@gmod/bbi 2.0.3 → 2.0.4
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/CHANGELOG.md +5 -1
- package/dist/bbi.js +4 -3
- package/dist/bbi.js.map +1 -1
- package/dist/blockView.js +2 -3
- package/dist/blockView.js.map +1 -1
- package/esm/bbi.js +4 -3
- package/esm/bbi.js.map +1 -1
- package/esm/blockView.js +2 -3
- package/esm/blockView.js.map +1 -1
- package/package.json +12 -12
- package/src/bbi.ts +5 -3
- package/src/blockView.ts +14 -4
package/CHANGELOG.md
CHANGED
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@@ -1,6 +1,10 @@
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1
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-
## [2.0.
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1
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+
## [2.0.4](https://github.com/GMOD/bbi-js/compare/v2.0.3...v2.0.4) (2022-10-15)
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2
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+
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2
3
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3
4
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5
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+
- Use plain TextDecoder for decoding autoSql
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6
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+
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7
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## [2.0.3](https://github.com/GMOD/bbi-js/compare/v2.0.2...v2.0.3) (2022-10-10)
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4
8
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9
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- Add BigInt64 polyfill for older safari
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6
10
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package/dist/bbi.js
CHANGED
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@@ -55,6 +55,9 @@ var operators_1 = require("rxjs/operators");
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var blockView_1 = require("./blockView");
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var BIG_WIG_MAGIC = -2003829722;
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var BIG_BED_MAGIC = -2021002517;
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58
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+
function toString(arr) {
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59
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+
return new TextDecoder().decode(arr);
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60
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+
}
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/* get the compiled parsers for different sections of the bigwig file
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*
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* @param isBE - is big endian, typically false
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@@ -187,9 +190,7 @@ var BBI = /** @class */ (function () {
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}
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if (asOffset) {
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off = Number(header.asOffset);
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190
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-
header.autoSql = buffer
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191
