fix unit tests

js/bam/bamReader.js

@@ -44,7 +44,7 @@ class BamReader {
 
             for (let c of chunks) {
                 const ba = await this._blockLoader.getData(c.minv, c.maxv)
-                const done = BamUtils.decodeBamRecords(ba, c.minv.offset, alignmentContainer, this.indexToChr, chrId, bpStart, bpEnd, this.filter)
+                const done = BamUtils.decodeBamRecords(ba, c.minv.offset, alignmentContainer, this.header.chrNames, chrId, bpStart, bpEnd, this.filter)
                 if (done) {
                     break
                 }

js/bam/bamReaderNonIndexed.js

@@ -37,6 +37,8 @@ import {buildOptions, isDataURL} from "../util/igvUtils.js"
  */
 class BamReaderNonIndexed {
 
+    chrAliasTable = new Map()
+
     constructor(config, genome) {
         this.config = config
         this.genome = genome
@@ -45,52 +47,75 @@ class BamReaderNonIndexed {
         BamUtils.setReaderDefaults(this, config)
     }
 
-    // Return an alignment container
+    /**
+     *
+     * @param chr
+     * @param bpStart
+     * @param bpEnd
+     * @returns {Promise<AlignmentContainer>}
+     */
     async readAlignments(chr, bpStart, bpEnd) {
 
-        if (this.alignmentCache) {
-            const header = this.header
-            const queryChr = header.chrAliasTable.hasOwnProperty(chr) ? header.chrAliasTable[chr] : chr
-            const qAlignments = this.alignmentCache.queryFeatures(queryChr, bpStart, bpEnd)
-            const alignmentContainer = new AlignmentContainer(chr, bpStart, bpEnd, this.config)
-            for (let a of qAlignments) {
-                alignmentContainer.push(a)
-            }
-            alignmentContainer.finish()
-            return alignmentContainer
-
-        } else {
+        if (!this.alignmentCache) {
+            // For a non-indexed BAM file all alignments are read at once and cached.
+            let unc
             if (this.isDataUri) {
                 const data = decodeDataURI(this.bamPath)
-                const unc = BGZip.unbgzf(data.buffer)
-                this.parseAlignments(unc)
-                return this.fetchAlignments(chr, bpStart, bpEnd)
+                unc = BGZip.unbgzf(data.buffer)
             } else {
                 const arrayBuffer = await igvxhr.loadArrayBuffer(this.bamPath, buildOptions(this.config))
-                const unc = BGZip.unbgzf(arrayBuffer)
-                this.parseAlignments(unc)
-                return this.fetchAlignments(chr, bpStart, bpEnd)
+                unc = BGZip.unbgzf(arrayBuffer)
             }
+            this.alignmentCache = this.#parseAlignments(unc)
         }
 
+        const queryChr = await this.#getQueryChr(chr)
+        const qAlignments = this.alignmentCache.queryFeatures(queryChr, bpStart, bpEnd)
+        const alignmentContainer = new AlignmentContainer(chr, bpStart, bpEnd, this.config)
+        for (let a of qAlignments) {
+            alignmentContainer.push(a)
+        }
+        alignmentContainer.finish()
+        return alignmentContainer
     }
 
-    parseAlignments(data) {
+    #parseAlignments(data) {
         const alignments = []
         this.header = BamUtils.decodeBamHeader(data)
-        BamUtils.  decodeBamRecords(data, this.header.size, alignments, this.header.chrNames)
-        this.alignmentCache = new FeatureCache(alignments, this.genome)
+        BamUtils.decodeBamRecords(data, this.header.size, alignments, this.header.chrNames)
+        return new FeatureCache(alignments, this.genome)
     }
 
-    fetchAlignments(chr, bpStart, bpEnd) {
-        const queryChr = this.header.chrAliasTable.hasOwnProperty(chr) ? this.header.chrAliasTable[chr] : chr
-        const features = this.alignmentCache.queryFeatures(queryChr, bpStart, bpEnd)
-        const alignmentContainer = new AlignmentContainer(chr, bpStart, bpEnd, this.config)
-        for (let feature of features) {
-            alignmentContainer.push(feature)
+    async #getQueryChr(chr) {
+
+        const ownNames = new Set(this.header.chrNames)
+        if (ownNames.has(chr)) {
+            return chr
         }
-        alignmentContainer.finish()
-        return alignmentContainer
+
+        if (this.chrAliasTable.has(chr)) {
+            return this.chrAliasTable.get(chr)
+        }
+
+        // Try alias
+
+        if (this.genome) {
+            const aliasRecord = await this.genome.getAliasRecord(chr)
+            let alias
+            if (aliasRecord) {
+                const aliases = Object.keys(aliasRecord)
+                    .filter(k => k !== "start" && k !== "end")
+                    .map(k => aliasRecord[k])
+                    .filter(a => ownNames.has(a))
+                if (aliases.length > 0) {
+                    alias = aliases[0]
+                }
+            }
+            this.chrAliasTable.set(chr, alias)  // alias may be undefined => no alias exists. Setting prevents repeated attempts
+            return alias
+        }
+
+        return chr
     }
 
