igv 3.7.1 → 3.7.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +10 -10
- package/dist/igv.esm.js +278 -81
- package/dist/igv.esm.min.js +9 -9
- package/dist/igv.esm.min.js.map +1 -1
- package/dist/igv.js +278 -81
- package/dist/igv.min.js +9 -9
- package/dist/igv.min.js.map +1 -1
- package/package.json +1 -1
- package/dist/igv.esm.js.gz +0 -0
- package/dist/igv.esm.min.js.gz +0 -0
- package/dist/igv.iife.js.map +0 -1
package/dist/igv.js
CHANGED
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@@ -10638,7 +10638,7 @@
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return list;
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}
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-
/*! @license DOMPurify 3.3.
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+
/*! @license DOMPurify 3.3.1 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.3.1/LICENSE */
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const {
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entries,
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@@ -10945,7 +10945,7 @@
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function createDOMPurify() {
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let window = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : getGlobal();
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const DOMPurify = root => createDOMPurify(root);
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-
DOMPurify.version = '3.3.
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+
DOMPurify.version = '3.3.1';
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DOMPurify.removed = [];
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if (!window || !window.document || window.document.nodeType !== NODE_TYPE.document || !window.Element) {
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// Not running in a browser, provide a factory function
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@@ -11291,6 +11291,12 @@
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}
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addToSet(FORBID_CONTENTS, cfg.FORBID_CONTENTS, transformCaseFunc);
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}
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if (cfg.ADD_FORBID_CONTENTS) {
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if (FORBID_CONTENTS === DEFAULT_FORBID_CONTENTS) {
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FORBID_CONTENTS = clone(FORBID_CONTENTS);
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}
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addToSet(FORBID_CONTENTS, cfg.ADD_FORBID_CONTENTS, transformCaseFunc);
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}
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/* Add #text in case KEEP_CONTENT is set to true */
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if (KEEP_CONTENT) {
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ALLOWED_TAGS['#text'] = true;
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@@ -31918,7 +31924,7 @@
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headers['Range'] = rangeString;
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let url = this.url.slice(); // slice => copy
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-
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+
headers['User-Agent'] = 'IGV';
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if (this.config.oauthToken) {
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const token = resolveToken(this.config.oauthToken);