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-
.subarray(off, buffer.indexOf(0, off))
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192
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-
.toString('utf8');
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+
header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)));
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}
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if (header.totalSummaryOffset > requestSize) {
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return [2 /*return*/, this._getMainHeader(opts, requestSize * 2)];
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package/dist/bbi.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAsC;AACtC,yDAA6E;AAC7E,6BAA2C;AAC3C,4CAAuC;AACvC,yCAAuC;AAEvC,IAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AACjC,IAAM,aAAa,GAAG,CAAC,UAAU,CAAA;
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1
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+
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAsC;AACtC,yDAA6E;AAC7E,6BAA2C;AAC3C,4CAAuC;AACvC,yCAAuC;AAEvC,IAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AACjC,IAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AAEjC,SAAS,QAAQ,CAAC,GAAe;IAC/B,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;AACtC,CAAC;AAyCD;;;;GAIG;AACH,SAAS,UAAU,CAAC,IAAa;IAC/B,IAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;IAClC,IAAM,YAAY,GAAG,IAAI,sBAAM,EAAE;SAC9B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,OAAO,CAAC;SACd,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,eAAe,CAAC;SACvB,MAAM,CAAC,iBAAiB,CAAC;SACzB,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,qBAAqB,CAAC;SAC7B,MAAM,CAAC,YAAY,CAAC;SACpB,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,UAAU,CAAC,CAAC,iCAAiC;SACpD,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,iBAAiB,CAAC,CAAC,oCAAoC;SAC9D,KAAK,CAAC,YAAY,EAAE;QACnB,MAAM,EAAE,eAAe;QACvB,IAAI,EAAE,IAAI,sBAAM,EAAE;aACf,SAAS,CAAC,EAAE,CAAC;aACb,MAAM,CAAC,gBAAgB,CAAC;aACxB,MAAM,CAAC,UAAU,CAAC;aAClB,MAAM,CAAC,YAAY,CAAC;aACpB,MAAM,CAAC,aAAa,CAAC;KACzB,CAAC,CAAA;IAEJ,IAAM,kBAAkB,GAAG,IAAI,sBAAM,EAAE;SACpC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,cAAc,CAAC;SACtB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,iBAAiB,CAAC,CAAA;IAE9B,IAAM,eAAe,GAAG,IAAI,sBAAM,EAAE;SACjC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,OAAO,CAAC;SACf,MAAM,CAAC,WAAW,CAAC;SACnB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,WAAW,CAAC,CAAA;IAEtB,IAAM,UAAU,GAAG,IAAI,sBAAM,EAAE;SAC5B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,YAAY,CAAC;SACnB,IAAI,CAAC,CAAC,CAAC;SACP,MAAM,CAAC,KAAK,CAAC;SACb,UAAU,CAAC,QAAQ,CAAC,CAAA;IAEvB,OAAO;QACL,eAAe,iBAAA;QACf,kBAAkB,oBAAA;QAClB,YAAY,cAAA;QACZ,UAAU,YAAA;KACX,CAAA;AACH,CAAC;AAQD;IAsBE;;;;;OAKG;IACH,aACE,OAKM;QALN,wBAAA,EAAA,YAKM;QAEE,IAAA,UAAU,GAAwC,OAAO,WAA/C,EAAE,KAAsC,OAAO,cAAvB,EAAtB,aAAa,mBAAG,UAAA,CAAC,IAAI,OAAA,CAAC,EAAD,CAAC,KAAA,EAAE,IAAI,GAAU,OAAO,KAAjB,EAAE,GAAG,GAAK,OAAO,IAAZ,CAAY;QACjE,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;QAClC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,GAAG,GAAG,UAAU,CAAA;SACtB;aAAM,IAAI,GAAG,EAAE;YACd,IAAI,CAAC,GAAG,GAAG,IAAI,+BAAU,CAAC,GAAG,CAAC,CAAA;SAC/B;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,GAAG,GAAG,IAAI,8BAAS,CAAC,IAAI,CAAC,CAAA;SAC/B;aAAM;YACL,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;SACjC;IACH,CAAC;IAxCD;;;OAGG;IACI,uBAAS,GAAhB,UAAiB,IAAuC;QAAxD,iBASC;QATgB,qBAAA,EAAA,SAAuC;QACtD,IAAM,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,IAAmB,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;QAC1E,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE;YACjB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,UAAA,CAAC;gBAC7C,KAAI,CAAC,OAAO,GAAG,SAAS,CAAA;gBACxB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,OAAO,CAAA;IACrB,CAAC;IA6Ba,wBAAU,GAAxB,UAAyB,IAAoB;;;;;4BAC5B,qBAAM,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,EAAA;;wBAAxC,MAAM,GAAG,SAA+B;wBAC/B,qBAAM,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,IAAI,CAAC,EAAA;;wBAAhD,MAAM,GAAG,SAAuC;wBACtD,4CAAY,MAAM,GAAK,MAAM,GAAE;;;;KAChC;IAEa,4BAAc,GAA5B,UACE,IAAoB,EACpB,WAAkB;QAAlB,4BAAA,EAAA,kBAAkB;;;;;4BAEC,qBAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,EACzB,CAAC,EACD,WAAW,EACX,CAAC,EACD,IAAI,CACL,EAAA;;wBANO,MAAM,GAAK,CAAA,SAMlB,CAAA,OANa;wBAOR,WAAW,GAAG,IAAI,CAAC,YAAY,CAAC,MAAM,CAAC,CAAA;wBACvC,GAAG,GAAG,UAAU,CAAC,WAAW,CAAC,CAAA;wBAC7B,MAAM,GAAG,GAAG,CAAC,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;wBACrC,KAAK,GAAmC,MAAM,MAAzC,EAAE,QAAQ,GAAyB,MAAM,SAA/B,EAAE,kBAAkB,GAAK,MAAM,mBAAX,CAAW;wBACtD,MAAM,CAAC,QAAQ,GAAG,KAAK,KAAK,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAA;wBAC/D,IAAI,QAAQ,GAAG,WAAW,IAAI,kBAAkB,GAAG,WAAW,EAAE;4BAC9D,sBAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,EAAA;yBAClD;wBACD,IAAI,QAAQ,EAAE;4BACN,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;4BACnC,MAAM,CAAC,OAAO,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAA;yBACxE;wBACD,IAAI,MAAM,CAAC,kBAAkB,GAAG,WAAW,EAAE;4BAC3C,sBAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,EAAA;yBAClD;wBACD,IAAI,MAAM,CAAC,kBAAkB,EAAE;4BACvB,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAC,CAAA;4BACzD,GAAG,GAAG,GAAG,CAAC,kBAAkB,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;4BAC9C,MAAM,CAAC,YAAY,yBAAQ,GAAG,KAAE,YAAY,EAAE,MAAM,CAAC,GAAG,CAAC,YAAY,CAAC,GAAE,CAAA;yBACzE;wBACD,4CAAY,MAAM,KAAE,WAAW,aAAA,KAAE;;;;KAClC;IAEO,0BAAY,GAApB,UAAqB,MAAc;QACjC,IAAI,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC/B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE;YAClD,OAAO,KAAK,CAAA;SACb;QACD,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE;YAClD,OAAO,IAAI,CAAA;SACZ;QACD,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;IAC7C,CAAC;IAED,qCAAqC;IACvB,4BAAc,GAA5B,UAA6B,MAAc,EAAE,IAA8B;;;;;;;wBACnE,IAAI,GAAG,MAAM,CAAC,WAAW,CAAA;wBACzB,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;wBAC5B,YAAY,GAEd,EAAE,CAAA;wBACA,UAAU,GAA8B,EAAE,CAAA;wBAE5C,kBAAkB,GAAG,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAA;wBACpD,eAAe,GAAG,MAAM,CAAC,MAAM,CAAC,eAAe,CAAC,CAAA;wBACtD,OAAO,kBAAkB,GAAG,CAAC,K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package/dist/blockView.js
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@@ -202,7 +202,7 @@ var BlockView = /** @class */ (function () {
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}
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BlockView.prototype.readWigData = function (chrName, start, end, observer, opts) {
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return __awaiter(this, void 0, void 0, function () {
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var _a, refsByName, bbi, cirTreeOffset, isBigEndian, chrId_1, request_1,
