@gmod/cram 1.6.0 → 1.6.1
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 +6 -2
- package/README.md +152 -114
- package/dist/craiIndex.js +2 -4
- package/dist/craiIndex.js.map +1 -1
- package/dist/cram-bundle.js +4 -15
- package/dist/cramFile/file.js +2 -2
- package/dist/cramFile/file.js.map +1 -1
- package/dist/unzip-pako.d.ts +2 -0
- package/dist/unzip-pako.js +9 -0
- package/dist/unzip-pako.js.map +1 -0
- package/dist/unzip.d.ts +2 -0
- package/dist/unzip.js +6 -0
- package/dist/unzip.js.map +1 -0
- package/esm/craiIndex.js +2 -4
- package/esm/craiIndex.js.map +1 -1
- package/esm/cramFile/file.js +2 -2
- package/esm/cramFile/file.js.map +1 -1
- package/esm/unzip-pako.d.ts +2 -0
- package/esm/unzip-pako.js +5 -0
- package/esm/unzip-pako.js.map +1 -0
- package/esm/unzip.d.ts +2 -0
- package/esm/unzip.js +3 -0
- package/esm/unzip.js.map +1 -0
- package/package.json +6 -2
package/dist/cramFile/file.js
CHANGED
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@@ -39,7 +39,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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39
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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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-
var
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+
var unzip_1 = require("../unzip");
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var buffer_crc32_1 = __importDefault(require("buffer-crc32"));
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var quick_lru_1 = __importDefault(require("quick-lru"));
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var errors_1 = require("../errors");
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@@ -356,7 +356,7 @@ var CramFile = /** @class */ (function () {
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};
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CramFile.prototype._uncompress = function (compressionMethod, inputBuffer, outputBuffer) {
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if (compressionMethod === 'gzip') {
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359
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-
var result =
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359
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+
var result = (0, unzip_1.unzip)(inputBuffer);
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result.copy(outputBuffer);
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}
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else if (compressionMethod === 'bzip2') {
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"file.js","sourceRoot":"","sources":["../../src/cramFile/file.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,
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1
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+
{"version":3,"file":"file.js","sourceRoot":"","sources":["../../src/cramFile/file.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kCAAgC;AAChC,8DAAgC;AAChC,wDAA2B;AAE3B,oCAAsE;AACtE,iDAAoC;AACpC,mDAGyB;AACzB,oEAA6C;AAC7C,0DAAuC;AAEvC,4BAA4B;AAC5B,+BAA+C;AAC/C,8BAAwC;AAExC;IACE;;;;;;;;;;;OAWG;IACH,kBAAY,IAAI;QACd,IAAI,CAAC,IAAI,GAAG,IAAA,SAAI,EAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QACtD,IAAI,CAAC,iBAAiB,GAAG,IAAI,CAAA;QAC7B,IAAI,CAAC,8BAA8B,GAAG,IAAI,CAAC,QAAQ,CAAA;QACnD,IAAI,CAAC,OAAO,GAAG;YACb,gBAAgB,EAAE,IAAI,CAAC,gBAAgB,KAAK,KAAK;YACjD,SAAS,EAAE,IAAI,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK;SACjE,CAAA;QAED,6CAA6C;QAC7C,gEAAgE;QAChE,4DAA4D;QAC5D,qCAAqC;QACrC,IAAI,CAAC,YAAY,GAAG,IAAI,mBAAG,CAAC;YAC1B,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