 }

js/bigwig/bwReader.js

@@ -251,10 +251,10 @@ class BWReader {
 
             // Use a trix index if we have one to map entered term to indexed value in bb file
             if (this._trix) {
-                term = term.toLowerCase()
-                const trixResults = await this._trix.search(term)
-                if (trixResults && trixResults.has(term)) {   // <= exact matches only for now
-                    term = trixResults.get(term)[0]
+                const termLower = term.toLowerCase()
+                const trixResults = await this._trix.search(termLower)
+                if (trixResults && trixResults.has(termLower)) {   // <= exact matches only for now
+                    term = trixResults.get(termLower)[0]
                 }
             }
 

js/genome/genome.js

@@ -64,7 +64,7 @@ class Genome {
             this.cytobandSource = new CytobandFile(config.cytobandURL, Object.assign({}, config))
         }
 
-        if (false !== config.wholeGenomeView) {
+        if (false !== config.wholeGenomeView && this.chromosomes.size > 0) {
             // Set chromosome order for WG view and chromosome pulldown.  If chromosome order is not specified sort
             if (config.chromosomeOrder) {
                 if (Array.isArray(config.chromosomeOrder)) {
@@ -73,7 +73,7 @@ class Genome {
                     this.wgChromosomeNames = config.chromosomeOrder.split(',').map(nm => nm.trim())
                 }
             } else {
-                this.wgChromosomeNames = trimSmallChromosomes(chromosomes)
+                this.wgChromosomeNames = trimSmallChromosomes(this.chromosomes)
             }
         }
 

test/testHtsgetReader.js → test/old/testHtsgetReader.js

@@ -1,8 +1,8 @@
-import "./utils/mockObjects.js"
+import "../utils/mockObjects.js"
 import {assert} from 'chai'
-import HtsgetBamReader from "../js/htsget/htsgetBamReader.js"
-import HtsgetVariantReader from "../js/htsget/htsgetVariantReader.js"
-import Browser from "../js/browser.js"
+import HtsgetBamReader from "../../js/htsget/htsgetBamReader.js"
+import HtsgetVariantReader from "../../js/htsget/htsgetVariantReader.js"
+import Browser from "../../js/browser.js"
 
 
 // Mock genome with "1,2,3..." name convention

test/testAlignmentUtils.js

@@ -8,46 +8,53 @@ suite("testAlignmentUtils", function () {
 
     test("Alignment packing", async function () {
         this.timeout(10000)
-        const chr = 'chr22'
-        const start = 24375132
-        const end = 24385311
 
-        const bamReader = new BamReaderNonIndexed({
-            type: 'bam',
-            url: 'test/data/bam/gstt1_sample.bam',
-            indexed: false
-        })
+        await _testPacking('chr22')
+        await _testPacking('22')      // Test aliasing
 
-        const alignmentContainer = await bamReader.readAlignments(chr, start, end)
 
-        const rows = packAlignmentRows(alignmentContainer.alignments, start, end, false)
+        async function _testPacking(chr) {
+            const start = 24375132
+            const end = 24385311
 
-        let count = 0
-        for (let r of rows) count += r.alignments.length
+            const bamReader = new BamReaderNonIndexed({
+                type: 'bam',
+                url: 'test/data/bam/gstt1_sample.bam',
+                indexed: false
+            })
 
-        // All alignments are packed
-        assert.equal(alignmentContainer.alignments.length, count)
+            const alignmentContainer = await bamReader.readAlignments(chr, start, end)
 
-        // No duplicates
-        const seen = new Set()
-        for (let r of rows) {
-            for (let a of r.alignments) {
-                if (seen.has(a)) {
-                    assert.fail(a, undefined, 'Alignment seen twice')
+            const rows = packAlignmentRows(alignmentContainer.alignments, start, end, false)
+
+            let count = 0
+            for (let r of rows) count += r.alignments.length
+
+            // All alignments are packed
+            assert.equal(alignmentContainer.alignments.length, count)
+
+            // No duplicates
+            const seen = new Set()
+            for (let r of rows) {
+                for (let a of r.alignments) {
+                    if (seen.has(a)) {
+                        assert.fail(a, undefined, 'Alignment seen twice')
+                    }
+                    seen.add(a)
                 }
-                seen.add(a)
             }
-        }
 
-        // No alignment overlaps
-        for (let r of rows) {
-            let lastEnd = -1
-            for (let a of r.alignments) {
-                assert.isAtLeast(a.start, lastEnd, 'Alignment start is < last end')
-                lastEnd = a.end
+            // No alignment overlaps
+            for (let r of rows) {
+                let lastEnd = -1
+                for (let a of r.alignments) {
+                    assert.isAtLeast(a.start, lastEnd, 'Alignment start is < last end')
+                    lastEnd = a.end
+                }
             }
         }
 
+
     })
 