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var _a, refsByName, bbi, cirTreeOffset, isBigEndian, chrId_1, request_1, buffer, cirBlockSize_1, blocksToFetch_1, outstanding_1, cirFobRecur2_1, filterFeats_1, cirFobStartFetch_1, cirFobRecur_1, e_1;
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var _this = this;
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return __generator(this, function (_b) {
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switch (_b.label) {
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}
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request_1 = { chrId: chrId_1, start: start, end: end };
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if (!this.cirTreePromise) {
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this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, off, opts);
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this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, Number(cirTreeOffset), opts);
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}
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return [4 /*yield*/, this.cirTreePromise];
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case 1:
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package/dist/blockView.js.map
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1
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+
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|
package/esm/bbi.js
CHANGED
|
@@ -5,6 +5,9 @@ import { reduce } from 'rxjs/operators';
|
|
|
5
5
|
import { BlockView } from './blockView';
|
|
6
6
|
const BIG_WIG_MAGIC = -2003829722;
|
|
7
7
|
const BIG_BED_MAGIC = -2021002517;
|
|
8
|
+
function toString(arr) {
|
|
9
|
+
return new TextDecoder().decode(arr);
|
|
10
|
+
}
|
|
8
11
|
/* get the compiled parsers for different sections of the bigwig file
|
|
9
12
|
*
|
|
10
13
|
* @param isBE - is big endian, typically false
|
|
@@ -116,9 +119,7 @@ export class BBI {
|
|
|
116
119
|
}
|
|
117
120
|
if (asOffset) {
|
|
118
121
|
const off = Number(header.asOffset);
|
|
119
|
-
header.autoSql = buffer
|
|
120
|
-
.subarray(off, buffer.indexOf(0, off))
|
|
121
|
-
.toString('utf8');
|
|
122
|
+
header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)));
|
|
122
123
|
}
|
|
123
124
|
if (header.totalSummaryOffset > requestSize) {
|
|
124
125
|
return this._getMainHeader(opts, requestSize * 2);
|
package/esm/bbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,SAAS,EAAE,UAAU,EAAqB,MAAM,oBAAoB,CAAA;AAC7E,OAAO,EAAE,UAAU,EAAY,MAAM,MAAM,CAAA;AAC3C,OAAO,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAA;AACvC,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAA;AAEvC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AACjC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;
|
|
1
|
+
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,SAAS,EAAE,UAAU,EAAqB,MAAM,oBAAoB,CAAA;AAC7E,OAAO,EAAE,UAAU,EAAY,MAAM,MAAM,CAAA;AAC3C,OAAO,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAA;AACvC,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAA;AAEvC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AACjC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AAEjC,SAAS,QAAQ,CAAC,GAAe;IAC/B,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;AACtC,CAAC;AAyCD;;;;GAIG;AACH,SAAS,UAAU,CAAC,IAAa;IAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;IAClC,MAAM,YAAY,GAAG,IAAI,MAAM,EAAE;SAC9B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,OAAO