utils/src/index.js"
 import Chromosome from "./chromosome.js"
-import {loadFasta} from "./fasta.js"
+import {loadSequence} from "./fasta.js"
 import ChromAliasBB from "./chromAliasBB.js"
 import ChromAliasFile from "./chromAliasFile.js"
 import CytobandFileBB from "./cytobandFileBB.js"
 import CytobandFile from "./cytobandFile.js"
 
 import {loadChromSizes} from "./chromSizes.js"
+import ChromAliasDefaults from "./chromAliasDefaults.js"
 
 /**
  * The Genome class represents an assembly and consists of the following elements
@@ -18,6 +19,8 @@ import {loadChromSizes} from "./chromSizes.js"
 
 class Genome {
 
+    #wgChromosomeNames
+
     static async createGenome(options) {
 
         const genome = new Genome(options)
@@ -37,16 +40,16 @@ class Genome {
 
         const config = this.config
 
-        this.sequence = await loadFasta(config)
+        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 {
-            this.chromosomes = this.sequence.chromosomes || new Map() // This might be undefined, depending on sequence type
+            // if the sequence defines chromosomes use them (fasta does, 2bit does not)
+            this.chromosomes = this.sequence.chromosomes || new Map()
         }
 
-        // For backward compatibility
         if (this.chromosomes.size > 0) {
             this.chromosomeNames = Array.from(this.chromosomes.keys())
         }
@@ -55,6 +58,8 @@ class Genome {
             this.chromAlias = new ChromAliasBB(config.chromAliasBbURL, Object.assign({}, config), this)
         } else if (config.aliasURL) {
             this.chromAlias = new ChromAliasFile(config.aliasURL, Object.assign({}, config), this)
+        } else {
+            this.chromAlias = new ChromAliasDefaults(this.id, this.chromosomeNames);
         }
 
         if (config.cytobandBbURL) {
@@ -67,19 +72,19 @@ class Genome {
             // Set chromosome order for WG view and chromosome pulldown.  If chromosome order is not specified sort
             if (config.chromosomeOrder) {
                 if (Array.isArray(config.chromosomeOrder)) {
-                    this.wgChromosomeNames = config.chromosomeOrder
+                    this.#wgChromosomeNames = config.chromosomeOrder
                 } else {
-                    this.wgChromosomeNames = config.chromosomeOrder.split(',').map(nm => nm.trim())
+                    this.#wgChromosomeNames = config.chromosomeOrder.split(',').map(nm => nm.trim())
                 }
             } else {
-                this.wgChromosomeNames = trimSmallChromosomes(this.chromosomes)
+                this.#wgChromosomeNames = trimSmallChromosomes(this.chromosomes)
             }
         }
 
         // Optionally create the psuedo chromosome "all" to support whole genome view
-        this.wholeGenomeView = config.wholeGenomeView !== false && this.wgChromosomeNames && this.chromosomes.size > 1
+        this.wholeGenomeView = config.wholeGenomeView !== false && this.#wgChromosomeNames && this.chromosomes.size > 1
         if (this.wholeGenomeView) {
-            const l = this.wgChromosomeNames.reduce((accumulator, currentValue) => accumulator += this.chromosomes.get(currentValue).bpLength, 0)
+            const l = this.#wgChromosomeNames.reduce((accumulator, currentValue) => accumulator += this.chromosomes.get(currentValue).bpLength, 0)
             this.chromosomes.set("all", new Chromosome("all", 0, l))
         }
     }
@@ -114,8 +119,7 @@ class Genome {
         if (this.showWholeGenomeView() && this.chromosomes.has("all")) {
             return "all"
         } else {
-            return this.sequence.getFirstChromosomeName()
-
+            return this.chromosomeNames[0]
         }
     }
 
@@ -140,9 +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
             }
@@ -160,14 +163,12 @@ class Genome {
 
         return this.chromosomes.get(chr)
     }
-
     async getAliasRecord(chr) {
         if (this.chromAlias) {
             return this.chromAlias.search(chr)
         }
     }
 
-
     getCytobands(chr) {
         if (this.cytobandSource) {
             const chrName = this.getChromosomeName(chr)
@@ -179,6 +180,10 @@ class Genome {
         return this.chromosomes
     }
 