 

test/testBAM.js

@@ -2,6 +2,10 @@ import "./utils/mockObjects.js"
 import BamReader from "../js/bam/bamReader.js"
 import {assert} from 'chai'
 import BamReaderNonIndexed from "../js/bam/bamReaderNonIndexed.js"
+import {createGenome} from "./utils/Genome.js"
+
+
+const genome = createGenome()
 
 suite("testBAM", function () {
 
@@ -12,28 +16,32 @@ suite("testBAM", function () {
         const end = 155160000
 
         const bamReader = new BamReader({
-            type: 'bam',
-            url: 'test/data/bam/na12889.bam',
-            indexURL: 'test/data/bam/na12889.bam.csi'
-        })
+                type: 'bam',
+                url: 'test/data/bam/na12889.bam',
+                indexURL: 'test/data/bam/na12889.bam.csi'
+            },
+            genome)
 
         const alignmentContainer = await bamReader.readAlignments(chr, start, end)
         validate(assert, alignmentContainer)
     })
 
     test("BAM alignments - non indexed", async function () {
 
-        const chr = 'chr1'
         const start = 155140000
         const end = 155160000
 
         const bamReader = new BamReaderNonIndexed({
-            type: 'bam',
-            url: 'test/data/bam/na12889.bam',
-            indexed: false
-        })
+                type: 'bam',
+                url: 'test/data/bam/na12889.bam',
+                indexed: false
+            },
+            genome)
 
-        const alignmentContainer = await bamReader.readAlignments(chr, start, end)
+        let alignmentContainer = await bamReader.readAlignments("chr1", start, end)
+        validate(assert, alignmentContainer)
+
+        alignmentContainer = await bamReader.readAlignments("1", start, end)
         validate(assert, alignmentContainer)
     })
 

test/testBED.js

@@ -5,7 +5,7 @@ import {assert} from 'chai'
 import {createGenome} from "./utils/Genome.js"
 
 const genome = createGenome()
-import GenomeUtils from "../js/genome/genomeUtils.js"
+import Genome from "../js/genome/genome.js"
 
 suite("testBed", function () {
 

test/testChromAlias.js

@@ -6,21 +6,35 @@ import {assert} from "chai"
 
 suite("chromAlias", function () {
 
+    const genome = {
+        chromosomes: new Map([
+            ["NC_007194.1", {name: "NC_007194.1", bpLength: 1}],
+        ])
+    }
+
+    /**
+     * Test a UCSC style chrom alias flat file
+     *
+     * # refseq	assembly	genbank	ncbi	ucsc
+     * NC_007194.1	1	CM000169.1	1	chr1
+     * NC_007195.1	2	CM000170.1	2	chr2
+     * NC_007196.1	3	CM000171.1	3	chr3
+     * NC_007197.1	4	CM000172.1	4	chr4
+     * NC_007198.1	5	CM000173.1	5	chr5
+     * NC_007199.1	6	CM000174.1	6	chr6
+     * NC_007200.1	7	CM000175.1	7	chr7
+     * NC_007201.1	8	CM000176.1	8	chr8
+     */
     test("test chromAlias.txt", async function () {
 
-        const url = "test/data/genomes/t2t.chromAlias.txt"
-
-        const chromosomeNames = ["CP068254.1", "CP068255.2", "CP068256.2", "CP068257.2", "CP068258.2", "CP068259.2",
-            "CP068260.2", "CP068261.2", "CP068262.2", "CP068263.2", "CP068264.2", "CP068265.2", "CP068266.2",
-            "CP068267.2", "CP068268.2", "CP068269.2", "CP068270.2", "CP068271.2", "CP068272.2", "CP068273.2",
-            "CP068274.2", "CP068275.2", "CP068276.2", "CP068277.2", "CP086569.2"
-        ]
-
-        const chromAlias = new ChromAliasFile(url, {})
-
-        await chromAlias.init(chromosomeNames)
-
+        const url = "test/data/genomes/GCF_000002655.1.chromAlias.txt"
 
+        const chromAlias = new ChromAliasFile(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")
     })
 
     test("test chromalias bb extra index search", async function () {
@@ -32,28 +46,6 @@ suite("chromAlias", function () {
 
         const bbReader = new BWReader(config)
 
-
-        // There are 5 extra indexes, 1 for each alias
-        const ncbiName = "3"
-        const f1 = await bbReader.search(ncbiName)
-        assert.equal(ncbiName, f1.ncbi)
-
-        const ucscName = "chr2"
-        const f2 = await bbReader.search(ucscName)
-        assert.equal(ucscName, f2.ucsc)
-    })
-
-    test("test chromalias bb remote", async function () {
-        this.timeout(200000)
-        const config = {
-            url: "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.chromAlias.bb",
-            format: "bigbed"
-        }
-
-        const bbReader = new BWReader(config)
-
-        const features = await bbReader.readFeatures("chr1")
-
         // There are 5 extra indexes, 1 for each alias
         const ncbiName = "3"
         const f1 = await bbReader.search(ncbiName)
@@ -63,5 +55,4 @@ suite("chromAlias", function () {
         const f2 = await bbReader.search(ucscName)
         assert.equal(ucscName, f2.ucsc)
     })
-    //                chromAliasBbURL: "https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.chromAlias.bb",
 })