,CAAC;SACd,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,eAAe,CAAC;SACvB,MAAM,CAAC,iBAAiB,CAAC;SACzB,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,qBAAqB,CAAC;SAC7B,MAAM,CAAC,YAAY,CAAC;SACpB,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,UAAU,CAAC,CAAC,iCAAiC;SACpD,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,iBAAiB,CAAC,CAAC,oCAAoC;SAC9D,KAAK,CAAC,YAAY,EAAE;QACnB,MAAM,EAAE,eAAe;QACvB,IAAI,EAAE,IAAI,MAAM,EAAE;aACf,SAAS,CAAC,EAAE,CAAC;aACb,MAAM,CAAC,gBAAgB,CAAC;aACxB,MAAM,CAAC,UAAU,CAAC;aAClB,MAAM,CAAC,YAAY,CAAC;aACpB,MAAM,CAAC,aAAa,CAAC;KACzB,CAAC,CAAA;IAEJ,MAAM,kBAAkB,GAAG,IAAI,MAAM,EAAE;SACpC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,cAAc,CAAC;SACtB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,iBAAiB,CAAC,CAAA;IAE9B,MAAM,eAAe,GAAG,IAAI,MAAM,EAAE;SACjC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,OAAO,CAAC;SACf,MAAM,CAAC,WAAW,CAAC;SACnB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,WAAW,CAAC,CAAA;IAEtB,MAAM,UAAU,GAAG,IAAI,MAAM,EAAE;SAC5B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,YAAY,CAAC;SACnB,IAAI,CAAC,CAAC,CAAC;SACP,MAAM,CAAC,KAAK,CAAC;SACb,UAAU,CAAC,QAAQ,CAAC,CAAA;IAEvB,OAAO;QACL,eAAe;QACf,kBAAkB;QAClB,YAAY;QACZ,UAAU;KACX,CAAA;AACH,CAAC;AAQD,MAAM,OAAgB,GAAG;IAsBvB;;;;;OAKG;IACH,YACE,UAKI,EAAE;QAEN,MAAM,EAAE,UAAU,EAAE,aAAa,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,OAAO,CAAA;QACjE,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;QAClC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,GAAG,GAAG,UAAU,CAAA;SACtB;aAAM,IAAI,GAAG,EAAE;YACd,IAAI,CAAC,GAAG,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;SAC/B;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,GAAG,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,CAAA;SAC/B;aAAM;YACL,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;SACjC;IACH,CAAC;IAxCD;;;OAGG;IACI,SAAS,CAAC,OAAqC,EAAE;QACtD,MAAM,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,IAAmB,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;QAC1E,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE;YACjB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAChD,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;gBACxB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,OAAO,CAAA;IACrB,CAAC;IA6BO,KAAK,CAAC,UAAU,CAAC,IAAoB;QAC3C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;QAC9C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACtD,OAAO,EAAE,GAAG,MAAM,EAAE,GAAG,MAAM,EAAE,CAAA;IACjC,CAAC;IAEO,KAAK,CAAC,cAAc,CAC1B,IAAoB,EACpB,WAAW,GAAG,IAAI;QAElB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,EACzB,CAAC,EACD,WAAW,EACX,CAAC,EACD,IAAI,CACL,CAAA;QACD,MAAM,WAAW,GAAG,IAAI,CAAC,YAAY,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,UAAU,CAAC,WAAW,CAAC,CAAA;QACnC,MAAM,MAAM,GAAG,GAAG,CAAC,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,kBAAkB,EAAE,GAAG,MAAM,CAAA;QACtD,MAAM,CAAC,QAAQ,GAAG,KAAK,KAAK,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAA;QAC/D,IAAI,QAAQ,GAAG,WAAW,IAAI,kBAAkB,GAAG,WAAW,EAAE;YAC9D,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;SAClD;QACD,IAAI,QAAQ,EAAE;YACZ,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;YACnC,MAAM,CAAC,OAAO,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAA;SACxE;QACD,IAAI,MAAM,CAAC,kBAAkB,GAAG,WAAW,EAAE;YAC3C,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;SAClD;QACD,IAAI,MAAM,CAAC,kBAAkB,EAAE;YAC7B,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAC,CAAA;YAC/D,MAAM,GAAG,GAAG,GAAG,CAAC,kBAAkB,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YAC9C,MAAM,CAAC,YAAY,GAAG,EAAE,GAAG,GAAG,EAAE,YAAY,EAAE,MAAM,CAAC,GAAG,CAAC,YAAY,CAAC,EAAE,CAAA;SACzE;QACD,OAAO,EAAE,GAAG,MAAM,EAAE,WAAW,EAAE,CAAA;IACnC,CAAC;IAEO,YAAY,CAAC,MAAc;QACjC,IAAI,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC/B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE;YAClD,OAAO,KAAK,CAAA;SACb;QACD,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE;YAClD,OAAO,IAAI,CAAA;SACZ;QACD,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;IAC7C,CAAC;IAED,qCAAqC;IAC7B,KAAK,CAAC,cAAc,CAAC,MAAc,EAAE,IAA8B;QACzE,MAAM,IAAI,GAAG,MAAM,CAAC,WAAW,CAAA;QAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;QAClC,MAAM,YAAY,GAEd,EAAE,CAAA;QACN,MAAM,UAAU,GAA8B,EAAE,CAAA;QAEhD,IAAI,kBAAkB,GAAG,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAA;QAC1D,MAAM,eAAe,GAAG,MAAM,CAAC,MAAM,CAAC,eAAe,CAAC,CAAA;QACtD,OAAO,kBAAkB,GAAG,CAAC,KAAK,CAAC,EAAE;YACnC,kBAAkB,IAAI,CAAC,CAAA;S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|
package/esm/blockView.js
CHANGED
|
@@ -146,8 +146,7 @@ export class BlockView {
|
|
|
146
146
|
}
|
|
147
147
|
const request = { chrId, start, end };
|
|
148
148
|
if (!this.cirTreePromise) {
|
|
149
|
-
|
|
150
|
-
this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, off, opts);
|
|
149
|
+
this.cirTreePromise = bbi.read(Buffer.alloc(48), 0, 48, Number(cirTreeOffset), opts);
|
|
151
150
|
}
|
|
152
151
|
const { buffer } = await this.cirTreePromise;
|
|
153
152
|
const cirBlockSize = isBigEndian
|
|
@@ -170,7 +169,7 @@ export class BlockView {
|
|
|
170
169
|
if (p.recurOffsets) {
|
|
171
170
|
const recurOffsets = p.recurOffsets
|
|
172
171
|
.filter(filterFeats)
|
|
173
|
-
.map(
|
|
172
|
+
.map(l => Number(l.blockOffset));
|
|
174
173
|
if (recurOffsets.length > 0) {
|
|
175
174
|
cirFobRecur(recurOffsets, level + 1);
|
|
176
175
|
}
|
package/esm/blockView.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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,CAAC,CAAA;QACX,MAAM,QAAQ,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACjD,MAAM,IAAI,CAAC,CAAA;QACX,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,IAAI,CAAC,CAAA;QACX,MAAM,SAAS,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QAClD,MAAM,IAAI,CAAC,CAAA;QACX,MAAM,KAAK,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;QAClC,QAAQ,SAAS,EAAE;YACjB,KAAK,CAAC;gBACJ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE;oBAClC,MAAM,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;oBAC7C,MAAM,IAAI,CAAC,CAAA;oBACX,MAAM,GAAG,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;oBAC3C,MAAM,IAAI,CAAC,CAAA;oBACX,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;oBAC/C,MAAM,IAAI,CAAC,CAAA;oBACX,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,CAAA;iBACjC;gBACD,MAAK;YACP,KAAK,CAAC;gBACJ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE;oBAClC,MAAM,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;oBAC7C,MAAM,IAAI,CAAC,CAAA;oBACX,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;oBAC/C,MAAM,IAAI,CAAC,CAAA;oBACX,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,GAAG,QAAQ,EAAE,CAAA;iBACnD;gBACD,MAAK;YACP,KAAK,CAAC;gBACJ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE;oBAClC,MAAM,KAAK,GAAG,QAAQ,CAAC,UAAU,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;oBAC/C,MAAM,IAAI,CAAC,CAAA;oBACX,MAAM,KAAK,GAAG,UAAU,GAAG,CAAC,GAAG,QAAQ,CAAA;oBACvC,KAAK,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,GAAG,QAAQ,EAAE,CAAA;iBACnD;gBACD,MAAK;SACR;QAED,OAAO,OAAO;YACZ,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAM,EAAE,EAAE,CACtB,WAAW,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,OAAO,CAAC,KAAK,EAAE,OAAO,CAAC,GAAG,CAAC,CACxD;YACH,CAAC,CAAC,KAAK,CAAA;IACX,CAAC;IAEM,KAAK,CAAC,YAAY,CACvB,QAA6B,EAC7B,MAA4C,EAC5C,OAAgB,EAAE;QAElB,IAAI;YACF,MAAM,EAAE,SAAS,EAAE,YAAY,EAAE,GAAG,IAAI,CAAA;YACxC,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;YAChC,MAAM,kBAAkB,GAAG,WAAW,CAAC,MAAM,CAAC,CAAA;YAC9C,gBAAgB,CAAC,MAAM,CAAC,CAAA;YACxB,MAAM,OAAO,CAAC,GAAG,CACf,kBAAkB,CAAC,GAAG,CAAC,KAAK,EAAC,UAAU,EAAC,EAAE;gBACxC,gBAAgB,CAAC,MAAM,CAAC,CAAA;gBACxB,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,UAAU,CAAA;gBACrC,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,YAAY,CAAC,GAAG,CACtC,GAAG,MAAM,IAAI,MAAM,EAAE,EACrB,UAAU,EACV,MAAM,CACP,CAAA;gBACD,UAAU,CAAC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;oBAChC,gBAAgB,CAAC,MAAM,CAAC,CAAA;oBACxB,IAAI,WAAW,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,UAAU,CAAC,MAAM,CAAC,CAAA;oBAClE,IAAI,UAAU,GAAG,IAAI,CAAA;oBACrB,IAAI,YAAY,EAAE;wBAChB,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,WAAW,CAAC,CAAC,CAAA;wBAC9C,WAAW,GAAG,CAAC,CAAA;qBAChB;oBACD,gBAAgB,CAAC,MAAM,CAAC,CAAA;oBAExB,QAAQ,SAAS,EAAE;wBACjB,KAAK,SAAS;4BACZ,QAAQ,CAAC,IAAI,CACX,IAAI,CAAC,iBAAiB,CAAC,UAAU,EAAE,WAAW,EAAE,OAAO,CAAC,CACzD,CAAA;4BACD,MAAK;wBACP,KAAK,QAAQ;4BACX,QAAQ,CAAC,IAAI,CACX,IAAI,CAAC,gBAAgB,CAAC,UAAU,EAAE,WAAW,EAAE,OAAO,CAAC,CACxD,CAAA;4BACD,MAAK;wBACP,KAAK,QAAQ;4BACX,QAAQ,CAAC,IAAI,CACX,IAAI,CAAC,gBAAgB,CACnB,UAAU,EACV,WAAW,EACX,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,EAC/B,OAAO,CACR,CACF,CAAA;4BACD,MAAK;wBACP;4BACE,OAAO,CAAC,IAAI,CAAC,8BAA8B,SAAS,EAAE,CAAC,CAAA;qBAC1D;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CACH,CAAA;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;SACpB;QAAC,OAAO,CAAC,EAAE;YACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;SAClB;IACH,CAAC;CACF"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/bbi",
|
|
3
|
-
"version": "2.0.
|
|
3
|
+
"version": "2.0.4",
|
|
4
4
|
"description": "Parser for BigWig/BigBed files",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/bbi-js",
|
|
@@ -49,25 +49,25 @@
|
|
|
49
49
|
"rxjs": "^6.5.2"
|
|
50
50
|
},
|
|
51
51
|
"devDependencies": {
|
|
52
|
-
"@gmod/bed": "^2.
|
|
53
|
-
"@types/jest": "^
|
|
54
|
-
"@types/long": "^
|
|
55
|
-
"@types/node": "^18.
|
|
52
|
+
"@gmod/bed": "^2.1.2",
|
|
53
|
+
"@types/jest": "^29.1.2",
|
|
54
|
+
"@types/long": "^5.0.0",
|
|
55
|
+
"@types/node": "^18.11.0",
|
|
56
56
|
"@types/pako": "^2.0.0",
|
|
57
|
-
"@typescript-eslint/eslint-plugin": "^5.
|
|
58
|
-
"@typescript-eslint/parser": "^5.
|
|
57
|
+
"@typescript-eslint/eslint-plugin": "^5.40.0",
|
|
58
|
+
"@typescript-eslint/parser": "^5.40.0",
|
|
59
59
|
"cross-fetch": "^3.0.2",
|
|
60
|
-
"eslint": "^8.
|
|
60
|
+
"eslint": "^8.25.0",
|
|
61
61
|
"eslint-config-prettier": "^8.3.0",
|
|
62
62
|
"eslint-plugin-import": "^2.25.3",
|
|
63
63
|
"eslint-plugin-prettier": "^4.0.0",
|
|
64
|
-
"jest": "^
|
|
65
|
-
"jest-environment-jsdom": "^
|
|
64
|
+
"jest": "^29.2.0",
|
|
65
|
+
"jest-environment-jsdom": "^29.2.0",
|
|
66
66
|
"prettier": "^2.5.1",
|
|
67
67
|
"rimraf": "^3.0.2",
|
|
68
68
|
"standard-changelog": "^2.0.11",
|
|
69
|
-
"ts-jest": "^
|
|
70
|
-
"typescript": "^4.