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headers['Authorization'] = `Bearer ${token}`;
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@@ -33983,7 +33989,166 @@
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|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F2232012c-4627-439b-9ce7-ad10a2bc3334%2F4DNFIESB8H1S.hic": "8654573338,25900",
|
|
34138
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F07c7a44f-cb01-4901-b591-051913e91353%2F4DNFIK3NAVTO.hic": "8415503170,25900",
|
|
34139
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fcabde890-f7cd-4916-a749-902673f6a716%2F4DNFIOTFSJFL.hic": "3455979876,22663",
|
|
34140
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F1878f6d9-cb86-4be3-baa6-9300d32a6b46%2F4DNFINCBG8I4.hic": "3356575145,22663",
|
|
34141
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F49813dc5-38c1-41d3-ad6a-b27e11f925fc%2F4DNFISZ88WZA.hic": "7739704623,22663",
|
|
34142
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F3fd4b6e2-2002-4897-91c1-ebea81ac7f56%2F4DNFI42A55E5.hic": "6954360693,22663",
|
|
34143
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F931eb1f3-c388-40c7-89e0-e995851650da%2F4DNFIJQO4MRF.hic": "16726884852,25900",
|
|
34144
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fe6ecfcb8-9ca6-44c3-9e27-b4e475a382e4%2F4DNFIZX79UT2.hic": "13334742903,25900",
|
|
34145
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fc62048ee-843f-40ee-81ad-f78d20266f7d%2F4DNFICZG2DYC.hic": "16057986680,25900",
|
|
34146
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F6694b1fb-7fdd-4c1d-9fc6-8dfc8f6b5b58%2F4DNFIK6TSF51.hic": "13887898680,25900",
|
|
34147
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F2ce3bdb5-84cb-4d31-abfa-e92a39889972%2F4DNFI1GY4LKB.hic": "15320828542,25900",
|
|
34148
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F10758c5f-f49a-4da5-9e4e-25907afe27e2%2F4DNFI86G6QZJ.hic": "13911815900,25900",
|
|
34149
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F15e818b8-346b-4f90-a321-b7dd72abb7dc%2F4DNFINFK9D35.hic": "17494323050,22663",
|
|
34150
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F5501e4db-e6a4-41da-85d4-9114ca5ba28e%2F4DNFIBFXR38K.hic": "17172205445,22663",
|
|
34151
|
+
"4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F378a1641-5894-475e-8614-bd016e8529d5%2F4DNFIMBPX8Q1.hic": "17880333903,22663"
|
|
33987
34152
|
};
|
|
33988
34153
|
|
|
33989
34154
|
const isNode = typeof process !== 'undefined' && process.versions != null && process.versions.node != null;
|
|
@@ -34010,6 +34175,8 @@
|
|
|
34010
34175
|
this.normalizationTypes = ['NONE'];
|
|
34011
34176
|
this.matrixCache = new LRU$1(10);
|
|
34012
34177
|
this.blockCache = new BlockCache();
|
|
34178
|
+
this.normVectorIndexPosition = -1;
|
|
34179
|
+
this.normVectorIndexSize = -1;
|
|
34013
34180
|
|
|
34014
34181
|
// args may specify an io.File object, a local path (Node only), or a url
|
|
34015
34182
|
if (args.file) {
|
|
@@ -34029,9 +34196,9 @@
|
|
|
34029
34196
|
}
|
|
34030
34197
|
} else if (args.path) {
|
|
34031
34198
|
// path argument, assumed local file
|
|
34032
|
-
throw Error(`path property is deprecated, use NodeLocalFile`)
|
|
34199
|
+
throw Error(`path property is deprecated, use NodeLocalFile`);
|
|
34033
34200
|
} else {
|
|
34034
|
-
throw Error("Arguments must include file, blob, url, or path")
|
|
34201
|
+
throw Error("Arguments must include file, blob, url, or path");
|
|
34035
34202
|
}
|
|
34036
34203
|
}
|
|
34037
34204
|
|
|
@@ -34056,15 +34223,15 @@
