reorg

Author: turner

.gitignore

@@ -9,4 +9,4 @@ igv.js.iml
 igv.css.map
 /deploy/
 /dev/oauth/oauthConfigPrivate.js
-/js/bigwig/bwReader_nochromtree.js
+/src/igvCore/bigwig/bwReader_nochromtree.js

helpful/knownGenomes.js

@@ -1,6 +1,6 @@
-import TextFeatureSource from "../js/feature/textFeatureSource.js"
-import QTLSelections from "../js/qtl/qtlSelections.js"
-import FeatureRenderer from "../js/feature/featureRenderer.js"
+import TextFeatureSource from "./igvCore/feature/textFeatureSource.js"
+import QTLSelections from "./igvCore/qtl/qtlSelections.js"
+import FeatureRenderer from "./igvCore/feature/featureRenderer.js"
 import AnnotationRenderService from './annotationRenderService.js'
 
 function createAnnotationRenderService(container, genome) {

src/annotationRenderServiceFactory.js

@@ -1,5 +1,5 @@
 import {buildOptions, isDataURL} from "../util/igvUtils.js"
-import {BGZip, igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
+import {BGZip, igvxhr, StringUtils} from "igv-utils"
 import {Cytoband} from "./cytoband.js"
 import Chromosome from "./chromosome.js"
 

js/bigwig/bbDecoders.js renamed to src/igvCore/bigwig/bbDecoders.js

@@ -23,7 +23,7 @@
  * THE SOFTWARE.
  */
 
-import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
+import {igvxhr} from "igv-utils"
 
 /**
  * EQTL reader for GTEX webservice
@@ -108,4 +108,4 @@ class EQTL {
 
 
 
-export default GtexReader
+export default GtexReader

js/bigwig/bpTree.js renamed to src/igvCore/bigwig/bpTree.js

@@ -26,7 +26,7 @@
 import TextFeatureSource from '../feature/textFeatureSource.js'
 import TrackBase from "../trackBase.js"
 import IGVGraphics from "../igv-canvas.js"
-import {IGVMath} from "../../node_modules/igv-utils/src/index.js"
+import {IGVMath} from "igv-utils"
 import {searchFeatures} from "../search.js"
 
 class QTLTrack extends TrackBase {

js/bigwig/bufferedReader.js renamed to src/igvCore/bigwig/bufferedReader.js

@@ -1,7 +1,8 @@
-import GenomeUtils from '../js/genome/genomeUtils.js';
-import Genome from '../js/genome/genome.js';
-import { searchFeatures } from "../js/search.js"
+import GenomeUtils from './igvCore/genome/genomeUtils.js';
+import Genome from './igvCore/genome/genome.js';
+import { searchFeatures } from "./igvCore/search.js"
 import { createAnnotationRenderService } from './annotationRenderServiceFactory.js'
+import { knownGenomes } from './knownGenomes.js'
 
 let annotationRenderService
 
@@ -11,15 +12,16 @@ document.addEventListener('DOMContentLoaded', async () => {
 
     const genomeName = 'hg19'
 
-    const genome = await Genome.createGenome(GenomeUtils.KNOWN_GENOMES[genomeName])
+    const genome = await Genome.createGenome(knownGenomes[genomeName])
 
     annotationRenderService = createAnnotationRenderService(document.querySelector('#dat-gene-render-container'), genome)
 
     // const { chr, start:bpStart, end:bpEnd, name } = await searchFeatures({ genome }, 'brca2')
 
-    const chr = 'chr5'
-    const bpStart = 60116410
-    const bpEnd = 71928691
+    // random locus
+    const chr = 'chr16'
+    const bpStart = 26716013
+    const bpEnd = 29371136
 
     const features = await annotationRenderService.getFeatures(chr, bpStart, bpEnd)
 

js/bigwig/bwReader.js renamed to src/igvCore/bigwig/bwReader.js

@@ -1,5 +1,5 @@
-import CramReader from "../../js/cram/cramReader.js"
-import FastaSequence from "../../js/genome/indexedFasta.js"
+import CramReader from "../../src/igvCore/cram/cramReader.js"
+import FastaSequence from "../../src/igvCore/genome/indexedFasta.js"
 import {assert} from 'chai'
 import {setup} from "../util/setup.js"
 

js/bigwig/bwSource.js renamed to src/igvCore/bigwig/bwSource.js

@@ -1,8 +1,8 @@
 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 "../../src/igvCore/htsget/htsgetBamReader.js"
+import HtsgetVariantReader from "../../src/igvCore/htsget/htsgetVariantReader.js"
+import Browser from "../../src/igvCore/browser.js"
 
