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turnerturner
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All npm imports updated to modern style
1 parent 5983851 commit f149b29

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‎js/bigwig/bbDecoders.js

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import {IGVColor} from "../../node_modules/igv-utils/src/index.js"
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import {IGVColor} from 'igv-utils'
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function getDecoder(definedFieldCount, fieldCount, autoSql, format) {
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‎js/bigwig/bpTree.js

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import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
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import {igvxhr} from 'igv-utils'
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import {buildOptions} from "../util/igvUtils.js"
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import BinaryParser from "../binary.js"
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‎js/bigwig/bufferedReader.js

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import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
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import {igvxhr} from 'igv-utils'
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import {buildOptions} from "../util/igvUtils.js"
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class BufferedReader {

‎js/bigwig/bwReader.js

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import RPTree from "./rpTree.js"
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import BinaryParser from "../binary.js"
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import {BGZip, igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
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import {BGZip, igvxhr, StringUtils} from 'igv-utils'
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import {buildOptions, isDataURL} from "../util/igvUtils.js"
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import getDecoder from "./bbDecoders.js"
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import {parseAutoSQL} from "../util/ucscUtils.js"

‎js/bigwig/rpTree.js

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import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
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import {igvxhr} from 'igv-utils'
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import BinaryParser from "../binary.js"
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import {buildOptions} from "../util/igvUtils.js"
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‎js/bigwig/trix.js

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// A copy of the license for the GMOD trix-js distribution on which this is based may be downloaded
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// from: https://raw.githubusercontent.com/GMOD/trix-js/ma
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import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
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import {igvxhr} from 'igv-utils'
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// this is the number of hex characters to use for the address in ixixx, see

‎js/feature/color/featureColorManager.js

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import {ColorTable, PaletteColorTable} from "../../util/colorPalletes.js"
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import {IGVColor} from "../../../node_modules/igv-utils/src/index.js"
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import {IGVColor} from 'igv-utils'
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export default class FeatureColorManager {
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static defaultColor = 'rgb(0,0,150)'
@@ -13,7 +13,7 @@ export default class FeatureColorManager {
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this._initialAltColor = this.altColor || this.constructor.defaultColor
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// Set up color table if colorBy is specified
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if (config.colorBy) {
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if (config.colorBy)
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if (config.colorBy.field) {
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config.colorTable = config.colorBy.pallete || config.colorBy.palette
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config.colorBy = config.colorBy.field
@@ -70,4 +70,4 @@ export default class FeatureColorManager {
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const binNumber = Math.floor((score - min) / binWidth)
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return Math.min(1.0, 0.2 + (binNumber * 0.8) / 9)
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}
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}
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}

‎js/feature/customServiceReader.js

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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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* THE SOFTWARE.
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*/
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import {igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
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import {igvxhr, StringUtils} from 'igv-utils'
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const isString = StringUtils.isString
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‎js/feature/decode/bedpe.js

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import {IGVColor} from "../../../node_modules/igv-utils/src/index.js"
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import {IGVColor} from 'igv-utils'
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import {isNumber} from "../../util/igvUtils.js"
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/**

‎js/feature/decode/ucsc.js

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import {IGVColor} from "../../../node_modules/igv-utils/src/index.js"
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import {IGVColor} from 'igv-utils'
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import DecodeError from "./decodeError.js"
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import {parseAttributeString} from "../gff/parseAttributeString.js"

‎js/feature/featureFileReader.js

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* THE SOFTWARE.
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*/
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import {BGZip, FileUtils, igvxhr, URIUtils} from "../../node_modules/igv-utils/src/index.js"
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import {BGZip, FileUtils, igvxhr, URIUtils} from 'igv-utils'
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import FeatureParser from "./featureParser.js"
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import {buildOptions, isDataURL} from "../util/igvUtils.js"
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import getDataWrapper from "./dataWrapper.js"

‎js/feature/gff/gff.js

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import {IGVColor} from "../../../node_modules/igv-utils/src/index.js"
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import {IGVColor} from 'igv-utils'
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import {GFFFeature} from "./gffFeature.js"
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import {decodeGFFAttribute, parseAttributeString} from "./parseAttributeString.js"
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‎js/feature/gff/gffFeature.js

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import {StringUtils} from "../../../node_modules/igv-utils/src/index.js"
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import {StringUtils} from 'igv-utils'
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import {isCoding, isIntron, isUTR} from "./so.js"
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‎js/feature/staticFeatureSource.js

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* THE SOFTWARE.
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*/
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import {FeatureCache} from "../../node_modules/igv-utils/src/index.js"
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import {FeatureCache} from 'igv-utils'
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import {computeWGFeatures, findFeatureAfterCenter, packFeatures} from "./featureUtils.js"
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import BaseFeatureSource from "./baseFeatureSource.js"
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‎js/feature/textFeatureSource.js

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import {FeatureCache} from "../../node_modules/igv-utils/src/index.js"
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import {FeatureCache} from 'igv-utils'
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import FeatureFileReader from "./featureFileReader.js"
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import GenomicInterval from "../genome/genomicInterval.js"
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import {packFeatures} from "./featureUtils.js"

‎js/gbk/genbankParser.js

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import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
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import {igvxhr} from 'igv-utils'
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import getDataWrapper from "../feature/dataWrapper.js"
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import Genbank from "./genbank.js"
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‎js/genome/chromAliasDefaults.js

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* Default chromosome aliases, mostly 1<->chr1 etc. Used if chrom alias file is not supplied.
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*
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*/
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import {isNumber, buildOptions} from "../util/igvUtils.js"
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import {igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
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class ChromAliasDefaults {
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‎js/genome/chromAliasFile.js

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* @returns {Promise<*[]>}
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*/
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import {buildOptions} from "../util/igvUtils.js"
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import {igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
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import {igvxhr, StringUtils} from 'igv-utils'
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import ChromAliasDefaults from "./chromAliasDefaults.js"
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class ChromAliasFile {

‎js/genome/chromSizes.js

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import {BGZip, igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
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import {BGZip, igvxhr, StringUtils} from 'igv-utils'
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import Chromosome from "./chromosome.js"
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import {isDataURL} from "../util/igvUtils.js"
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‎js/genome/genome.js

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import {StringUtils} from "../../node_modules/igv-utils/src/index.js"
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import {StringUtils} from 'igv-utils'
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import Chromosome from "./chromosome.js"
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import {loadSequence} from "./loadSequence.js"
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import ChromAliasBB from "./chromAliasBB.js"

‎js/genome/genomeUtils.js

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import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
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import {igvxhr} from 'igv-utils'
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const DEFAULT_GENOMES_URL = "https://igv.org/genomes/genomes3.json"
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const BACKUP_GENOMES_URL = "https://raw.githubusercontent.com/igvteam/igv-data/refs/heads/main/genomes/web/genomes.json"

‎js/genome/indexedFasta.js

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*/
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// Indexed fasta files
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import {BGZip, igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
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import {BGZip, igvxhr, StringUtils} from 'igv-utils'
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import GenomicInterval from "./genomicInterval.js"
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import Chromosome from "./chromosome.js"
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import {buildOptions} from "../util/igvUtils.js"
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//The Fasta-index gives a byte-position of the chromosomal sequences within the FASTA file.
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//These locations need to be remapped to the locations within the zipped reference genome, using the GZI index
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//This function provides this functionality by
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//This function provides this functionality by
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//1) taking the indicated start/stop byte locations within the UNCOMPRESSED FASTA file
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//2) remapping these byte locations to the correct blocks (and associated positions) within the COMPRESSED FASTA file
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//Subsequently, the calling method can then extract the correct blocks from the compressed FASTA files and uncompressed the data
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//It is possible that the query end position lies AFTER the start of the final block
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//If this is the case, we add a 'fake' negative index which will be interpreted by the loadAndUncompressBlocks method as an indicator
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//to read until the end of the file
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//to read until the end of the file
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const finalRelevantBlock = result[result.length - 1]
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const finalIndexBlock = this.compressedIndex.length - 1
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if (finalRelevantBlock === finalIndexBlock && (this.compressedIndex)[finalRelevantBlock][UNCOMPRESSED_POSITION] < queryPositionEnd) {
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}
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//postprocess this data: because entire blocks are read we need to remove the first N bases of the first used block,
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//postprocess this data: because entire blocks are read we need to remove the first N bases of the first used block,
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//which are not included in the original query positions
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const firstBlockInfo = (this.compressedIndex)[blockIndices[0]]
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const offset = startByte - firstBlockInfo[UNCOMPRESSED_POSITION]