|
|
|
34056
34223
|
const binaryParser = new BinaryParser(new DataView(data));
|
|
34057
34224
|
this.magic = binaryParser.getString();
|
|
34058
34225
|
this.version = binaryParser.getInt();
|
|
34059
|
-
return this.version
|
|
34226
|
+
return this.version;
|
|
34060
34227
|
} else {
|
|
34061
|
-
return this.version
|
|
34228
|
+
return this.version;
|
|
34062
34229
|
}
|
|
34063
34230
|
}
|
|
34064
34231
|
|
|
34065
34232
|
async getMetaData() {
|
|
34066
34233
|
await this.init();
|
|
34067
|
-
return this.meta
|
|
34234
|
+
return this.meta;
|
|
34068
34235
|
}
|
|
34069
34236
|
|
|
34070
34237
|
async readHeaderAndFooter() {
|
|
@@ -34072,13 +34239,13 @@
|
|
|
34072
34239
|
// Read initial fields magic, version, and footer position
|
|
34073
34240
|
let data = await this.file.read(0, 16);
|
|
34074
34241
|
if (!data || data.byteLength === 0) {
|
|
34075
|
-
throw Error("File content is empty")
|
|
34242
|
+
throw Error("File content is empty");
|
|
34076
34243
|
}
|
|
34077
34244
|
let binaryParser = new BinaryParser(new DataView(data));
|
|
34078
34245
|
this.magic = binaryParser.getString();
|
|
34079
34246
|
this.version = binaryParser.getInt();
|
|
34080
34247
|
if (this.version < 5) {
|
|
34081
|
-
throw Error("Unsupported hic version: " + this.version)
|
|
34248
|
+
throw Error("Unsupported hic version: " + this.version);
|
|
34082
34249
|
}
|
|
34083
34250
|
this.footerPosition = binaryParser.getLong();
|
|
34084
34251
|
|
|
@@ -34087,7 +34254,7 @@
|
|
|
34087
34254
|
await this.readFooter();
|
|
34088
34255
|
|
|
34089
34256
|
const bodyPostion = Object.values(this.masterIndex).reduce((min, currentValue) => {
|
|
34090
|
-
return Math.min(min, currentValue.start)
|
|
34257
|
+
return Math.min(min, currentValue.start);
|
|
34091
34258
|
}, Number.MAX_VALUE);
|
|
34092
34259
|
|
|
34093
34260
|
const remainingSize = bodyPostion - 16;
|
|
@@ -34172,7 +34339,7 @@
|
|
|
34172
34339
|
"version": this.version,
|
|
34173
34340
|
"genome": this.genomeId,
|
|
34174
34341
|
"chromosomes": this.chromosomes,
|
|
34175
|
-
"resolutions": this.bpResolutions
|
|
34342
|
+
"resolutions": this.bpResolutions
|
|
34176
34343
|
};
|
|
34177
34344
|
|
|
34178
34345
|
|
|
@@ -34280,14 +34447,14 @@
|
|
|
34280
34447
|
chrIdx2 = tmp;
|
|
34281
34448
|
}
|
|
34282
34449
|
|
|
34283
|
-
const key = Matrix$2.getKey(chrIdx1
|
|
34450
|
+
const key = Matrix$2.getKey(chrIdx1, chrIdx2);
|
|
34284
34451
|
const idx = this.masterIndex[key];
|
|
34285
34452
|
if (!idx) {
|
|
34286
|
-
return undefined
|
|
34453
|
+
return undefined;
|
|
34287
34454
|
}
|
|
34288
34455
|
const data = await this.file.read(idx.start, idx.size);
|
|
34289
34456
|
if (!data) {
|
|
34290
|
-
return undefined
|
|
34457
|
+
return undefined;
|
|
34291
34458
|
}
|
|
34292
34459
|
|
|
34293
34460
|
return Matrix$2.parseMatrix(data, this.chromosomes);
|
|
@@ -34310,7 +34477,7 @@
|
|
|
34310
34477
|
|
|
34311
34478
|
const blocks = await this.getBlocks(region1, region2, units, binsize);
|
|
34312
34479
|
if (!blocks || blocks.length === 0) {
|
|
34313
|
-
return []
|
|
34480
|
+
return [];
|
|
34314
34481
|
}
|
|
34315
34482
|
|
|
34316
34483
|
const contactRecords = [];
|
|
@@ -34376,23 +34543,23 @@
|
|
|
34376
34543
|
|
|
34377
34544
|
if (idx1 === undefined) {
|
|
34378
34545
|
console.log("No chromosome named: " + region1.chr);
|
|
34379
|
-
return []
|
|
34546
|
+
return [];
|
|
34380
34547
|
}
|
|
34381
34548
|
if (idx2 === undefined) {
|
|
34382
34549
|
console.log("No chromosome named: " + region2.chr);
|
|
34383
|
-