 
 // Mock genome with "1,2,3..." name convention

js/bigwig/chromTree.js renamed to src/igvCore/bigwig/chromTree.js

@@ -9,7 +9,7 @@
 
     <script type="text/javascript" src="testInflate.js"></script>
     <script type="text/javascript" src="../vendor/qunit.js"></script>
-    <script type="text/javascript" src="../../js/vendor/zlib_and_gzip.js"></script>
+    <script type="text/javascript" src="../../src/igvCore/vendor/zlib_and_gzip.js"></script>
     <script type="text/javascript" src="../../node_modules/igv-utils/src/index.js"></script>
 </head>
 <body>

js/bigwig/rpTree.js renamed to src/igvCore/bigwig/rpTree.js

@@ -1,6 +1,6 @@
 import "./utils/mockObjects.js"
 import {createFile} from "./utils/File.js"
-import TextFeatureSource from "../js/feature/textFeatureSource.js"
+import TextFeatureSource from "../src/igvCore/feature/textFeatureSource.js"
 import {assert} from 'chai'
 import {createGenome} from "./utils/MockGenome.js"
 

js/bigwig/trix.js renamed to src/igvCore/bigwig/trix.js

@@ -1,6 +1,6 @@
 import "./utils/mockObjects.js"
 import {assert} from 'chai'
-import BamReaderNonIndexed from "../js/bam/bamReaderNonIndexed.js"
+import BamReaderNonIndexed from "../src/igvCore/bam/bamReaderNonIndexed.js"
 
 suite("testAlignmentUtils", function () {
 

js/binary.js renamed to src/igvCore/binary.js

@@ -1,7 +1,7 @@
 import "./utils/mockObjects.js"
-import BamReader from "../js/bam/bamReader.js"
+import BamReader from "../src/igvCore/bam/bamReader.js"
 import {assert} from 'chai'
-import BamReaderNonIndexed from "../js/bam/bamReaderNonIndexed.js"
+import BamReaderNonIndexed from "../src/igvCore/bam/bamReaderNonIndexed.js"
 import {createGenome} from "./utils/MockGenome.js"
 
 

js/feature/baseFeatureSource.js renamed to src/igvCore/feature/baseFeatureSource.js

@@ -1,9 +1,9 @@
 import "./utils/mockObjects.js"
-import FeatureFileReader from "../js/feature/featureFileReader.js"
-import TextFeatureSource from "../js/feature/textFeatureSource.js"
+import FeatureFileReader from "../src/igvCore/feature/featureFileReader.js"
+import TextFeatureSource from "../src/igvCore/feature/textFeatureSource.js"
 import {assert} from 'chai'
 import {createGenome} from "./utils/MockGenome.js"
-import Genome from "../js/genome/genome.js"
+import Genome from "../src/igvCore/genome/genome.js"
 
 const genome = createGenome()
 

js/feature/chromAliasManager.js renamed to src/igvCore/feature/chromAliasManager.js

@@ -1,5 +1,5 @@
 import "./utils/mockObjects.js"
-import TextFeatureSource from "../js/feature/textFeatureSource.js"
+import TextFeatureSource from "../src/igvCore/feature/textFeatureSource.js"
 import {assert} from 'chai'
 import {createGenome} from "./utils/MockGenome.js"
 

js/feature/customServiceReader.js renamed to src/igvCore/feature/customServiceReader.js

@@ -1,11 +1,11 @@
 import "./utils/mockObjects.js"
-import FeatureFileReader from "../js/feature/featureFileReader.js"
-import FeatureSource from "../js/feature/featureSource.js"
+import FeatureFileReader from "../src/igvCore/feature/featureFileReader.js"
+import FeatureSource from "../src/igvCore/feature/featureSource.js"
 import {assert} from 'chai'
 import {createGenome} from "./utils/MockGenome.js"
 
 const genome = createGenome()
-import GenomeUtils from "../js/genome/genomeUtils.js"
+import GenomeUtils from "../src/igvCore/genome/genomeUtils.js"
 
 suite("testBed", function () {
 

js/feature/dataWrapper.js renamed to src/igvCore/feature/dataWrapper.js

@@ -1,5 +1,5 @@
 import "./utils/mockObjects.js"
-import BGZBlockLoader, {inflateBlocks, findBlockBoundaries} from "../js/bam/bgzBlockLoader.js"
+import BGZBlockLoader, {inflateBlocks, findBlockBoundaries} from "../src/igvCore/bam/bgzBlockLoader.js"
 import {assert} from 'chai'
 import fs from 'fs'
 

js/feature/decode/bedpe.js renamed to src/igvCore/feature/decode/bedpe.js

@@ -1,4 +1,4 @@
-import BGZLineReader from "../js/util/bgzLineReader.js"
+import BGZLineReader from "../src/igvCore/util/bgzLineReader.js"
 import "./utils/mockObjects.js"
 import {assert} from 'chai'
 

js/feature/decode/custom.js renamed to src/igvCore/feature/decode/custom.js

@@ -1,5 +1,5 @@
 import "./utils/mockObjects.js"
-import {loadIndex} from "../js/bam/indexFactory.js"
+import {loadIndex} from "../src/igvCore/bam/indexFactory.js"
 import {assert} from 'chai'
 
