@gmod/cram 2.0.2 → 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 +9 -0
- package/README.md +0 -4
- package/dist/craiIndex.js +1 -1
- package/dist/craiIndex.js.map +1 -1
- package/dist/cram-bundle.js +1 -1
- package/dist/cram-bundle.js.LICENSE.txt +0 -2
- package/dist/cramFile/codecs/byteArrayStop.d.ts +0 -1
- package/dist/cramFile/codecs/getBits.d.ts +0 -1
- package/dist/cramFile/codecs/getBits.js +2 -2
- package/dist/cramFile/codecs/getBits.js.map +1 -1
- package/dist/cramFile/codecs/index.js +1 -2
- package/dist/cramFile/codecs/index.js.map +1 -1
- package/dist/cramFile/container/index.d.ts +1 -2
- package/dist/cramFile/file.d.ts +1 -3
- package/dist/cramFile/file.js +2 -2
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/sectionParsers.d.ts +0 -1
- package/dist/cramFile/sectionParsers.js +3 -3
- package/dist/cramFile/sectionParsers.js.map +1 -1
- package/dist/cramFile/slice/decodeRecord.js +1 -1
- package/dist/cramFile/slice/decodeRecord.js.map +1 -1
- package/dist/cramFile/util.d.ts +0 -2
- package/dist/cramFile/util.js +5 -6
- package/dist/cramFile/util.js.map +1 -1
- package/dist/indexedCramFile.d.ts +0 -3
- package/dist/indexedCramFile.js +4 -16
- package/dist/indexedCramFile.js.map +1 -1
- package/dist/io/index.d.ts +1 -3
- package/dist/io/index.js +3 -16
- package/dist/io/index.js.map +1 -1
- package/dist/rans/d04.js +1 -1
- package/dist/rans/d04.js.map +1 -1
- package/dist/rans/d14.js +1 -1
- package/dist/rans/d14.js.map +1 -1
- package/dist/rans/frequencies.js +2 -3
- package/dist/rans/frequencies.js.map +1 -1
- package/dist/rans/index.js +1 -1
- package/dist/rans/index.js.map +1 -1
- package/dist/sam.d.ts +1 -1
- package/dist/sam.js +3 -4
- package/dist/sam.js.map +1 -1
- package/dist/typescript.d.ts +0 -1
- package/dist/typescript.js +0 -8
- package/dist/typescript.js.map +1 -1
- package/dist/unzip-pako.d.ts +0 -1
- package/dist/unzip-pako.js +1 -2
- package/dist/unzip-pako.js.map +1 -1
- package/dist/unzip.d.ts +0 -1
- package/esm/craiIndex.js +1 -1
- package/esm/craiIndex.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayStop.d.ts +0 -1
- package/esm/cramFile/codecs/getBits.d.ts +0 -1
- package/esm/cramFile/container/index.d.ts +1 -2
- package/esm/cramFile/file.d.ts +1 -3
- package/esm/cramFile/sectionParsers.d.ts +0 -1
- package/esm/cramFile/util.d.ts +0 -2
- package/esm/indexedCramFile.d.ts +0 -3
- package/esm/indexedCramFile.js +3 -15
- package/esm/indexedCramFile.js.map +1 -1
- package/esm/io/index.d.ts +1 -3
- package/esm/io/index.js +2 -11
- package/esm/io/index.js.map +1 -1
- package/esm/sam.d.ts +1 -1
- package/esm/sam.js +2 -2
- package/esm/sam.js.map +1 -1
- package/esm/typescript.d.ts +0 -1
- package/esm/typescript.js +1 -6
- package/esm/typescript.js.map +1 -1
- package/esm/unzip-pako.d.ts +0 -1
- package/esm/unzip.d.ts +0 -1
- package/package.json +5 -10
- package/src/craiIndex.ts +1 -1
- package/src/indexedCramFile.ts +3 -25
- package/src/io/index.ts +2 -12
- package/src/sam.ts +3 -3
- package/src/typescript.ts +0 -7
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@@ -1,6 +1,7 @@
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"use strict";
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.