return []
|
|
34550
|
+
return [];
|
|
34384
34551
|
}
|
|
34385
34552
|
|
|
34386
34553
|
const matrix = await this.getMatrix(idx1, idx2);
|
|
34387
34554
|
if (!matrix) {
|
|
34388
34555
|
console.log("No matrix for " + region1.chr + "-" + region2.chr);
|
|
34389
|
-
return []
|
|
34556
|
+
return [];
|
|
34390
34557
|
}
|
|
34391
34558
|
|
|
34392
34559
|
const zd = matrix.getZoomData(binSize, unit);
|
|
34393
34560
|
if (!zd) {
|
|
34394
|
-
let msg = `No data
|
|
34395
|
-
throw new Error(msg)
|
|
34561
|
+
let msg = `No data available for resolution: ${binSize} for map ${region1.chr}-${region2.chr}`;
|
|
34562
|
+
throw new Error(msg);
|
|
34396
34563
|
}
|
|
34397
34564
|
|
|
34398
34565
|
const blockNumbers = zd.getBlockNumbers(region1, region2, this.version);
|
|
@@ -34423,7 +34590,7 @@
|
|
|
34423
34590
|
const idx = await zd.blockIndex.getBlockIndexEntry(blockNumber);
|
|
34424
34591
|
|
|
34425
34592
|
if (!idx) {
|
|
34426
|
-
return undefined
|
|
34593
|
+
return undefined;
|
|
34427
34594
|
} else {
|
|
34428
34595
|
let data = await this.file.read(idx.filePosition, idx.size);
|
|
34429
34596
|
if (!data) {
|
|
@@ -34536,7 +34703,7 @@
|
|
|
34536
34703
|
|
|
34537
34704
|
const index = normVectorIndex[key];
|
|
34538
34705
|
|
|
34539
|
-
return undefined !== index
|
|
34706
|
+
return undefined !== index;
|
|
34540
34707
|
|
|
34541
34708
|
}
|
|
34542
34709
|
|
|
@@ -34562,20 +34729,20 @@
|
|
|
34562
34729
|
|
|
34563
34730
|
if (!normVectorIndex) {
|
|
34564
34731
|
console.log("Normalization vectors not present in this file");
|
|
34565
|
-
return undefined
|
|
34732
|
+
return undefined;
|
|
34566
34733
|
}
|
|
34567
34734
|
|
|
34568
34735
|
const status = await this.isNormalizationValueAvailableAtResolution(type, chr, unit, binSize);
|
|
34569
34736
|
|
|
34570
34737
|
if (false === status) {
|
|
34571
34738
|
|
|
34572
|
-
const str = `Normalization option ${
|
|
34739
|
+
const str = `Normalization option ${type} not available at resolution ${binSize}. Will use NONE.`;
|
|
34573
34740
|
console.log(str);
|
|
34574
34741
|
|
|
34575
34742
|
if (this.alert) {
|
|
34576
34743
|
this.alert(str);
|
|
34577
|
-
}
|
|
34578
|
-
return undefined
|
|
34744
|
+
}
|
|
34745
|
+
return undefined;
|
|
34579
34746
|
}
|
|
34580
34747
|
|
|
34581
34748
|
const idx = normVectorIndex[key];
|
|
@@ -34602,37 +34769,44 @@
|
|
|
34602
34769
|
return undefined;
|
|
34603
34770
|
}
|
|
34604
34771
|
|
|
34605
|
-
if (
|
|
34772
|
+
if (this.normVectorIndex) {
|
|
34773
|
+
return this.normVectorIndex;
|
|
34774
|
+
}
|
|
34775
|
+
|
|
34606
34776
|
|
|
34607
|
-
|
|
34608
|
-
|
|
34609
|
-
|
|
34610
|
-
|
|
34611
|
-
|
|
34612
|
-
|
|
34613
|
-
|
|
34777
|
+
// If we know the position of the norm vector index, read it directly. This is the case for hic v9 files
|
|
34778
|
+
if (this.normVectorIndexPosition > 0 && this.normVectorIndexSize > 0) {
|
|
34779
|
+
const range = {start: this.normVectorIndexPosition, size: this.normVectorIndexSize};
|
|
34780
|
+
return this.readNormVectorIndex(range);
|
|
34781
|
+
}
|
|
34782
|
+
|
|
34783
|
+
// See if nvi (normVector position and size) is provided in config or can be inferred from url
|
|
34784
|
+
if (!this.config.nvi && this.remote && this.url) {
|
|
34785
|
+
const url = new URL(this.url);
|
|
34786
|
+
const key = encodeURIComponent(url.hostname + url.pathname);
|
|
34787
|
+
if (nvi.hasOwnProperty(key)) {
|
|
34788
|
+
this.config.nvi = nvi[key];
|
|
34614
34789
|
}
|
|
34790
|
+
}
|
|
34615
34791
|
|
|
34616
|
-
|
|
34617
|
-
|
|
34618
