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/dist/igv.js CHANGED
@@ -10638,7 +10638,7 @@
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  return list;
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  }
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- /*! @license DOMPurify 3.3.0 | (c) Cure53 and other contributors | Released under the Apache license 2.0 and Mozilla Public License 2.0 | github.com/cure53/DOMPurify/blob/3.3.0/LICENSE */
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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,
@@ -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 = '3.3.0';
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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
@@ -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;
@@ -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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- // headers['User-Agent'] = 'straw'
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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}`;
@@ -33983,7 +33989,166 @@
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34079
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34080
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34081
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34082
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34083
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34084
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34085
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34086
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34087
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fae0abe8b-41c6-455e-a466-96cda0b2583b%2F4DNFI6C7TKI7.hic": "2357341855,22663",
34088
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F8ea50b3a-b753-426f-bcde-d438bb046ca9%2F4DNFIAXX5DW8.hic": "2753362470,22663",
34089
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F4900dce0-61a6-447f-ac6c-ab305018b9c7%2F4DNFIBY3K18K.hic": "4559946251,22663",
34090
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F7da49fc1-76aa-4c98-98a0-5d3c2b038b48%2F4DNFIOYBTKML.hic": "3184716393,22663",
34091
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F15555ede-38ed-41bc-8360-b7199ef78905%2F4DNFI1AM5YH5.hic": "2297316945,22663",
34092
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F03bdcf69-274b-4032-9f97-c3801eaff73c%2F4DNFICF19STL.hic": "1147374802,22663",
34093
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F38cdfddb-14e4-4975-aa40-32d8755c1c3f%2F4DNFIJOJW15R.hic": "3691597417,22663",
34094
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F9590c872-52ad-4b3f-acb2-c53adedba82a%2F4DNFIM391G1I.hic": "1440905789,22663",
34095
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fe576ec24-0e4f-45eb-8a1a-a3224a4745b0%2F4DNFIDB95IFX.hic": "1297694240,22663",
34096
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F52a81c80-1e92-4f6a-86d9-55e5c51f6a1a%2F4DNFIN5ROA5D.hic": "1518878546,22663",
34097
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fef1c70d3-7183-4d68-89f3-84f40be4754a%2F4DNFI4WHVND7.hic": "905267421,22663",
34098
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F07a2daaa-eceb-413f-9db8-a29804f60e47%2F4DNFIQEYK87U.hic": "1887807641,22663",
34099
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fff393095-88d1-474d-8147-b170895f49e5%2F4DNFIIHXG8KW.hic": "990948025,22663",
34100
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F14475927-663a-46ea-87e5-262b2b63d4cd%2F4DNFI7RGXYFY.hic": "1995218925,25900",
34101
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fe801f002-d414-42ff-a4d6-5fb41700f8ef%2F4DNFI3NN1U8T.hic": "1411001640,25900",
34102
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Ff0d46aa0-ddf5-4cda-af89-52f94a5e2e71%2F4DNFIKCEWMIA.hic": "2428803282,25900",
34103
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fbf511667-f8a9-447f-939a-2f4a6be9e375%2F4DNFII78SGLC.hic": "1346970600,25900",
34104
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fbb09b17a-4913-4b9e-a012-e9479fc61486%2F4DNFIQBPRZZD.hic": "6069682291,25900",
34105
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fba6ff162-dd84-4b2c-ba2d-f07a0b2e4b3f%2F4DNFIRLG5UWL.hic": "2403291005,25900",
34106
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F2b047495-6f82-4500-b544-a1aa76997e28%2F4DNFIGEI2UJ5.hic": "1172022205,25900",
34107
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F5608ab84-424a-4959-a8ff-d30e02b2f7f6%2F4DNFIR3Y85FX.hic": "2506972674,22663",
34108
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F87b3ffac-31fd-453d-848c-701d7f6cfc59%2F4DNFIGXWABZ8.hic": "1822988545,22663",
34109
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F0d791b5a-804c-43a0-b1ff-29934f743de0%2F4DNFIAZ2BC1Z.hic": "2418357843,22663",
34110
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F140f5862-a950-4d6d-b73c-0c25aa3c4625%2F4DNFINL956G3.hic": "2822207807,22663",
34111
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fe1286ed7-6935-45d6-a551-4e23b0f04ab0%2F4DNFIPJBFDS7.hic": "2549466943,22663",
34112
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Ffb268240-1da9-45e0-bdf3-322e8f83479f%2F4DNFI6OVJGRB.hic": "3977878338,22663",
34113
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fae8036e4-c01f-4685-aad1-c9165ea20da9%2F4DNFIY9S5ZOF.hic": "4376491213,22663",
34114
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fe1f7e790-ec33-40bb-a487-da303818d806%2F4DNFI9S2EX2W.hic": "2018000408,22663",
34115
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fb1005a45-2702-4e42-8da0-725cc3b7bd5e%2F4DNFISAAJ8ZA.hic": "1969820347,22663",
34116
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Ff94abe7a-4241-4127-9e4e-ad5c9e097537%2F4DNFIEHRX3PO.hic": "1812900014,22663",
34117