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exports.CramBufferOverrunError = void 0;
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exports.getBits = getBits;
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class CramBufferOverrunError extends Error {
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}
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exports.CramBufferOverrunError = CramBufferOverrunError;
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@@ -22,5 +23,4 @@ function getBits(data, cursor, numBits) {
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}
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return val;
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}
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exports.getBits = getBits;
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//# sourceMappingURL=getBits.js.map
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@@ -1 +1 @@
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{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":";;;
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{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":";;;AAEA,0BAyBC;AA3BD,MAAa,sBAAuB,SAAQ,KAAK;CAAG;AAApD,wDAAoD;AAEpD,SAAgB,OAAO,CACrB,IAAY,EACZ,MAAqD,EACrD,OAAe;IAEf,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IACE,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC;QAC5D,IAAI,CAAC,MAAM,EACX,CAAC;QACD,MAAM,IAAI,sBAAsB,CAC9B,6DAA6D,CAC9D,CAAA;IACH,CAAC;IACD,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;QACtC,yDAAyD;QACzD,GAAG,KAAK,CAAC,CAAA;QACT,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QAC5D,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;QACvB,IAAI,MAAM,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;QAC1B,CAAC;QACD,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
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@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.instantiateCodec =
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exports.instantiateCodec = instantiateCodec;
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const errors_1 = require("../../errors");
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const huffman_1 = __importDefault(require("./huffman"));
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const external_1 = __importDefault(require("./external"));
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}
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return new CodecClass(encodingData.parameters, dataType, instantiateCodec);
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}
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exports.instantiateCodec = instantiateCodec;
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//# sourceMappingURL=index.js.map
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.ts"],"names":[],"mappings":"
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.ts"],"names":[],"mappings":";;;;;AA6BA,4CAcC;AA3CD,yCAAqD;AAErD,wDAAuC;AACvC,0DAAsC;AACtC,oEAAgD;AAChD,wEAAoD;AACpD,kDAA8B;AAC9B,oDAAgC;AAChC,sDAAkC;AAKlC,MAAM,YAAY,GAAG;IACnB,CAAC,EAAE,kBAAa;IAChB,kBAAkB;IAClB,CAAC,EAAE,iBAAe;IAClB,CAAC,EAAE,yBAAoB;IACvB,CAAC,EAAE,uBAAkB;IACrB,CAAC,EAAE,cAAS;IACZ,CAAC,EAAE,gBAAW;IACd,sBAAsB;IACtB,CAAC,EAAE,eAAU;CACd,CAAA;AAED,SAAS,mBAAmB,CAAC,EAAU;IACrC,OAAQ,YAAoB,CAAC,EAAE,CAAC,CAAA;AAClC,CAAC;AAED,SAAgB,gBAAgB,CAC9B,YAA0B,EAC1B,QAA6B;IAE7B,MAAM,UAAU,GAAG,mBAAmB,CACpC,QAAQ,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,OAAO,CACjD,CAAA;IACD,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,MAAM,IAAI,+BAAsB,CAC9B,qCAAqC,YAAY,CAAC,OAAO,EAAE,CAC5D,CAAA;IACH,CAAC;IAED,OAAO,IAAI,UAAU,CAAC,YAAY,CAAC,UAAU,EAAE,QAAQ,EAAE,gBAAgB,CAAC,CAAA;AAC5E,CAAC"}
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/// <reference types="node" />
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import CramSlice from '../slice';
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import CramContainerCompressionScheme from './compressionScheme';
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import CramFile from '../file';
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@@ -18,7 +17,7 @@ export default class CramContainer {
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contentPosition: number;
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_size: number;
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content: Buffer;
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crc32?: number
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crc32?: number;
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} | null | undefined>;
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getFirstBlock(): Promise<import("../file").CramFileBlock | undefined>;
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getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
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package/dist/cramFile/file.d.ts
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/// <reference path="../../src/typings/binary-parser.d.ts" />
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/// <reference types="node" />
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import QuickLRU from 'quick-lru';
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import { Parser } from '@gmod/binary-parser';
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import { BlockHeader, CompressionMethod } from './sectionParsers';
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tag: string;
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data: {
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tag: string;
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value: string
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value: string;
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}[];
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}[]>;
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getHeaderText(): Promise<string | undefined>;
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package/dist/cramFile/file.js
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return (0, util_1.parseItem)(buffer, cramBlockHeader.parser, 0, position);
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});
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}
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_parseSection(
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return __awaiter(this,
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_parseSection(section_1, position_1) {
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return __awaiter(this, arguments, void 0, function* (section, position, size = section.maxLength, preReadBuffer = undefined) {
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let buffer;
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if (preReadBuffer) {
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buffer = preReadBuffer;
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+
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@@ -1,6 +1,8 @@
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1
1
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"use strict";
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2
2
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Object.defineProperty(exports, "__esModule", { value: true });
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3
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-
exports.