 

js/feature/decode/decodeError.js renamed to src/igvCore/feature/decode/decodeError.js

@@ -1,6 +1,6 @@
 import "./utils/mockObjects.js"
 import {assert} from 'chai'
-import {computeLengthOnReference} from "../js/bam/supplementaryAlignment.js"
+import {computeLengthOnReference} from "../src/igvCore/bam/supplementaryAlignment.js"
 
 suite("testBAMUtils", function () {
 

js/feature/decode/fusionJuncSpan.js renamed to src/igvCore/feature/decode/fusionJuncSpan.js

@@ -1,6 +1,6 @@
 import "./utils/mockObjects.js"
-import TextFeatureSource from "../js/feature/textFeatureSource.js"
-import FeatureFileReader from "../js/feature/featureFileReader.js"
+import TextFeatureSource from "../src/igvCore/feature/textFeatureSource.js"
+import FeatureFileReader from "../src/igvCore/feature/featureFileReader.js"
 import {assert} from 'chai'
 import {createGenome} from "./utils/MockGenome.js"
 

js/feature/decode/gtexGWAS.js renamed to src/igvCore/feature/decode/gtexGWAS.js

@@ -1,11 +1,11 @@
 import "./utils/mockObjects.js"
-import BWSource from "../js/bigwig/bwSource.js"
-import {parseAutoSQL} from "../js/util/ucscUtils.js"
+import BWSource from "../src/igvCore/bigwig/bwSource.js"
+import {parseAutoSQL} from "../src/igvCore/util/ucscUtils.js"
 import {assert} from 'chai'
 import {fileToDataURL} from "./utils/URLUtils.js"
-import BWReader from "../js/bigwig/bwReader.js"
+import BWReader from "../src/igvCore/bigwig/bwReader.js"
 import {createGenome} from "./utils/MockGenome.js"
-import ChromAliasBB from "../js/genome/chromAliasBB.js"
+import ChromAliasBB from "../src/igvCore/genome/chromAliasBB.js"
 
 function getWGChromosomeNames() {
     const chromosomeNames = []

js/feature/decode/ucsc.js renamed to src/igvCore/feature/decode/ucsc.js

@@ -1,7 +1,7 @@
 import "./utils/mockObjects.js"
-import BWSource from "../js/bigwig/bwSource.js"
-import BWReader from "../js/bigwig/bwReader.js"
-import FeatureSource from "../js/feature/featureSource.js"
+import BWSource from "../src/igvCore/bigwig/bwSource.js"
+import BWReader from "../src/igvCore/bigwig/bwReader.js"
+import FeatureSource from "../src/igvCore/feature/featureSource.js"
 import {assert} from 'chai'
 import {createGenome} from "./utils/MockGenome.js"
 
@@ -113,4 +113,4 @@ suite("testBigWig", function () {
         assert.equal(zoomLevelHeaders.length, 0)
     })
 
-})
+})

js/feature/exonUtils.js renamed to src/igvCore/feature/exonUtils.js

@@ -1,8 +1,8 @@
 import "./utils/mockObjects.js"
 import {assert} from 'chai'
-import Browser from "../js/browser.js"
-import FeatureSource from "../js/feature/featureSource.js"
-import search from "../js/search.js"
+import Browser from "../src/igvCore/browser.js"
+import FeatureSource from "../src/igvCore/feature/featureSource.js"
+import search from "../src/igvCore/search.js"
 
 const MockBrowser = {
     toJSON: function () {

js/feature/featureColorManager.js renamed to src/igvCore/feature/featureColorManager.js

@@ -1,5 +1,5 @@
 import "./utils/mockObjects.js"
-import BufferedReader from "../js/bigwig/bufferedReader.js"
+import BufferedReader from "../src/igvCore/bigwig/bufferedReader.js"
 import {assert} from 'chai'
 
 suite("testBigWig", function () {

js/feature/featureFileReader.js renamed to src/igvCore/feature/featureFileReader.js

@@ -1,5 +1,5 @@
 import "./utils/mockObjects.js"
-import BamReader from "../js/bam/bamReader.js"
+import BamReader from "../src/igvCore/bam/bamReader.js"
 import {assert} from 'chai'
 import {createGenome} from "./utils/MockGenome.js"
 