|
-
|
|
34619
|
-
|
|
34620
|
-
|
|
34621
|
-
|
|
34622
|
-
|
|
34623
|
-
|
|
34624
|
-
|
|
34625
|
-
|
|
34626
|
-
|
|
34627
|
-
|
|
34628
|
-
|
|
34629
|
-
|
|
34630
|
-
}
|
|
34792
|
+
if (this.config.nvi) {
|
|
34793
|
+
const nviArray = decodeURIComponent(this.config.nvi).split(",");
|
|
34794
|
+
const range = {start: parseInt(nviArray[0]), size: parseInt(nviArray[1])};
|
|
34795
|
+
return this.readNormVectorIndex(range);
|
|
34796
|
+
} else {
|
|
34797
|
+
try {
|
|
34798
|
+
await this.readNormExpectedValuesAndNormVectorIndex();
|
|
34799
|
+
return this.normVectorIndex;
|
|
34800
|
+
} catch (e) {
|
|
34801
|
+
if (e.code === "416" || e.code === 416) {
|
|
34802
|
+
// This is expected if file does not contain norm vectors
|
|
34803
|
+
this.normExpectedValueVectorsPosition = undefined;
|
|
34804
|
+
} else {
|
|
34805
|
+
console.error(e);
|
|
34631
34806
|
}
|
|
34632
34807
|
}
|
|
34633
34808
|
}
|
|
34634
34809
|
|
|
34635
|
-
return this.normVectorIndex
|
|
34636
34810
|
}
|
|
34637
34811
|
|
|
34638
34812
|
async getNormalizationOptions() {
|
|
@@ -34822,9 +34996,9 @@
|
|
|
34822
34996
|
|
|
34823
34997
|
getFileChrName(chrAlias) {
|
|
34824
34998
|
if (this.chrAliasTable.hasOwnProperty(chrAlias)) {
|
|
34825
|
-
return this.chrAliasTable[chrAlias]
|
|
34999
|
+
return this.chrAliasTable[chrAlias];
|
|
34826
35000
|
} else {
|
|
34827
|
-
return chrAlias
|
|
35001
|
+
return chrAlias;
|
|
34828
35002
|
}
|
|
34829
35003
|
}
|
|
34830
35004
|
|
|
@@ -34853,7 +35027,7 @@
|
|
|
34853
35027
|
}
|
|
34854
35028
|
|
|
34855
35029
|
function isGoogleDrive(url) {
|
|
34856
|
-
return url.indexOf("drive.google.com") >= 0 || url.indexOf("www.googleapis.com/drive") > 0
|
|
35030
|
+
return url.indexOf("drive.google.com") >= 0 || url.indexOf("www.googleapis.com/drive") > 0;
|
|
34857
35031
|
}
|
|
34858
35032
|
|
|
34859
35033
|
class Block {
|
|
@@ -76482,7 +76656,7 @@ ${indent}columns: ${matrix.columns}
|
|
|
76482
76656
|
})
|
|
76483
76657
|
}
|
|
76484
76658
|
|
|
76485
|
-
const _version = "3.7.
|
|
76659
|
+
const _version = "3.7.2";
|
|
76486
76660
|
function version() {
|
|
76487
76661
|
return _version
|
|
76488
76662
|
}
|
|
@@ -76546,10 +76720,13 @@ ${indent}columns: ${matrix.columns}
|
|
|
76546
76720
|
genome.wgChromosomeNames.map(nm => genome.getChromosomeDisplayName(nm)) :
|
|
76547
76721
|
[];
|
|
76548
76722
|
|
|
76723
|
+
const alreadyAdded = genome.wgChromosomeNames ? new Set(genome.wgChromosomeNames) : new Set();
|
|
76724
|
+
|
|
76549
76725
|
if (this.showAllChromosomes && genome.chromosomeNames.length > 1) {
|
|
76550
76726
|
const exclude = new Set(list);
|
|
76551
|
-
let count =
|
|
76727
|
+
let count = alreadyAdded.size;
|
|
76552
76728
|
for (let nm of genome.chromosomeNames) {
|
|
76729
|
+
if(alreadyAdded.has(nm)) continue
|
|
76553
76730
|
if (++count === 1000) {
|
|
76554
76731
|
list.push(maximumSequenceCountExceeded);
|
|
76555
76732
|
break
|
|
@@ -79135,6 +79312,15 @@ ${indent}columns: ${matrix.columns}
|
|
|
79135
79312
|
}
|
|
79136
79313
|
}
|
|
79137
79314
|
|
|
79315
|
+
/**
|
|
79316
|
+
* Search for chromosome alias record. If found, cache results in the alias -> chr map
|
|
79317
|
+
*
|
|
79318
|
+
* An alias record is an object with keys corresponding to the chromosome name set (e.g. "ucsc", "refseq", etc) and
|
|
79319
|
+
* value the corresponding chromosome alias for that name set.
|
|
79320
|
+
*
|
|
79321
|
+
* @param alias - the sequence name or alias
|
|
79322
|
+
* @returns {Promise<any>} promise to resolve to the alias record.