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3
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+
exports.cramFileDefinition = void 0;
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4
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+
exports.isMappedSliceHeader = isMappedSliceHeader;
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5
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+
exports.getSectionParsers = getSectionParsers;
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4
6
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const binary_parser_1 = require("@gmod/binary-parser");
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5
7
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const singleItf8 = new binary_parser_1.Parser().itf8();
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6
8
|
const cramFileDefinition = {
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@@ -137,7 +139,6 @@ const unversionedParsers = {
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137
139
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function isMappedSliceHeader(header) {
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138
140
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return typeof header.refSeqId === 'number';
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139
141
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}
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140
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-
exports.isMappedSliceHeader = isMappedSliceHeader;
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141
142
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// each of these is a function of the major and minor version
|
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142
143
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const versionedParsers = {
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143
144
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// assemble a section parser for the unmapped slice header, with slight
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@@ -337,5 +338,4 @@ function getSectionParsers(majorVersion) {
|
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|
337
338
|
});
|
|
338
339
|
return parsers;
|
|
339
340
|
}
|
|
340
|
-
exports.getSectionParsers = getSectionParsers;
|
|
341
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//# sourceMappingURL=sectionParsers.js.map
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1
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+
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@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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+
exports.default = decodeRecord;
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const long_1 = __importDefault(require("long"));
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const errors_1 = require("../../errors");
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const record_1 = require("../record");
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@@ -337,5 +338,4 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
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tags,
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}
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-
exports.default = decodeRecord;
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//# sourceMappingURL=decodeRecord.js.map
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@@ -1 +1 @@
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1
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-
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+
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|
package/dist/cramFile/util.d.ts
CHANGED
|
@@ -1,5 +1,3 @@
|
|
|
1
|
-
/// <reference path="../../src/typings/binary-parser.d.ts" />
|
|
2
|
-
/// <reference types="node" />
|
|
3
1
|
import { Parser } from '@gmod/binary-parser';
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4
2
|
export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
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5
3
|
export declare function parseItf8(buffer: Uint8Array, initialOffset: number): [number, number];
|
package/dist/cramFile/util.js
CHANGED
|
@@ -3,7 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
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4
4
|
};
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5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
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6
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-
exports.
