@gmod/bam 1.1.8 → 1.1.9
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 +8 -0
- package/README.md +2 -3
- package/dist/bai.d.ts +2 -0
- package/dist/bai.js +300 -548
- package/dist/bai.js.map +1 -0
- package/dist/bamFile.d.ts +4 -6
- package/dist/bamFile.js +675 -1203
- package/dist/bamFile.js.map +1 -0
- package/dist/chunk.js +34 -69
- package/dist/chunk.js.map +1 -0
- package/dist/constants.js +27 -35
- package/dist/constants.js.map +1 -0
- package/dist/csi.js +317 -515
- package/dist/csi.js.map +1 -0
- package/dist/errors.js +64 -120
- package/dist/errors.js.map +1 -0
- package/dist/htsget.js +275 -396
- package/dist/htsget.js.map +1 -0
- package/dist/index.js +16 -54
- package/dist/index.js.map +1 -0
- package/dist/indexFile.d.ts +1 -2
- package/dist/indexFile.js +77 -163
- package/dist/indexFile.js.map +1 -0
- package/dist/record.js +496 -707
- package/dist/record.js.map +1 -0
- package/dist/sam.js +16 -49
- package/dist/sam.js.map +1 -0
- package/dist/util.d.ts +0 -1
- package/dist/util.js +115 -126
- package/dist/util.js.map +1 -0
- package/dist/virtualOffset.js +44 -77
- package/dist/virtualOffset.js.map +1 -0
- package/esm/bai.d.ts +26 -0
- package/esm/bai.js +191 -0
- package/esm/bai.js.map +1 -0
- package/esm/bamFile.d.ts +77 -0
- package/esm/bamFile.js +388 -0
- package/esm/bamFile.js.map +1 -0
- package/esm/chunk.d.ts +18 -0
- package/esm/chunk.js +33 -0
- package/esm/chunk.js.map +1 -0
- package/esm/constants.d.ts +15 -0
- package/esm/constants.js +27 -0
- package/esm/constants.js.map +1 -0
- package/esm/csi.d.ts +35 -0
- package/esm/csi.js +209 -0
- package/esm/csi.js.map +1 -0
- package/esm/errors.d.ts +23 -0
- package/esm/errors.js +24 -0
- package/esm/errors.js.map +1 -0
- package/esm/htsget.d.ts +33 -0
- package/esm/htsget.js +100 -0
- package/esm/htsget.js.map +1 -0
- package/esm/index.d.ts +6 -0
- package/esm/index.js +7 -0
- package/esm/index.js.map +1 -0
- package/esm/indexFile.d.ts +27 -0
- package/esm/indexFile.js +27 -0
- package/esm/indexFile.js.map +1 -0
- package/esm/record.d.ts +88 -0
- package/esm/record.js +534 -0
- package/esm/record.js.map +1 -0
- package/esm/sam.d.ts +7 -0
- package/esm/sam.js +16 -0
- package/esm/sam.js.map +1 -0
- package/esm/util.d.ts +35 -0
- package/esm/util.js +92 -0
- package/esm/util.js.map +1 -0
- package/esm/virtualOffset.d.ts +10 -0
- package/esm/virtualOffset.js +37 -0
- package/esm/virtualOffset.js.map +1 -0
- package/package.json +21 -29
- package/dist/declare.d.js +0 -2
package/dist/csi.js.map
ADDED
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{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,yDAA6C;AAC7C,+DAA0D;AAC1D,kDAA2B;AAC3B,+BAAgF;AAEhF,0DAAmC;AAEnC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,IAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED;IAAiC,uBAAS;IAIxC,aAAY,IAAS;QAArB,YACE,kBAAM,IAAI,CAAC,SAIZ;QAHC,KAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,KAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,KAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;;IACnB,CAAC;IACK,uBAAS,GAAf,UAAgB,KAAa;;;;;4BACT,qBAAM,IAAI,CAAC,KAAK,EAAE,EAAA;;wBAA9B,SAAS,GAAG,SAAkB;wBACpC,IAAI,CAAC,SAAS,EAAE;4BACd,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACK,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACpC,IAAI,CAAC,GAAG,EAAE;4BACR,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACO,KAAK,GAAK,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,MAA7B,CAA6B;wBAC1C,IAAI,KAAK,EAAE;4BACT,sBAAO,KAAK,CAAC,SAAS,EAAA;yBACvB;wBACD,sBAAO,CAAC,CAAC,EAAA;;;;KACV;IAEK,sBAAQ,GAAd;;;gBACE,sBAAO,EAAE,EAAA;;;KACV;IAED,0BAAY,GAAZ,UAAa,KAAa,EAAE,MAAc,EAAE,SAAiB;QAC3D,IAAI,SAAS,GAAG,EAAE,EAAE;YAClB,OAAO,EAAE,CAAA;SACV;QAED,IAAM,IAAI,GAA2B,EAAE,CAAA;QACvC,IAAI,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC5C,IAAI,CAAC,cAAc;YACjB,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACxE,IAAI,CAAC,MAAM,GACT,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAGnC,CAAC,IAAI,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACzB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,4CAAqC,IAAI,CAAC,WAAW,CAAE,CAAC,CAAA;SACzE;QACD,IAAI,CAAC,aAAa,GAAG;YACnB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QACzE,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,CAAC,MAAM,CACX,IAAI,EACJ,IAAI,CAAC,eAAe,CAClB,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC1D,CACF,CAAA;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,6BAAe,GAAf,UAAgB,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,IAAM,WAAW,GAAG,EAAE,CAAA;QACtB,IAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,aAAA,EAAE,WAAW,aAAA,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IACtB,oBAAM,GAAZ,UAAa,IAA8B;;;;;;;wBACnC,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;wBACzD,qBAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,EAAA;;wBAA9C,MAAM,GAAG,CAAC,SAAoC,CAAW;wBACjD,qBAAM,IAAA,uBAAK,EAAC,MAAM,CAAC;4BAEjC,0BAA0B;0BAFO;;wBAA3B,KAAK,GAAG,SAAmB;wBAEjC,0BAA0B;wBAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BACxC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;yBACpB;6BAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;4BAC/C,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;yBACpB;6BAAM;4BACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;4BACjC,oDAAoD;yBACrD;wBAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;wBACrD,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;wBACvC,IAAI,SAAS,EAAE;4BACb,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,EAAE,SAAS,CAAC,CAAC,CAAA;yBAC7D;wBACD,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