@@ -46,4 +46,4 @@ suite("testCSIIndex", function () {
 
         assert.equal(firstAlignment.start, 121976)
         }
-})
+})

js/feature/featurePacker.js renamed to src/igvCore/feature/featurePacker.js

@@ -1,5 +1,5 @@
 import "./utils/mockObjects.js"
-import {loadSequence} from "../js/genome/loadSequence.js"
+import {loadSequence} from "../src/igvCore/genome/loadSequence.js"
 import {assert} from 'chai'
 
 suite("testCachedSequence", function () {

js/feature/featureParser.js renamed to src/igvCore/feature/featureParser.js

@@ -1,9 +1,9 @@
 import "./utils/mockObjects.js"
-import ChromAliasFile from "../js/genome/chromAliasFile.js"
-import BWReader from "../js/bigwig/bwReader.js"
+import ChromAliasFile from "../src/igvCore/genome/chromAliasFile.js"
+import BWReader from "../src/igvCore/bigwig/bwReader.js"
 import {assert} from "chai"
-import ChromAliasDefaults from "../js/genome/chromAliasDefaults.js"
-import ChromAliasBB from "../js/genome/chromAliasBB.js"
+import ChromAliasDefaults from "../src/igvCore/genome/chromAliasDefaults.js"
+import ChromAliasBB from "../src/igvCore/genome/chromAliasBB.js"
 
 
 suite("chromAlias", function () {

js/feature/featureRenderer.js renamed to src/igvCore/feature/featureRenderer.js

@@ -1,6 +1,6 @@
 import "./utils/mockObjects.js"
 import {assert} from 'chai'
-import ChromTree from "../js/bigwig/chromTree.js"
+import ChromTree from "../src/igvCore/bigwig/chromTree.js"
 
 suite("test bbChromTree", function () {
 
@@ -65,4 +65,4 @@ suite("test bbChromTree", function () {
 
     })
 
-})
+})

js/feature/featureRendererUtils.js renamed to src/igvCore/feature/featureRendererUtils.js

@@ -1,7 +1,7 @@
 import "./utils/mockObjects.js"
 import {assert} from 'chai'
-import Genome from "../js/genome/genome.js"
-import CramReader from "../js/cram/cramReader.js"
+import Genome from "../src/igvCore/genome/genome.js"
+import CramReader from "../src/igvCore/cram/cramReader.js"
 import LocalFile from "./utils/JBrowseFileHandler.js"
 
 // Hack neccessary for unit testing cram bundle

js/feature/featureUtils.js renamed to src/igvCore/feature/featureUtils.js

@@ -1,8 +1,8 @@
 import "./utils/mockObjects.js"
 import {assert} from 'chai'
-import CytobandFileBB from "../js/genome/cytobandFileBB.js"
+import CytobandFileBB from "../src/igvCore/genome/cytobandFileBB.js"
 import {createGenome} from "./utils/MockGenome.js"
-import CytobandFile from "../js/genome/cytobandFile.js"
+import CytobandFile from "../src/igvCore/genome/cytobandFile.js"
 
 
 suite("test cytobands", function () {

js/feature/fileFormats.js renamed to src/igvCore/feature/fileFormats.js

@@ -1,7 +1,7 @@
 import "./utils/mockObjects.js"
 import {assert} from 'chai'
-import FastaSequence from "../js/genome/indexedFasta.js"
-import NonIndexedFasta from "../js/genome/nonIndexedFasta.js"
+import FastaSequence from "../src/igvCore/genome/indexedFasta.js"
+import NonIndexedFasta from "../src/igvCore/genome/nonIndexedFasta.js"
 
 suite("testFasta", function () {
 
@@ -126,4 +126,4 @@ suite("testFasta", function () {
     })
 
 
-})
+})

js/feature/gff/gff.js renamed to src/igvCore/feature/gff/gff.js

@@ -1,5 +1,5 @@
 import "./utils/mockObjects.js"
-import FeatureFileReader from '../js/feature/featureFileReader.js'
+import FeatureFileReader from '../src/igvCore/feature/featureFileReader.js'
 import {assert} from 'chai'
 
 suite("testTrackLine", function () {

js/feature/gff/gffFeature.js renamed to src/igvCore/feature/gff/gffFeature.js

@@ -1,8 +1,8 @@
 import "./utils/mockObjects.js"
 import {assert} from 'chai'
-import FastaSequence from "../js/genome/indexedFasta.js"
-import NonIndexedFasta from "../js/genome/nonIndexedFasta.js"
-import {findFeatureAfterCenter} from "../js/feature/featureUtils.js"
+import FastaSequence from "../src/igvCore/genome/indexedFasta.js"
+import NonIndexedFasta from "../src/igvCore/genome/nonIndexedFasta.js"
+import {findFeatureAfterCenter} from "../src/igvCore/feature/featureUtils.js"
 
 suite("testFeatureUtils", function () {
 
@@ -60,4 +60,4 @@ suite("testFeatureUtils", function () {
 
     })
 
-})
+})