|
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6
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+
exports.itf8Size = itf8Size;
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7
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+
exports.parseItf8 = parseItf8;
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8
|
+
exports.parseItem = parseItem;
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9
|
+
exports.tinyMemoize = tinyMemoize;
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10
|
+
exports.sequenceMD5 = sequenceMD5;
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|
7
11
|
const md5_1 = __importDefault(require("md5"));
|
|
8
12
|
const getBits_1 = require("./codecs/getBits");
|
|
9
13
|
function itf8Size(v) {
|
|
@@ -21,7 +25,6 @@ function itf8Size(v) {
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21
25
|
}
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22
26
|
return 5;
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23
27
|
}
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24
|
-
exports.itf8Size = itf8Size;
|
|
25
28
|
function parseItf8(buffer, initialOffset) {
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|
26
29
|
let offset = initialOffset;
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|
27
30
|
const countFlags = buffer[offset];
|
|
@@ -65,12 +68,10 @@ function parseItf8(buffer, initialOffset) {
|
|
|
65
68
|
}
|
|
66
69
|
return [result, offset - initialOffset];
|
|
67
70
|
}
|
|
68
|
-
exports.parseItf8 = parseItf8;
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|
69
71
|
function parseItem(buffer, parser, startBufferPosition = 0, startFilePosition = 0) {
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|
70
72
|
const { offset, result } = parser.parse(buffer);
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71
73
|
return Object.assign(Object.assign({}, result), { _endPosition: offset + startFilePosition, _size: offset - startBufferPosition });
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72
74
|
}
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73
|
-
exports.parseItem = parseItem;
|
|
74
75
|
// this would be nice as a decorator, but i'm a little worried about
|
|
75
76
|
// babel support for it going away or changing.
|
|
76
77
|
// memoizes a method in the stupidest possible way, with no regard for the
|
|
@@ -89,9 +90,7 @@ function tinyMemoize(_class, methodName) {
|
|
|
89
90
|
return this[memoAttrName];
|
|
90
91
|
};
|
|
91
92
|
}
|
|
92
|
-
exports.tinyMemoize = tinyMemoize;
|
|
93
93
|
function sequenceMD5(seq) {
|
|
94
94
|
return (0, md5_1.default)(seq.toUpperCase().replaceAll(/[^\u0021-\u007e]/g, ''));
|
|
95
95
|
}
|
|
96
|
-
exports.sequenceMD5 = sequenceMD5;
|
|
97
96
|
//# sourceMappingURL=util.js.map
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|
@@ -1 +1 @@
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|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/cramFile/util.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/cramFile/util.ts"],"names":[],"mappings":";;;;;AAIA,4BAcC;AAED,8BA2CC;AAiFD,8BAYC;AAMD,kCAaC;AAED,kCAEC;AAnLD,8CAAqB;AAErB,8CAAyD;AAEzD,SAAgB,QAAQ,CAAC,CAAS;IAChC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;QACjB,OAAO,CAAC,CAAA;IACV,CAAC;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC;QACnB,OAAO,CAAC,CAAA;IACV,CAAC;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC;QACrB,OAAO,CAAC,CAAA;IACV,CAAC;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC;QACtB,OAAO,CAAC,CAAA;IACV,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,SAAgB,SAAS,CACvB,MAAkB,EAClB,aAAqB;IAErB,IAAI,MAAM,GAAG,aAAa,CAAA;IAC1B,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,CAAC,CAAA;IACjC,IAAI,MAAM,CAAA;IACV,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QACtB,MAAM,GAAG,UAAU,CAAA;QACnB,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;IACrB,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,MAAM,GAAG,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;QAC1D,