;wBAEjD,+CAA+C;wBAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;wBACnC,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;wBAC1B,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAA;wBAC/B,qBAAM,IAAA,sBAAe,EAAC,IAAI,CAAC,MAAM,CAAC;4BAClC,oBAAoB;0BADc;;wBAAlC,SAAkC,CAAA;wBAE5B,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAC9C,UAAU,IAAI,CAAC,CAAA;wBACT,QAAQ,GAA+B,EAAE,CAAA;wBAC3C,KAAK,SAAA,CAAA;wBACT,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;4BAC9B,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;4BAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;gCAC3B,yDAAyD;gCACzD,qCAAqC;gCACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;gCAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;6BAClC;iCAAM;gCACC,OAAO,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,G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function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !_construct.default) return false; if (_construct.default.sham) return false; if (typeof Proxy === "function") return true; try { Date.prototype.toString.call((0, _construct.default)(Date, [], function () {})); return true; } catch (e) { return false; } }
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var BamError = /*#__PURE__*/function (_Error) {
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(0, _inherits2.default)(BamError, _Error);
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var _super = _createSuper(BamError);
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function BamError() {
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(0, _classCallCheck2.default)(this, BamError);
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return _super.apply(this, arguments);
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}
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return BamError;
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}( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
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/** Error caused by encountering a part of the BAM spec that has not yet been implemented */
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var BamError = /** @class */ (function (_super) {
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__extends(BamError, _super);
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function BamError() {
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return _super !== null && _super.apply(this, arguments) || this;
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}
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return BamError;
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}(Error));
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exports.BamError = BamError;
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var BamUnimplementedError =
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return _super2.apply(this, arguments);
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}
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return BamUnimplementedError;
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}( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
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/** An error caused by malformed data. */
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/** Error caused by encountering a part of the BAM spec that has not yet been implemented */
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var BamUnimplementedError = /** @class */ (function (_super) {
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__extends(BamUnimplementedError, _super);
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function BamUnimplementedError() {
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return _super !== null && _super.apply(this, arguments) || this;
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}
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return BamUnimplementedError;
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}(Error));
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exports.BamUnimplementedError = BamUnimplementedError;
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var BamMalformedError =
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}
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return BamMalformedError;
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}(BamError);
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/** An error caused by malformed data. */
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var BamMalformedError = /** @class */ (function (_super) {
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__extends(BamMalformedError, _super);
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function BamMalformedError() {
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return _super !== null && _super.apply(this, arguments) || this;
|
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}
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return BamMalformedError;
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}(BamError));
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+
exports.BamMalformedError = BamMalformedError;
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45
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/**
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46
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* An error caused by attempting to read beyond the end of the defined data.