,SAAS;SAChC,CAAC,CAAA;IACJ,CAAC;IAED,2BAAQ,GAAR;QACE,IAAI,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE;YACtB,OAAO,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAA;SAC1B;QACD,IAAI,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE;YACjB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAA;SACrB;QAED,OAAO,aAAa,CAAA;IACtB,CAAC;IAED,8CAA8C;IAC9C,uBAAI,GAAJ,UAAK,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ;QACnC,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;IACzD,CAAC;IAED,8CAA8C;IAC9C,uBAAI,GAAJ;QACE,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACzB,CAAC;IAED,WAAW;IACL,gCAAa,GAAnB;;;;;;wBACQ,SAAS,GAAG,MAAM,CAAC,WAAW,CAAC,mCAAwB,CAAC,SAAS,CAAC,CAAA;wBACxE,qBAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,EAAE,mCAAwB,CAAC,SAAS,EAAE,CAAC,CAAC,EAAA;;wBAAzE,SAAyE,CAAA;wBACnE,UAAU,GAAG,mCAAwB,CAAC,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAA;wBAC1E,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,EAAE;4BAClE,MAAM,IAAI,+BAAsB,CAC9B,uBAAgB,UAAU,CAAC,YAAY,mBAAgB,CACxD,CAAA;yBACF;wBACD,sBAAO,UAAU,EAAA;;;;KAClB;IAED,UAAU;IACJ,+BAAY,GAAlB;;;;;4BACyB,qBAAM,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAA;;wBAA/C,cAAc,GAAG,SAA8B;wBACrD,IAAI,CAAC,cAAc,EAAE;4BACnB,MAAM,IAAI,2BAAkB,CAAC,6BAA6B,CAAC,CAAA;yBAC5D;wBAEmB,qBAAM,cAAc,CAAC,aAAa,EAAE;4BACxD,wDAAwD;0BADA;;wBAAhD,OAAO,GAAK,CAAA,SAAoC,CAAA,QAAzC;wBAET,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACrC,SAAS,GAAG,CAAC,CAAA;wBAIb,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,MAAM,EAAE,SAAS,EAAE,SAAS,GAAG,YAAY,CAAC,CAAA;wBAC1E,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;wBAClB,sBAAO,IAAA,qBAAe,EAAC,IAAI,CAAC,EAAA;;;;KAC7B;IAEK,gCAAa,GAAnB;;;;4BACE,qBAAM,IAAI,CAAC,YAAY,EAAE,EAAA;;wBAAzB,SAAyB,CAAA;wBACzB,sBAAO,IAAI,CAAC,MAAM,EAAA;;;;KACnB;IAED,UAAU;IACJ,oCAAiB,GAAvB;;;;;4BAC2B,qBAAM,IAAI,CAAC,aAAa,EAAE,EAAA;;wBAA3C,YAAY,GAAK,CAAA,SAA0B,CAAA,aAA/B;wBACpB,sBAAO,IAAA,kCAAiB,EAAC,YAAY,CAAC,EAAA;;;;KACvC;IAEK,mCAAgB,GAAtB,UAAuB,eAAe;;;;;4BACb,qBAAM,IAAI,CAAC,iBAAiB,EAAE,EAAA;;wBAA/C,cAAc,GAAG,SAA8B;wBACjD,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;wBAC/B,qBAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,EAAA;;wBAAnC,QAAQ,GAAK,CAAA,SAAsB,CAAA,KAA3B;wBACd,oBAAoB,GAAK,cAAc,qBAAnB,CAAmB;wBAItC,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,IAAI,eAAe,CAAA;wBAClC,gDAAgD;wBAChD,uDAAuD;wBACvD,IAAI,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,IAAI,QAAQ,EAAE;4BAC7D,sBAAO,SAAS,EAAA;yBACjB;wBAED,gBAAgB,GAAG,IAAI,CAAC,sBAAsB,CAAC,QAAQ,CAAC,CAAA;wBAClC,qBAAM,gBAAgB,CAAC,SAAS,EAAE,EAAA;;wBAAlD,aAAa,GAAG,SAAkC;wBACxD,IAAI,CAAC,aAAa,EAAE;4BAClB,MAAM,IAAI,2BAAkB,CAC1B,oBAAa,eAAe,uBAAoB,CACjD,CAAA;yBACF;6BAKG,CAAA,CAAC,KAAK,CAAC,CAAA,EAAP,wBAAO;wBACT,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;wBAC5B,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,GAAG,aAAa,CAAC,SAAS,CAAA;wBAC3B,qBAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,EAAA;;wBAAtC,KAAK,GAAG,SAA8B;wBAC5C,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;;;wBAFc,CAAC,IAAI,CAAC,CAAA;;;;wBAKnD,8EAA8E;wBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;;;wBA1BpB,CAAC,IAAI,CAAC,CAAA;;6BA8B5C,sBAAO,gBAAgB,EAAA;;;;KACxB;IAEK,6BAAU,GAAhB,UAAiB,QAAQ,EAAE,MAAM,EAAE,aAAa,EAAE,WAAW;;;;;;wBACrD,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;wBACpC,qBAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAA;;wBAA5C,SAA4C,CAAA;wBACtC,eAAe,GAAG,sBAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACzC,IAAI,eAAe,KAAK,aAAa,EAAE;4BACrC,MAAM,IAAI,2BAAkB,CAC1B,0BAAmB,WAAW,gCAAsB,aAAa,sCAA4B,eAAe,CAAE,CAC/G,CAAA;yBACF;;;;;KACF;IAED;;OAEG;IACG,iCAAc,GAApB;;;;;4BACyB,qBAAM,IAAI,CAAC,iBAAiB,EAAE,EAAA;;wBAA/C,cAAc,GAAG,SAA8B;wBAC1B,qBAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,EAAA;;wBAAnC,QAAQ,GAAK,CAAA,SAAsB,CAAA,KAA3B;wBACd,oBAAoB,GAAK,cAAc,qBAAnB,CAAmB;wBAE3C,cAAc,GAAG,CAAC,CAAA;wBAClB,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;;;6BACnD,CAAA,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,GAAG,QAAQ,CAAA;wBACvC,qBAAM,IAAI,CAAC,sBAAsB,CACrD,QAAQ,CACT,CAAC,SAAS,EAAE,EAAA;;wBAFP,aAAa,GAAG,SAET;wBACb,IAAI,CAAC,aAAa,EAAE;4BAClB,yBAAK;yBACN;6BAIG,CAAA,cAAc,KAAK,CAAC,CAAA,EAApB,wBAAoB;wBACtB,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;wBAC5B,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,GAAG,aAAa,CAAC,SAAS,CAAA;wBAC3B,qBAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,EAAA;;wBAAtC,KAAK,GAAG,SAA8B;wBAC5C,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;;;wBAFc,CAAC,IAAI,CAAC,CAAA;;;;wBAKnD,8EAA8E;wBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;;;wBAExD,cAAc,IAAI,CAAC,CAAA;;6BAGrB,sBAAO,cAAc,EAAA;;;;KACtB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1
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"use strict";
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2
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Object.defineProperty(exports, "__esModule", { value: true });
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3
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exports.unzip = void 0;
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4
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var pako_1 = require("pako");
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5
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function unzip(input) {
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return Buffer.from((0, pako_1.inflate)(input));
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7
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}
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8
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exports.unzip = unzip;
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9
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//# sourceMappingURL=unzip-pako.js.map
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@@ -0,0 +1 @@
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1
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{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;;AAAA,6BAA8B;AAE9B,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,MAAM,CAAC,IAAI,CAAC,IAAA,cAAO,EAAC,KAAK,CAAC,CAAC,CAAA;AACpC,CAAC;AAFD,sBAEC"}
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package/dist/unzip.d.ts
ADDED
package/dist/unzip.js
ADDED
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@@ -0,0 +1,6 @@
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|
|
1
|
+
"use strict";
|
|
2
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
+
exports.unzip = void 0;
|
|
4
|
+
var zlib_1 = require("zlib");
|
|
5
|
+
Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.gunzipSync; } });
|
|
6
|
+
//# sourceMappingURL=unzip.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,6BAAiC;AACV,sFADd,iBAAU,OACS"}
|
package/esm/craiIndex.js
CHANGED
|
@@ -1,10 +1,8 @@
|
|
|
1
1
|
import AbortablePromiseCache from 'abortable-promise-cache';
|
|
2
2
|
import QuickLRU from 'quick-lru';
|
|
3
|
-
import {
|
|
4
|
-
import zlib from 'zlib';
|
|
3
|
+
import { unzip } from './unzip';
|
|
5
4
|
import { open } from './io';
|
|
6
5
|
import { CramMalformedError } from './errors';
|
|
7
|
-
const gunzip = promisify(zlib.gunzip);
|
|
8
6
|
const BAI_MAGIC = 21578050; // BAI\1
|
|
9
7
|
class Slice {
|
|
10
8
|
constructor(args) {