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;IACrB,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,MAAM;YACJ,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACrE,QAAQ,CAAA;QACV,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;IACrB,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,MAAM;YACJ,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC;gBACjB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACrB,UAAU,CAAA;QACZ,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;IACrB,CAAC;SAAM,CAAC;QACN,MAAM;YACJ,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC;gBAC3B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,CAAA;QAC7B,+EAA+E;QAC/E,+EAA+E;QAC/E,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;IACrB,CAAC;IACD,IAAI,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC;QAC3B,MAAM,IAAI,gCAAsB,CAC9B,oEAAoE,CACrE,CAAA;IACH,CAAC;IACD,OAAO,CAAC,MAAM,EAAE,MAAM,GAAG,aAAa,CAAC,CAAA;AACzC,CAAC;AAiFD,SAAgB,SAAS,CACvB,MAAc,EACd,MAAiB,EACjB,mBAAmB,GAAG,CAAC,EACvB,iBAAiB,GAAG,CAAC;IAErB,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAC/C,uCACK,MAAM,KACT,YAAY,EAAE,MAAM,GAAG,iBAAiB,EACxC,KAAK,EAAE,MAAM,GAAG,mBAAmB,IACpC;AACH,CAAC;AAED,oEAAoE;AACpE,+CAA+C;AAC/C,0EAA0E;AAC1E,0EAA0E;AAC1E,SAAgB,WAAW,CAAC,MAAW,EAAE,UAAe;IACtD,MAAM,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,CAAA;IAC3C,MAAM,YAAY,GAAG,SAAS,UAAU,EAAE,CAAA;IAC1C,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,GAAG,SAAS,aAAa;QACnD,IAAI,CAAC,CAAC,YAAY,IAAI,IAAI,CAAC,EAAE,CAAC;YAC5B,MAAM,GAAG,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAC7B,IAAI,CAAC,YAAY,CAAC,GAAG,GAAG,CAAA;YACxB,OAAO,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE;gBAC9B,OAAO,IAAI,CAAC,YAAY,CAAC,CAAA;YAC3B,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,YAAY,CAAC,CAAA;IAC3B,CAAC,CAAA;AACH,CAAC;AAED,SAAgB,WAAW,CAAC,GAAW;IACrC,OAAO,IAAA,aAAG,EAAC,GAAG,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,mBAAmB,EAAE,EAAE,CAAC,CAAC,CAAA;AACnE,CAAC"}
|
|
@@ -15,20 +15,17 @@ export interface CramIndexLike {
|
|
|
15
15
|
export default class IndexedCramFile {
|
|
16
16
|
cram: CramFile;
|
|
17
17
|
index: CramIndexLike;
|
|
18
|
-
private fetchSizeLimit;
|
|
19
18
|
/**
|
|
20
19
|
*
|
|
21
20
|
* @param {object} args
|
|
22
21
|
* @param {CramFile} args.cram
|
|
23
22
|
* @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
|
|
24
23
|
* @param {number} [args.cacheSize] optional maximum number of CRAM records to cache. default 20,000
|
|
25
|
-
* @param {number} [args.fetchSizeLimit] optional maximum number of bytes to fetch in a single getRecordsForRange call. Default 3 MiB.
|
|
26
24
|
* @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
|
|
27
25
|
* checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
|
|
28
26
|
*/
|
|
29
27
|
constructor(args: {
|
|
30
28
|
index: CramIndexLike;
|
|
31
|
-
fetchSizeLimit?: number;
|
|
32
29
|
} & ({
|
|
33
30
|
cram: CramFile;
|
|
34
31
|
} | ({
|
package/dist/indexedCramFile.js
CHANGED
|
@@ -21,7 +21,6 @@ class IndexedCramFile {
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|
|
21
21
|
* @param {CramFile} args.cram
|
|
22
22
|
* @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
|
|
23
23
|
* @param {number} [args.cacheSize] optional maximum number of CRAM records to cache. default 20,000
|
|
24
|
-
* @param {number} [args.fetchSizeLimit] optional maximum number of bytes to fetch in a single getRecordsForRange call. Default 3 MiB.
|
|
25
24
|
* @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
|
|
26
25
|
* checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
|
|
27
26
|
*/
|
|
@@ -44,7 +43,6 @@ class IndexedCramFile {
|
|
|
44
43
|
if (!this.index.getEntriesForRange) {
|
|
45
44
|
throw new Error('invalid arguments: not an index');
|
|
46
45
|
}
|
|
47
|
-
this.fetchSizeLimit = args.fetchSizeLimit || 3000000;
|
|
48
46
|
}
|
|
49
47
|
/**
|
|
50
48
|
*
|
|
@@ -53,8 +51,8 @@ class IndexedCramFile {
|
|
|
53
51
|
* @param {number} end end of the range of interest. 1-based closed coordinates.