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*/
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function BamBufferOverrunError() {
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(0, _classCallCheck2.default)(this, BamBufferOverrunError);
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return _super4.apply(this, arguments);
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}
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91
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|
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92
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return BamBufferOverrunError;
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93
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-
}(BamMalformedError);
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48
|
+
var BamBufferOverrunError = /** @class */ (function (_super) {
|
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49
|
+
__extends(BamBufferOverrunError, _super);
|
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|
+
function BamBufferOverrunError() {
|
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+
return _super !== null && _super.apply(this, arguments) || this;
|
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52
|
+
}
|
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53
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+
return BamBufferOverrunError;
|
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54
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+
}(BamMalformedError));
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55
|
+
exports.BamBufferOverrunError = BamBufferOverrunError;
|
|
94
56
|
/**
|
|
95
57
|
* An error caused by data being too big, exceeding a size limit.
|
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96
58
|
*/
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|
97
|
-
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98
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function BamSizeLimitError() {
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(0, _classCallCheck2.default)(this, BamSizeLimitError);
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return _super5.apply(this, arguments);
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}
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|
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111
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return BamSizeLimitError;
|
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112
|
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}(BamError);
|
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59
|
+
var BamSizeLimitError = /** @class */ (function (_super) {
|
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60
|
+
__extends(BamSizeLimitError, _super);
|
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61
|
+
function BamSizeLimitError() {
|
|
62
|
+
return _super !== null && _super.apply(this, arguments) || this;
|
|
63
|
+
}
|
|
64
|
+
return BamSizeLimitError;
|
|
65
|
+
}(BamError));
|
|
66
|
+
exports.BamSizeLimitError = BamSizeLimitError;
|
|
113
67
|
/**
|
|
114
68
|
* An invalid argument was supplied to a bam-js method or object.
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115
69
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*/
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|
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var _super6 = _createSuper(BamArgumentError);
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124
|
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|
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125
|
-
function BamArgumentError() {
|
|
126
|
-
(0, _classCallCheck2.default)(this, BamArgumentError);
|
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127
|
-
return _super6.apply(this, arguments);
|
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128
|
-
}
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129
|
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|
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130
|
-
return BamArgumentError;
|
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131
|
-
}(BamError);
|
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132
|
-
|
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70
|
+
var BamArgumentError = /** @class */ (function (_super) {
|
|
71
|
+
__extends(BamArgumentError, _super);
|
|
72
|
+
function BamArgumentError() {
|
|
73
|
+
return _super !== null && _super.apply(this, arguments) || this;
|
|
74
|
+
}
|
|
75
|
+
return BamArgumentError;
|
|
76
|
+
}(BamError));
|
|
133
77
|
exports.BamArgumentError = BamArgumentError;
|
|
134
|
-
//# sourceMappingURL=
|
|
78
|
+
//# sourceMappingURL=errors.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"errors.js","sourceRoot":"","sources":["../src/errors.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;AAAA;IAA8B,4BAAK;IAAnC;;IAAqC,CAAC;IAAD,eAAC;AAAD,CAAC,AAAtC,CAA8B,KAAK,GAAG;AAAzB,4BAAQ;AAErB,4FAA4F;AAC5F;IAA2C,yCAAK;IAAhD;;IAAkD,CAAC;IAAD,4BAAC;AAAD,CAAC,AAAnD,CAA2C,KAAK,GAAG;AAAtC,sDAAqB;AAElC,0CAA0C;AAC1C;IAAuC,qCAAQ;IAA/C;;IAAiD,CAAC;IAAD,wBAAC;AAAD,CAAC,AAAlD,CAAuC,QAAQ,GAAG;AAArC,8CAAiB;AAE9B;;GAEG;AACH;IAA2C,yCAAiB;IAA5D;;IAA8D,CAAC;IAAD,4BAAC;AAAD,CAAC,AAA/D,CAA2C,iBAAiB,GAAG;AAAlD,sDAAqB;AAElC;;GAEG;AACH;IAAuC,qCAAQ;IAA/C;;IAAiD,CAAC;IAAD,wBAAC;AAAD,CAAC,AAAlD,CAAuC,QAAQ,GAAG;AAArC,8CAAiB;AAE9B;;GAEG;AACH;IAAsC,oCAAQ;IAA9C;;IAAgD,CAAC;IAAD,uBAAC;AAAD,CAAC,AAAjD,CAAsC,QAAQ,GAAG;AAApC,4CAAgB"}
|