|
|
79323
|
+
*/
|
|
79138
79324
|
async search(alias) {
|
|
79139
79325
|
if(this.aliasRecordCache.size === 0) {
|
|
79140
79326
|
await this.loadAliases();
|
|
@@ -79482,7 +79668,7 @@ ${indent}columns: ${matrix.columns}
|
|
|
79482
79668
|
this.ucscID = config.ucscID || ucsdIDMap.get(this.id) || this.id;
|
|
79483
79669
|
this.blatDB = config.blatDB || this.ucscID;
|
|
79484
79670
|
this.name = config.name;
|
|
79485
|
-
this.nameSet = config.nameSet
|
|
79671
|
+
this.nameSet = config.nameSet;
|
|
79486
79672
|
}
|
|
79487
79673
|
|
|
79488
79674
|
|
|
@@ -80784,7 +80970,7 @@ ${indent}columns: ${matrix.columns}
|
|
|
80784
80970
|
}
|
|
80785
80971
|
}
|
|
80786
80972
|
|
|
80787
|
-
const genomeOrReference = session.reference || session.genome;
|
|
80973
|
+
const genomeOrReference = session.reference || session.genome || session.genarkAccession;
|
|
80788
80974
|
if (!genomeOrReference) {
|
|
80789
80975
|
console.warn("No genome or reference object specified");
|
|
80790
80976
|
return
|
|
@@ -81001,6 +81187,15 @@ ${indent}columns: ${matrix.columns}
|
|
|
81001
81187
|
return genome
|
|
81002
81188
|
}
|
|
81003
81189
|
|
|
81190
|
+
async expandGenarkAccession(genarkAccession) {
|
|
81191
|
+
|
|
81192
|
+
const url = convertToHubURL(genarkAccession);
|
|
81193
|
+
const hub = await loadHub(url);
|
|
81194
|
+
const genomeConfig = hub.getGenomeConfig();
|
|
81195
|
+
genomeConfig.nameSet = "ucsc";
|
|
81196
|
+
return genomeConfig
|
|
81197
|
+
}
|
|
81198
|
+
|
|
81004
81199
|
/**
|
|
81005
81200
|
* Load a genome, defined by a string ID or a json-like configuration object. This includes a fasta reference
|
|
81006
81201
|
* as well as optional cytoband and annotation tracks.
|
|
@@ -81010,31 +81205,33 @@ ${indent}columns: ${matrix.columns}
|
|
|
81010
81205
|
*/
|
|
81011
81206
|
async loadGenome(idOrConfig) {
|
|
81012
81207
|
|
|
81013
|
-
|
|
81014
|
-
idOrConfig.url = convertToHubURL(idOrConfig.genarkAccession);
|
|
81015
|
-
}
|
|
81208
|
+
let genomeConfig;
|
|
81016
81209
|
|
|
81017
|
-
|
|
81018
|
-
|
|
81019
|
-
|
|
81020
|
-
|
|
81021
|
-
|
|
81022
|
-
|
|
81023
|
-
|
|
81024
|
-
|
|
81210
|
+
if (idOrConfig.genarkAccession) {
|
|
81211
|
+
genomeConfig = await this.expandGenarkAccession(idOrConfig.genarkAccession);
|
|
81212
|
+
} else {
|
|
81213
|
+
// Translate the generic "url" field, used by clients such as igv-webapp
|
|
81214
|
+
if (idOrConfig.url) {
|
|
81215
|
+
if (isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt")) {
|
|
81216
|
+
idOrConfig.hubURL = idOrConfig.url;
|
|
81217
|
+
delete idOrConfig.url;
|
|
81218
|
+
} else if ("gbk" === getFileExtension(idOrConfig.url)) {
|
|
81219
|
+
idOrConfig.gbkURL = idOrConfig.url;
|
|
81220
|
+
delete idOrConfig.url;
|
|
81221
|
+
}
|
|
81025
81222
|
}
|
|
81026
|
-
}
|
|
81027
81223
|
|
|
81028
|
-
|
|
81029
|
-
|
|
81030
|
-
|
|
81031
|
-
|
|
81032
|
-
|
|
81033
|
-
|
|
81034
|
-
|
|
81035
|
-
|
|
81036
|
-
|
|
81037
|
-
|
|
81224
|
+
|
|
81225
|
+
const isHubGenome = idOrConfig.hubURL || (idOrConfig.url && isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt"));
|
|
81226
|
+
if (isHubGenome) {
|
|
81227
|
+
const hub = await loadHub(idOrConfig.hubURL || idOrConfig.url);
|
|
81228
|
+
genomeConfig = hub.getGenomeConfig();
|
|
81229
|
+
} else if (isString$3(idOrConfig) || !(idOrConfig.url || idOrConfig.fastaURL || idOrConfig.twoBitURL || idOrConfig.gbkURL)) {
|
|
81230
|
+
// Either an ID, a json string, or an object missing required properties.
|
|
81231
|
+
genomeConfig = await GenomeUtils.expandReference(this.alert, idOrConfig);
|
|
81232
|
+
} else {
|
|
81233
|
+
genomeConfig = idOrConfig;
|
|
81234
|
+
}
|
|
81038
81235
|
}
|
|
81039
81236
|
|
|
81040
81237
|
await this.loadReference(genomeConfig);
|