|
|
54
52
|
* @returns {Promise[Array[CramRecord]]}
|
|
55
53
|
*/
|
|
56
|
-
getRecordsForRange(
|
|
57
|
-
return __awaiter(this,
|
|
54
|
+
getRecordsForRange(seq_1, start_1, end_1) {
|
|
55
|
+
return __awaiter(this, arguments, void 0, function* (seq, start, end, opts = {}) {
|
|
58
56
|
opts.viewAsPairs = opts.viewAsPairs || false;
|
|
59
57
|
opts.pairAcrossChr = opts.pairAcrossChr || false;
|
|
60
58
|
opts.maxInsertSize = opts.maxInsertSize || 200000;
|
|
@@ -64,10 +62,6 @@ class IndexedCramFile {
|
|
|
64
62
|
}
|
|
65
63
|
const seqId = seq;
|
|
66
64
|
const slices = yield this.index.getEntriesForRange(seqId, start, end);
|
|
67
|
-
const totalSize = slices.map(s => s.sliceBytes).reduce((a, b) => a + b, 0);
|
|
68
|
-
if (totalSize > this.fetchSizeLimit) {
|
|
69
|
-
throw new errors_1.CramSizeLimitError(`data size of ${totalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
|
|
70
|
-
}
|
|
71
65
|
// TODO: do we need to merge or de-duplicate the blocks?
|
|
72
66
|
// fetch all the slices and parse the feature data
|
|
73
67
|
const filter = (feature) => feature.sequenceId === seq &&
|
|
@@ -123,13 +117,7 @@ class IndexedCramFile {
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|
|
123
117
|
.filter((item, pos, ary) => !pos || item.toString() !== ary[pos - 1].toString());
|
|
124
118
|
const mateRecordPromises = [];
|
|
125
119
|
const mateFeatPromises = [];
|
|
126
|
-
const
|
|
127
|
-
.map(s => s.sliceBytes)
|
|
128
|
-
.reduce((a, b) => a + b, 0);
|
|
129
|
-
if (mateTotalSize > this.fetchSizeLimit) {
|
|
130
|
-
throw new Error(`mate data size of ${mateTotalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
|
|
131
|
-
}
|
|
132
|
-
mateChunks.forEach(c => {
|
|
120
|
+
for (const c of mateChunks) {
|
|
133
121
|
let recordPromise = this.cram.featureCache.get(c.toString());
|
|
134
122
|
if (!recordPromise) {
|
|
135
123
|
recordPromise = this.getRecordsInSlice(c, () => true);
|
|
@@ -149,7 +137,7 @@ class IndexedCramFile {
|
|
|
149
137
|
return mateRecs;
|
|
150
138
|
});
|
|
151
139
|
mateFeatPromises.push(featPromise);
|
|
152
|
-
}
|
|
140
|
+
}
|
|
153
141
|
const newMateFeats = yield Promise.all(mateFeatPromises);
|
|
154
142
|
if (newMateFeats.length) {
|
|
155
143
|
const newMates = newMateFeats.reduce((result, current) => result.concat(current));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,
|
|
1
|
+
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|
package/dist/io/index.d.ts
CHANGED
|
@@ -1,6 +1,4 @@
|
|
|
1
1
|
import { Filehandle } from '../cramFile/filehandle';
|
|
2
|
-
import { LocalFile, RemoteFile } from 'generic-filehandle';
|
|
3
|
-
declare function fromUrl(source: string): LocalFile | RemoteFile;
|
|
4
2
|
declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: Filehandle): Filehandle;
|
|
5
|
-
export {
|
|
3
|
+
export { open };
|
|
6
4
|
export { LocalFile, RemoteFile } from 'generic-filehandle';
|
package/dist/io/index.js
CHANGED
|
@@ -1,33 +1,20 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
3
|
-
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
|
-
};
|
|
5
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.RemoteFile = exports.LocalFile =
|
|
7
|
-
|
|
8
|
-
const typescript_1 = require("../typescript");
|