+    get wgChromosomeNames() {
+        return this.#wgChromosomeNames.slice()
+    }
+
     /**
      * Return the genome coordinate in kb for the give chromosome and position.
      * NOTE: This might return undefined if the chr is filtered from whole genome view.
@@ -202,7 +207,7 @@ class Genome {
 
         let lastChr = undefined
         let lastCoord = 0
-        for (let name of this.wgChromosomeNames) {
+        for (let name of this.#wgChromosomeNames) {
 
             const cumulativeOffset = this.cumulativeOffsets[name]
             if (cumulativeOffset > genomeCoordinate) {
@@ -214,7 +219,7 @@ class Genome {
         }
 
         // If we get here off the end
-        return {chr: this.wgChromosomeNames[this.wgChromosomeNames.length - 1], position: 0}
+        return {chr: this.#wgChromosomeNames[this.#wgChromosomeNames.length - 1], position: 0}
 
     };
 
@@ -234,15 +239,11 @@ class Genome {
 
         function computeCumulativeOffsets() {
 
-            let self = this
             let acc = {}
             let offset = 0
-            for (let name of self.wgChromosomeNames) {
-
+            for (let name of this.#wgChromosomeNames) {
                 acc[name] = Math.floor(offset)
-
-                const chromosome = self.getChromosome(name)
-
+                const chromosome = this.getChromosome(name)
                 offset += chromosome.bpLength
             }
 
@@ -257,7 +258,7 @@ class Genome {
 
         if (!this.bpLength) {
             let bpLength = 0
-            for (let cname of this.wgChromosomeNames) {
+            for (let cname of this.#wgChromosomeNames) {
                 let c = this.chromosomes.get(cname)
                 bpLength += c.bpLength
             }
@@ -271,13 +272,6 @@ class Genome {
         return this.sequence.getSequence(chr, start, end)
     }
 
-    constructWG(config) {
-
-        // Compute psuedo-chromosome "all"
-        const l = this.wgChromosomeNames.reduce((accumulator, currentValue) => accumulator += this.chromosomes.get(currentValue).bpLength, 0)
-        this.chromosomes.set("all", new Chromosome("all", 0, l))
-    }
-
 }
 
 /**
diff --git a/js/sequenceTrack.js b/js/sequenceTrack.js
index cc17e0977..d697e2bd0 100755
--- a/js/sequenceTrack.js
+++ b/js/sequenceTrack.js
@@ -26,7 +26,7 @@
 import IGVGraphics from "./igv-canvas.js"
 import {isSecureContext} from "./util/igvUtils.js"
 import {reverseComplementSequence} from "./util/sequenceUtils.js"
-import {loadFasta} from "./genome/fasta.js"
+import {loadSequence} from "./genome/fasta.js"
 import {defaultNucleotideColors} from "./util/nucleotideColors.js";
 
 const defaultSequenceTrackOrder = Number.MIN_SAFE_INTEGER
@@ -441,7 +441,7 @@ class WrappedFasta {
     }
 
     async init() {
-        this.fasta = await loadFasta(this.config)
+        this.fasta = await loadSequence(this.config)
         this.chrNameMap = new Map()
         for(let name of this.fasta.chromosomeNames) {
             this.chrNameMap.set(this.genome.getChromosomeName(name), name)
diff --git a/test/testChromAlias.js b/test/testChromAlias.js
index d14bde29b..b57554fb4 100644
--- a/test/testChromAlias.js
+++ b/test/testChromAlias.js
@@ -2,6 +2,8 @@ import "./utils/mockObjects.js"
 import ChromAliasFile from "../js/genome/chromAliasFile.js"
 import BWReader from "../js/bigwig/bwReader.js"
 import {assert} from "chai"
+import ChromAliasDefaults from "../js/genome/chromAliasDefaults.js"
+import ChromAliasBB from "../js/genome/chromAliasBB.js"
 
 
 suite("chromAlias", function () {
@@ -9,7 +11,10 @@ suite("chromAlias", function () {
     const genome = {
         chromosomes: new Map([
             ["NC_007194.1", {name: "NC_007194.1", bpLength: 1}],
-        ])
+        ]),
+        getChromosomeName: function (ignore) {
+            return "NC_007194.1"
+        }
     }
 