|
|
69
|
+
"ts-jest": "^29.0.3",
|
|
70
|
+
"typescript": "^4.8.4"
|
|
71
71
|
},
|
|
72
72
|
"publishConfig": {
|
|
73
73
|
"access": "public"
|
package/src/bbi.ts
CHANGED
|
@@ -7,6 +7,10 @@ import { BlockView } from './blockView'
|
|
|
7
7
|
const BIG_WIG_MAGIC = -2003829722
|
|
8
8
|
const BIG_BED_MAGIC = -2021002517
|
|
9
9
|
|
|
10
|
+
function toString(arr: Uint8Array) {
|
|
11
|
+
return new TextDecoder().decode(arr)
|
|
12
|
+
}
|
|
13
|
+
|
|
10
14
|
export interface Feature {
|
|
11
15
|
start: number
|
|
12
16
|
end: number
|
|
@@ -190,9 +194,7 @@ export abstract class BBI {
|
|
|
190
194
|
}
|
|
191
195
|
if (asOffset) {
|
|
192
196
|
const off = Number(header.asOffset)
|
|
193
|
-
header.autoSql = buffer
|
|
194
|
-
.subarray(off, buffer.indexOf(0, off))
|
|
195
|
-
.toString('utf8')
|
|
197
|
+
header.autoSql = toString(buffer.subarray(off, buffer.indexOf(0, off)))
|
|
196
198
|
}
|
|
197
199
|
if (header.totalSummaryOffset > requestSize) {
|
|
198
200
|
return this._getMainHeader(opts, requestSize * 2)
|
package/src/blockView.ts
CHANGED
|
@@ -16,6 +16,8 @@ interface CoordRequest {
|
|
|
16
16
|
end: number
|
|
17
17
|
}
|
|
18
18
|
interface DataBlock {
|
|
19
|
+
blockOffset: bigint
|
|
20
|
+
blockSize: bigint
|
|
19
21
|
startChrom: number
|
|
20
22
|
endChrom: number
|
|
21
23
|
startBase: number
|
|
@@ -200,8 +202,13 @@ export class BlockView {
|
|
|
200
202
|
}
|
|
201
203
|
const request = { chrId, start, end }
|
|
202
204
|
if (!this.cirTreePromise) {
|
|
203
|
-
|
|
204
|
-
|
|
205
|
+
this.cirTreePromise = bbi.read(
|
|
206
|
+
Buffer.alloc(48),
|
|
207
|
+
0,
|
|
208
|
+
48,
|
|
209
|
+
Number(cirTreeOffset),
|
|
210
|
+
opts,
|
|
211
|
+
)
|
|
205
212
|
}
|
|
206
213
|
const { buffer } = await this.cirTreePromise
|
|
207
214
|
const cirBlockSize = isBigEndian
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@@ -218,7 +225,10 @@ export class BlockView {
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218
225
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try {
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219
226
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const data = cirBlockData.subarray(offset)
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220
227
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221
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-
const p = this.leafParser.parse(data)
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228
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+
const p = this.leafParser.parse(data) as {
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229
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+
blocksToFetch: DataBlock[]
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230
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+
recurOffsets: DataBlock[]
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231
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+
}
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222
232
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if (p.blocksToFetch) {
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223
233
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blocksToFetch = blocksToFetch.concat(
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224
234
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p.blocksToFetch
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@@ -232,7 +242,7 @@ export class BlockView {
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232
242
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if (p.recurOffsets) {
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233
243
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const recurOffsets = p.recurOffsets
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234
244
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.filter(filterFeats)
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235
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-
.map(
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245
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+
.map(l => Number(l.blockOffset))
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236
246
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if (recurOffsets.length > 0) {
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237
247
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cirFobRecur(recurOffsets, level + 1)
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238
248
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}
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