|
3
|
+
exports.RemoteFile = exports.LocalFile = void 0;
|
|
4
|
+
exports.open = open;
|
|
9
5
|
const generic_filehandle_1 = require("generic-filehandle");
|
|
10
|
-
function fromUrl(source) {
|
|
11
|
-
const { protocol, pathname } = url_1.default.parse(source);
|
|
12
|
-
if (protocol === 'file:') {
|
|
13
|
-
return new generic_filehandle_1.LocalFile(unescape((0, typescript_1.ensureNotNullish)(pathname)));
|
|
14
|
-
}
|
|
15
|
-
return new generic_filehandle_1.RemoteFile(source);
|
|
16
|
-
}
|
|
17
|
-
exports.fromUrl = fromUrl;
|
|
18
6
|
function open(maybeUrl, maybePath, maybeFilehandle) {
|
|
19
7
|
if (maybeFilehandle) {
|
|
20
8
|
return maybeFilehandle;
|
|
21
9
|
}
|
|
22
10
|
if (maybeUrl) {
|
|
23
|
-
return
|
|
11
|
+
return new generic_filehandle_1.RemoteFile(maybeUrl);
|
|
24
12
|
}
|
|
25
13
|
if (maybePath) {
|
|
26
14
|
return new generic_filehandle_1.LocalFile(maybePath);
|
|
27
15
|
}
|
|
28
16
|
throw new Error('no url, path, or filehandle provided, cannot open');
|
|
29
17
|
}
|
|
30
|
-
exports.open = open;
|
|
31
18
|
var generic_filehandle_2 = require("generic-filehandle");
|
|
32
19
|
Object.defineProperty(exports, "LocalFile", { enumerable: true, get: function () { return generic_filehandle_2.LocalFile; } });
|
|
33
20
|
Object.defineProperty(exports, "RemoteFile", { enumerable: true, get: function () { return generic_filehandle_2.RemoteFile; } });
|
package/dist/io/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":";;;AAoBS,oBAAI;AAnBb,2DAA0D;AAE1D,SAAS,IAAI,CACX,QAAiB,EACjB,SAAkB,EAClB,eAA4B;IAE5B,IAAI,eAAe,EAAE,CAAC;QACpB,OAAO,eAAe,CAAA;IACxB,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,IAAI,+BAAU,CAAC,QAAQ,CAAC,CAAA;IACjC,CAAC;IACD,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,IAAI,8BAAS,CAAC,SAAS,CAAC,CAAA;IACjC,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAID,yDAA0D;AAAjD,+GAAA,SAAS,OAAA;AAAE,gHAAA,UAAU,OAAA"}
|
package/dist/rans/d04.js
CHANGED
|
@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
+
exports.default = uncompress;
|
|
6
7
|
//@ts-nocheck
|
|
7
8
|
const errors_1 = require("../errors");
|
|
8
9
|
const constants_1 = require("./constants");
|
|
@@ -70,5 +71,4 @@ function uncompress(
|
|
|
70
71
|
}
|
|
71
72
|
out.setPosition(0);
|
|
72
73
|
}
|
|
73
|
-
exports.default = uncompress;
|
|
74
74
|
//# sourceMappingURL=d04.js.map
|
package/dist/rans/d04.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"d04.js","sourceRoot":"","sources":["../../src/rans/d04.ts"],"names":[],"mappings":";;;;;
|
|
1
|
+
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package/dist/rans/d14.js
CHANGED
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@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
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|
4
4
|
};
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|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
+
exports.default = uncompress;
|
|
6
7
|
//@ts-nocheck
|
|
7
8
|
const constants_1 = require("./constants");
|
|
8
9
|
const decoding_1 = __importDefault(require("./decoding"));
|
|
@@ -55,5 +56,4 @@ function uncompress(
|
|
|
55
56
|
l7 = c7;
|
|
56
57
|
}
|
|
57
58
|
}
|
|
58
|
-
exports.default = uncompress;
|
|
59
59
|
//# sourceMappingURL=d14.js.map
|