     /**
@@ -35,6 +40,22 @@ suite("chromAlias", function () {
         assert.equal(chromAliasRecord.genbank, "CM000169.1")
         assert.equal(chromAliasRecord.ncbi, "1")
         assert.equal(chromAliasRecord.ucsc, "chr1")
+
+        assert.equal(chromAlias.getChromosomeAlias("NC_007194.1", "genbank"), "CM000169.1")
+    })
+
+    test("test chromAlias.bb", async function () {
+
+        const url = "test/data/genomes/GCF_000002655.1.chromAlias.bb"
+
+        const chromAlias = new ChromAliasBB(url, {}, genome)
+        const chromAliasRecord = await chromAlias.search("1")
+        assert.equal(chromAliasRecord.chr, "NC_007194.1")
+        assert.equal(chromAliasRecord.genbank, "CM000169.1")
+        assert.equal(chromAliasRecord.ncbi, "1")
+        assert.equal(chromAliasRecord.ucsc, "chr1")
+
+        assert.equal(chromAlias.getChromosomeAlias("NC_007194.1", "genbank"), "CM000169.1")
     })
 
     test("test chromalias bb extra index search", async function () {
@@ -55,4 +76,42 @@ suite("chromAlias", function () {
         const f2 = await bbReader.search(ucscName)
         assert.equal(ucscName, f2.ucsc)
     })
+
+
+    test("test defaults", async function () {
+
+        const genomeID = "hg*"
+
+        // NCBI convention
+        let chrNames = []
+        for (let i = 1; i < 25; i++) {
+            chrNames.push(i.toString())
+        }
+        chrNames.push("MT")
+
+        let chromAlias = new ChromAliasDefaults(genomeID, chrNames)
+        let chromAliasRecord = await chromAlias.search("chr1")
+        assert.equal(chromAliasRecord.chr, "1")
+        assert.equal(chromAlias.getChromosomeName("chrX"), "23")
+        assert.equal(chromAlias.getChromosomeName("chrM"), "MT")
+
+        // UCSC convention
+        chrNames = []
+        for (let i = 1; i < 23; i++) {
+            chrNames.push("chr" + i)
+            chrNames.push("chrX")
+            chrNames.push("chrY")
+            chrNames.push("chrM")
+        }
+
+        chromAlias = new ChromAliasDefaults(genomeID, chrNames)
+        chromAliasRecord = await chromAlias.search("1")
+        assert.equal(chromAliasRecord.chr, "chr1")
+        assert.equal(chromAlias.getChromosomeName("23"), "chrX")
+        assert.equal(chromAlias.getChromosomeName("MT"), "chrM")
+
+        // Defaults don't support name sets,
+        assert.equal(chromAlias.getChromosomeAlias("NC_007194.1", "genbank"), "NC_007194.1")
+
+    })
 })
diff --git a/test/testCytobands.js b/test/testCytobands.js
index ecbe2fe6e..a5b3ea774 100644
--- a/test/testCytobands.js
+++ b/test/testCytobands.js
@@ -28,15 +28,5 @@ suite("test cytobands", function () {
 
     })
 
-    test("test cytoband bigbed remote", async function () {
 
-        const url = "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/bbi/GCA_009914755.4_T2T-CHM13v2.0.cytoBandMapped/cytoBandMapped.bb"
-        const src = new CytobandFileBB(url)
-
-        const cytobands = await src.getCytobands("chr1")  // "CP068269.2
-        const last = cytobands[cytobands.length-1];
-        assert.equal(248387328, last.end)
-
-    })
-    //CP068269.2
 })
diff --git a/test/testFasta.js b/test/testFasta.js
index 642613941..2a65b0844 100644
--- a/test/testFasta.js
+++ b/test/testFasta.js
@@ -1,5 +1,5 @@
 import "./utils/mockObjects.js"
-import {loadFasta} from "../js/genome/fasta.js"
+import {loadSequence} from "../js/genome/fasta.js"
 import {assert} from 'chai'
 
 suite("testFasta", function () {
@@ -29,7 +29,7 @@ suite("testFasta", function () {
 
         this.timeout(100000)
 
-        const fasta = await loadFasta({
+        const fasta = await loadSequence({
                 fastaURL: "https://www.dropbox.com/s/bpf7g2ynx8qep73/chr22.fa?dl=0",
                 indexURL: "https://www.dropbox.com/s/1jx9327vjkd87w5/chr22.fa.fai?dl=0"
             }
@@ -76,7 +76,7 @@ suite("testFasta", function () {
         // >chr1:1000001-1000025
         // GGGCACAGCCTCACCCAGGAAAGCA
 
-        const fasta = await loadFasta({
+        const fasta = await loadSequence({
             fastaURL: "test/data/fasta/sliced.fasta", indexed: false
         })
 
@@ -115,7 +115,7 @@ suite("testFasta", function () {
         // >chr1:1000001-1000025 @len=249250621
         // GGGCACAGCCTCACCCAGGAAAGCA
 