|
|
@@ -59,7 +57,7 @@ export default class CraiIndex {
|
|
|
59
57
|
return this.readFile()
|
|
60
58
|
.then(data => {
|
|
61
59
|
if (data[0] === 31 && data[1] === 139) {
|
|
62
|
-
return
|
|
60
|
+
return unzip(data);
|
|
63
61
|
}
|
|
64
62
|
return data;
|
|
65
63
|
})
|
package/esm/craiIndex.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.js"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,QAAQ,MAAM,WAAW,CAAA;AAChC,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.js"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,QAAQ,MAAM,WAAW,CAAA;AAChC,OAAO,EAAE,KAAK,EAAE,MAAM,SAAS,CAAA;AAC/B,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAC3B,OAAO,EAAE,kBAAkB,EAAE,MAAM,UAAU,CAAA;AAE7C,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,MAAM,KAAK;IACT,YAAY,IAAI;QACd,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAC3B,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,UAAU,IAAI,IAAI,CAAC,UAAU,EAAE,CAAA;IAClG,CAAC;CACF;AAED,SAAS,gBAAgB,CAAC,KAAK,EAAE,MAAM;IACrC,IAAI,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,KAAK,SAAS,CAAC,EAAE;QACvC,MAAM,IAAI,kBAAkB,CAAC,0BAA0B,CAAC,CAAA;KACzD;IAED,MAAM,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,cAAc,EAAE,UAAU,EAAE,UAAU,CAAC,GAAG,MAAM,CAAA;IAE3E,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE;QACjB,KAAK,CAAC,KAAK,CAAC,GAAG,EAAE,CAAA;KAClB;IAED,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CACf,IAAI,KAAK,CAAC;QACR,KAAK;QACL,IAAI;QACJ,cAAc;QACd,UAAU;QACV,UAAU;KACX,CAAC,CACH,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,SAAS;IAC5B,yFAAyF;IACzF,iBAAiB;IACjB,qBAAqB;IACrB,oBAAoB;IACpB,+CAA+C;IAC/C,gEAAgE;IAChE,yBAAyB;IACzB,2GAA2G;IAE3G;;;;;;OAMG;IACH,YAAY,IAAI;QACd,MAAM,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QAC7D,IAAI,CAAC,WAAW,GAAG,IAAI,qBAAqB,CAAC;YAC3C,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;YACnC,IAAI,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;SACpD,CAAC,CAAA;QACF,IAAI,CAAC,QAAQ,GAAG,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;IACtD,CAAC;IAED,UAAU;QACR,MAAM,KAAK,GAAG,EAAE,CAAA;QAChB,OAAO,IAAI,CAAC,QAAQ,EAAE;aACnB,IAAI,CAAC,IAAI,CAAC,EAAE;YACX,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;gBACrC,OAAO,KAAK,CAAC,IAAI,CAAC,CAAA;aACnB;YACD,OAAO,IAAI,CAAA;QACb,CAAC,CAAC;aACD,IAAI,CAAC,kBAAkB,CAAC,EAAE;YACzB,IACE,kBAAkB,CAAC,MAAM,GAAG,CAAC;gBAC7B,kBAAkB,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAChD;gBACA,MAAM,IAAI,kBAAkB,CAC1B,+IAA+I,CAChJ,CAAA;aACF;YACD,mDAAmD;YACnD,uDAAuD;YACvD,uEAAuE;YACvE,gDAAgD;YAChD,IAAI,aAAa,GAAG,EAAE,CAAA;YACtB,IAAI,aAAa,GAAG,EAAE,CAAA;YACtB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,kBAAkB,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;gBACrD,MAAM,QAAQ,GAAG,kBAAkB,CAAC,CAAC,CAAC,CAAA;gBACtC,IACE,CAAC,QAAQ,IAAI,EAAE,IAAI,QAAQ,IAAI,EAAE,CAAC,CAAC,SAAS;oBAC5C,CAAC,CAAC,aAAa,IAAI,QAAQ,KAAK,EAAE,CAAC,CAAC,eAAe,EACnD;oBACA,aAAa,IAAI,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAA;iBAC/C;qBAAM,IAAI,QAAQ,KAAK,CAAC,CAAC,QAAQ,EAAE;oBAClC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;oBACtD,aAAa,GAAG,EAAE,CAAA;iBACnB;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,EAAE;oBACnC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;oBACtD,aAAa,GAAG,EAAE,CAAA;oBAClB,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;oBACtC,aAAa,GAAG,EAAE,CAAA;iBACnB;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,IAAI,QAAQ,KAAK,EAAE,CAAC,WAAW,EAAE;oBAClE,oDAAoD;oBACpD,oCAAoC;oBACpC,MAAM,IAAI,kBAAkB,CAAC,0BAA0B,CAAC,CAAA;iBACzD;aACF;YAED,8DAA8D;YAC9D,IAAI,aAAa,EAAE;gBACjB,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;aACvD;YACD,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC,EAAE;gBAC9B,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;aACvC;YAED,6BAA6B;YAC7B,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,EAAE;gBAC7C,KAAK,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,CACrB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,CAC/C,CAAA;YACH,CAAC,CAAC,CAAA;YACF,OAAO,KAAK,CAAA;QACd,CAAC,CAAC,CAAA;IACN,CAAC;IAED,QAAQ,CAAC,IAAI,GAAG,EAAE;QAChB,OAAO,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACzD,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,2BAA2B,CAAC,KAAK;QACrC,OAAO,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;IACzC,CAAC;IAED;;;;;;;;;;OAUG;IACH,KAAK,CAAC,kBAAkB,CAAC,KAAK,EAAE,UAAU,EAAE,QAAQ;QAClD,MAAM,UAAU,GAAG,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;QACjD,IAAI,CAAC,UAAU,EAAE;YACf,OAAO,EAAE,CAAA;SACV;QAED,MAAM,OAAO,GAAG,KAAK,CAAC,EAAE;YACtB,MAAM,UAAU,GAAG,KAAK,CAAC,KAAK,CAAA;YAC9B,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,IAAI,CAAA;YACzC,IAAI,UAAU,IAAI,QAAQ,EAAE;gBAC1B,OAAO,CAAC,CAAC,CAAA;aACV,CAAC,0BAA0B;YAC5B,IAAI,QAAQ,IAAI,UAAU,EAAE;gBAC1B,OAAO,CAAC,CAAA;aACT,CAAC,wBAAwB;YAC1B,OAAO,CAAC,CAAA,CAAC,uBAAuB;QAClC,CAAC,CAAA;QACD,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;gBAChC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA;aACzB;SACF;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
|
package/esm/cramFile/file.js
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import
|
|
1
|
+
import { unzip } from '../unzip';
|
|
2
2
|
import crc32 from 'buffer-crc32';
|
|
3
3
|
import LRU from 'quick-lru';
|
|
4
4
|
import { CramUnimplementedError, CramMalformedError } from '../errors';
|
|
@@ -202,7 +202,7 @@ export default class CramFile {
|
|
|
202
202
|
}
|
|
203
203
|
_uncompress(compressionMethod, inputBuffer, outputBuffer) {
|
|
204
204
|
if (compressionMethod === 'gzip') {
|
|
205
|
-
const result =
|
|
205
|
+
const result = unzip(inputBuffer);
|
|
206
206
|
result.copy(outputBuffer);
|
|
207
207
|
}
|
|
208
208
|
else if (compressionMethod === 'bzip2') {
|
package/esm/cramFile/file.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"file.js","sourceRoot":"","sources":["../../src/cramFile/file.js"],"names":[],"mappings":"AAAA,OAAO,
|
|
1
|
+
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|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9B,MAAM,UAAU,KAAK,CAAC,KAAa;IACjC,OAAO,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAA;AACpC,CAAC"}
|
package/esm/unzip.d.ts
ADDED
package/esm/unzip.js
ADDED
package/esm/unzip.js.map
ADDED
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AACjC,OAAO,EAAE,UAAU,IAAI,KAAK,EAAE,CAAA"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/cram",
|
|
3
|
-
"version": "1.6.
|
|
3
|
+
"version": "1.6.1",
|
|
4
4
|
"description": "read CRAM files with pure Javascript",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/cram-js",
|
|
@@ -49,11 +49,13 @@
|
|
|
49
49
|
"es6-promisify": "^6.0.1",
|
|
50
50
|
"long": "^4.0.0",
|
|
51
51
|
"md5": "^2.2.1",
|
|
52
|
+
"pako": "^1.0.4",
|
|
52
53
|
"quick-lru": "^2.0.0"
|
|
53
54
|
},
|
|
54
55
|
"devDependencies": {
|
|
55
56
|
"@gmod/indexedfasta": "^2.0.2",
|
|
56
57
|
"@types/jest": "^27.4.0",
|
|
58
|
+
"@types/pako": "^1.0.3",
|
|
57
59
|
"@typescript-eslint/eslint-plugin": "^5.9.1",
|
|
58
60
|
"@typescript-eslint/parser": "^5.9.1",
|
|
59
61
|
"documentation": "^13.2.5",
|
|
@@ -76,6 +78,8 @@
|
|
|
76
78
|
},
|
|
77
79
|
"browser": {
|
|
78
80
|
"./dist/io/localFile.js": false,
|
|
79
|
-
"./esm/io/localFile.js": false
|
|
81
|
+
"./esm/io/localFile.js": false,
|
|
82
|
+
"./esm/unzip.js": "./esm/unzip-pako.js",
|
|
83
|
+
"./dist/unzip.js": "./dist/unzip-pako.js"
|
|
80
84
|
}
|
|
81
85
|
}
|