‎js/genome/nonIndexedFasta.js

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import {BGZip, igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
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import {BGZip, igvxhr, StringUtils} from 'igv-utils'
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import Chromosome from "./chromosome.js"
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import {buildOptions, isDataURL} from "../util/igvUtils.js"
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import SequenceInterval from "./sequenceInterval.js"

‎js/genome/twobit.js

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*/
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import {igvxhr} from "../../node_modules/igv-utils/src/index.js"
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import {igvxhr} from 'igv-utils'
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import BinaryParser from "../binary.js"
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import BPTree from "../bigwig/bpTree.js"
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}
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export default TwobitSequence
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export default TwobitSequence

‎js/search.js

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import {igvxhr, StringUtils} from "../node_modules/igv-utils/src/index.js"
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import {igvxhr, StringUtils} from 'igv-utils'
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const DEFAULT_SEARCH_CONFIG = {

‎js/util/colorPalletes.js

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import {IGVMath} from "../../node_modules/igv-utils/src/index.js"
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import {IGVMath} from 'igv-utils'
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function hexToRGB(hex) {
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// Ensure the hex value is in the proper format

‎js/util/colorScale.js

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import {IGVColor} from "../../node_modules/igv-utils/src/index.js"
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import {IGVColor} from 'igv-utils'
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const ColorScaleFactory = {

‎js/util/deepCopy.js

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* Fast deep copy function, copied from https://github.com/davidmarkclements/rfdc
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* Function is copied rather than imported because project does not support es6 import, only 'require'
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*/
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import {FileUtils} from "../../node_modules/igv-utils/src/index.js"
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import {FileUtils} from 'igv-utils'
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function cloneArray(a, fn) {
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}
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export default deepCopy
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export default deepCopy

‎js/util/fileFormatUtils.js

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import {buildOptions, getFilename} from "./igvUtils.js"
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import BinaryParser from "../binary.js"
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import {BGZip, igvxhr, StringUtils} from "../../node_modules/igv-utils/src/index.js"
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import {BGZip, igvxhr, StringUtils} from 'igv-utils'
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const BIGWIG_MAGIC_LTH = 0x888FFC26 // BigWig Magic Low to High
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const BIGWIG_MAGIC_HTL = 0x26FC8F66 // BigWig Magic High to Low

‎js/util/getChrColor.js

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import {IGVColor} from "../../node_modules/igv-utils/src/index.js"
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import {IGVColor} from 'igv-utils'
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export function getChrColor(chr) {
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if (chrColorMap[chr]) {
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"chr46": "rgb(255, 20, 99)",
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"chr47": "rgb(0, 214, 143)",
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"chr48": "rgb(20, 255, 177)",
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}
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}

‎js/util/igvUtils.js

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* THE SOFTWARE.
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*/
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import {FileUtils, StringUtils} from "../../node_modules/igv-utils/src/index.js"
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import {FileUtils, StringUtils} from 'igv-utils'
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import * as DOMUtils from "./dom-utils.js"
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const extend = function (parent, child) {

‎js/util/paintAxis.js

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‎js/util/viewportUtils.js

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