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fc280624f-895f-4ae1-bf79-7dc3b9f3b7b0%2F4DNFID9DXKIA.hic": "725923849,22663",
34118
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fcab608ee-4a04-4778-ac76-6f35f749cf77%2F4DNFIYZY8FRZ.hic": "1740798405,22663",
34119
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Faf129845-3b27-4ef1-9d06-c1874d96678f%2F4DNFI7TWN65F.hic": "734312298,22663",
34120
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fda348dd8-6e9d-42f6-a4f3-33ccee122b5d%2F4DNFIQY1WZG2.hic": "709100099,22663",
34121
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F201f494f-44a5-47b4-84f1-a51589e20475%2F4DNFI1OAGRV3.hic": "687695123,22663",
34122
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F54ba0756-0e28-4362-a6c8-305484c80352%2F4DNFINROFYOA.hic": "701869003,22663",
34123
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F3d1254c1-c8b5-450b-8829-1f410da9411f%2F4DNFII9NVNO3.hic": "9088194137,25900",
34124
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F1a1cc3cc-15a7-4ddf-9eea-b96400def819%2F4DNFIGU793GK.hic": "10224339103,25900",
34125
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F91a5a87a-7e53-4170-9f98-8df880205806%2F4DNFIYU853WO.hic": "5831941450,25900",
34126
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F0695c0b4-8b0e-4a78-a4f9-be8e148eaade%2F4DNFISDI5IAS.hic": "6338256623,25900",
34127
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F2118aed0-8a60-43c7-b204-b326c5ec063e%2F4DNFINR2MFSM.hic": "6918790050,25900",
34128
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F3e956c4d-9520-4275-9d54-480add2831e9%2F4DNFI9FI1WN4.hic": "6077420687,25900",
34129
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F7f902a51-7a0a-41d8-acfa-c29b3420faac%2F4DNFIM351CAA.hic": "7415860197,25900",
34130
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F8c304c3b-71f3-4302-8fe8-989d881d32ae%2F4DNFI176BGDG.hic": "7148579858,25900",
34131
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F74dd94fb-47ea-47e7-94cf-a909e521dc9a%2F4DNFI76TVWF9.hic": "4335721284,22663",
34132
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2Fce6512f3-2c5e-441a-9e20-d025629fddbe%2F4DNFIU8ET5TP.hic": "5420195714,22663",
34133
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F4ea59850-2c40-4a92-a245-76a7893001f2%2F4DNFI6XB8HB4.hic": "5192691591,22663",
34134
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F5d254a61-9894-4c88-a005-31c08155aa14%2F4DNFI6QRXTH3.hic": "3969529135,22663",
34135
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F0fe92b41-3a75-4665-86cf-b39f4cf94aa6%2F4DNFIPVMIIRE.hic": "8681423658,25900",
34136
+ "4dn-open-data-public.s3.amazonaws.com%2Ffourfront-webprod%2Fwfoutput%2F8538b53a-eb26-40cb-9ec3-a61028f43e2b%2F4DNFIPTFHCFP.hic": "8285769882,25900",
34137
+ "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 , chrIdx2);
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 avalailble for resolution: ${binSize} for map ${region1.chr}-${region2.chr}`;
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 ${ type } not available at resolution ${ binSize }. Will use NONE.`;
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 (!this.normVectorIndex) {
34772
+ if (this.normVectorIndex) {
34773
+ return this.normVectorIndex;
34774
+ }
34775
+
34606
34776
 
34607
- // If nvi is not supplied, try reading from remote lambda service
34608
- if (!this.config.nvi && this.remote && this.url) {
34609
- const url = new URL(this.url);
34610
- const key = encodeURIComponent(url.hostname + url.pathname);
34611
- if(nvi.hasOwnProperty(key)) {
34612
- this.config.nvi = nvi[key];
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
- if (this.config.nvi) {
34617
- const nviArray = decodeURIComponent(this.config.nvi).split(",");
34618
- const range = {start: parseInt(nviArray[0]), size: parseInt(nviArray[1])};
34619
- return this.readNormVectorIndex(range)
34620
- } else {
34621
- try {
34622
- await this.readNormExpectedValuesAndNormVectorIndex();
34623
- return this.normVectorIndex
34624
- } catch (e) {
34625
- if (e.code === "416" || e.code === 416) {
34626
- // This is expected if file does not contain norm vectors
34627
- this.normExpectedValueVectorsPosition = undefined;
34628
- } else {
34629
- console.error(e);
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 = "3.7.1";
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 = 0;
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 || 'ucsc';
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
- if (idOrConfig.genarkAccession) {
81014
- idOrConfig.url = convertToHubURL(idOrConfig.genarkAccession);
81015
- }
81208
+ let genomeConfig;
81016
81209
 
81017
- // Translate the generic "url" field, used by clients such as igv-webapp
81018
- if (idOrConfig.url) {
81019
- if (isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt")) {
81020
- idOrConfig.hubURL = idOrConfig.url;
81021
- delete idOrConfig.url;
81022
- } else if ("gbk" === getFileExtension(idOrConfig.url)) {
81023
- idOrConfig.gbkURL = idOrConfig.url;
81024
- delete idOrConfig.url;
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
- let genomeConfig;
81029
- const isHubGenome = idOrConfig.hubURL || (idOrConfig.url && isString$3(idOrConfig.url) && idOrConfig.url.endsWith("/hub.txt"));
81030
- if (isHubGenome) {
81031
- const hub = await loadHub(idOrConfig.hubURL || idOrConfig.url);
81032
- genomeConfig = hub.getGenomeConfig();
81033
- } else if (isString$3(idOrConfig) || !(idOrConfig.url || idOrConfig.fastaURL || idOrConfig.twoBitURL || idOrConfig.gbkURL)) {
81034
- // Either an ID, a json string, or an object missing required properties.
81035
- genomeConfig = await GenomeUtils.expandReference(this.alert, idOrConfig);
81036
- } else {
81037
- genomeConfig = idOrConfig;
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);