-        const fasta = await loadFasta({
+        const fasta = await loadSequence({
             fastaURL: "test/data/fasta/sliced2.fasta", indexed: false
         })
 
@@ -157,7 +157,7 @@ suite("testFasta", function () {
         const expectedSequence = "CGGGGAGAGAGAGAGAGCGAGCCAGGTTCAGGTCCAGGGAGGAGAGAGACAGCGCGCGCGAGGCGGAGACCTGGAGGGAGAGGAGCTGCGGAGAGGGGTTAGGCGGGGAGGGAGAGAGCCAGGTTCAGGTCCAGGGAGGAGAGAGACAGCGCGCGCGAGGCGGAGACCTGGAGGGAGAGGAGCTGCGGAGAGGGGTTAGGCGGGGAGAGAGAGAGCGAGCCAGGTTCAGGTCCAGGGAGGAGAGAGACAGCGCGCGCGAGGCGGAGACCTGGAGGGAGAGGAGCTGCGGAGAGGGGTTAGGCGGGGAGGGAGAGAGACAGCGCGCGCGAGGCGGAGACCTGGAGGGAGAGGAGCTGCGGAGAGGGGTTAGGCGGCGGGAGGCCCGGGAGCGTTACATGTGTGTGGACTCGGGGAGGGCGGCGGGGGGCCGCTCCTCGGGGCCGTCTGCCTGCAGGAAGGAGTCCACGGACTTGCTGCTGAGGCGGAAGGGCATCAGGCGGCAGAAGGTGCCGGGAGAGTAGGGAATCTGCGTGCGGGCCCTCTGCGAGGGGACCACCGTCTCCCCGGGAGACAGCCAGGGCGGCAGCCTGGCCAGGAGGCTGCGGTCCAGGGCCTCGTCCGGAGAAAACACAGGGTTGTCAATTCCTAGGAGAGAGGGCAGCGGCTAGTCAGCCTTCGGAGAGCCCCACGGCGGCAGGGGAGACCTCGCCGGGGCCGTCACCTGCTGGGTGCCTTGGAAAGTTAGGGTCACCGGGAAGGTTAGGGTCACGTGCCTTTCAGGTTGCGGGCCCTTCCCCCACATCCATGACCCCACACGCCACAGGCAGCACAGGTAACGTCTCGCTTCCCTCAAGACATACCCCACCTGCTCCCTGCCCGGCCCACGTCTCCCCGGACAGCAGCCTCCGAGTTGGTTGAGGGGGCACTCAGTGGGTGCCAAGCAGGGCCCTTGAGAACCCACAGGAGACCCCACCCCcccaggtcccagtgcccctggtccaa"
         const dataUri = "data:application/gzip;base64,H4sIANLFrF8C/71SO07FMBDsuQudn16gQFpN4QvMBSIXoUa5v9iZtRNqJLCVF3u9nl/ex/j8ery3Z2vb9tqej7a9vaDniB8TehC9k/71OmurAWqpmUW4DtAt7tB9zgOBk9V3d/whwb+6+D0KCgeoBXSAYK+ZILyoZrdWyZNG6ig3FLQe8ZhLNuHrNC+XLAOFoxBeuKLbUyctOIzYLVjaamvhIWRTYom2eyyJYSlVEItBZuzWTFQMORAup8hUFJSn68sUlABkx6ic+Yk5sOj6ShtloxJx/BJid1SWadWx12mvNO7KbKy/yW3dPiVUHigi70Rm9ZLmBSMql16XZEnZcF6xHvgl9vJw5egQ7RJKWoLJilz4UrXMRPSZJtwSgakllrwcY4z9OE6/ziNf4/R2378BIJQ+9/4DAAA="
 
-        const fasta = await loadFasta({
+        const fasta = await loadSequence({
             fastaURL: dataUri
         })
 
diff --git a/test/testGenome.js b/test/testGenome.js
index c798eb3a1..35f62649f 100644
--- a/test/testGenome.js
+++ b/test/testGenome.js
@@ -32,7 +32,7 @@ suite("testGenome", function () {
             id: "GCF_016699485.2",
             format: "2bit",
             twoBitURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.2bit",
-            chromSizes: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt"
+            chromSizesURL: "https://hgdownload.gi.ucsc.edu/hubs//GCA/011/100/615/GCA_011100615.1/GCA_011100615.1.chrom.sizes.txt"
         }
 
         const genome = await Genome.createGenome(reference)
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 () {
