@gmod/cram 3.0.7 → 4.0.1

package/dist/cram-bundle.js.LICENSE.txt

@@ -10,12 +10,3 @@
  * @author   Feross Aboukhadijeh <https://feross.org>
  * @license  MIT
  */
-
-/*!
- * The buffer module from node.js, for the browser.
- *
- * @author   Feross Aboukhadijeh <https://feross.org>
- * @license  MIT
- */
-
-/*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */

package/dist/cramFile/codecs/_base.d.ts

@@ -1,5 +1,5 @@
-import CramSlice from '../slice';
 import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 import { DataType } from './dataSeriesTypes';
 export interface DataTypeMapping {
     byte: number;

package/dist/cramFile/codecs/beta.d.ts

@@ -1,7 +1,7 @@
 import CramCodec, { Cursors } from './_base';
-import CramSlice from '../slice';
-import { CramFileBlock } from '../file';
 import { BetaEncoding } from '../encoding';
+import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 export default class BetaCodec extends CramCodec<'int', BetaEncoding['parameters']> {
     constructor(parameters: BetaEncoding['parameters'], dataType: 'int');
     decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;

package/dist/cramFile/codecs/beta.js

@@ -3,9 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
 const getBits_1 = require("./getBits");
+const errors_1 = require("../../errors");
 class BetaCodec extends _base_1.default {
     constructor(parameters, dataType) {
         super(parameters, dataType);

package/dist/cramFile/codecs/beta.js.map

@@ -1 +1 @@
-{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,SAAU,SAAQ,eAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,6CAA6C,CAC9D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,QAAQ,GAAG,IAAA,iBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;QACD,OAAO,QAAQ,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IAC1C,CAAC;CACF;AA1BD,4BA0BC"}
+{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":";;;;;AAAA,oDAA4C;AAC5C,uCAAmC;AACnC,yCAAqD;AAKrD,MAAqB,SAAU,SAAQ,eAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,6CAA6C,CAC9D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,QAAQ,GAAG,IAAA,iBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;QACD,OAAO,QAAQ,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IAC1C,CAAC;CACF;AA1BD,4BA0BC"}

package/dist/cramFile/codecs/byteArrayLength.d.ts

@@ -1,13 +1,13 @@
 import CramCodec, { Cursors } from './_base';
 import { ByteArrayLengthEncoding, CramEncoding } from '../encoding';
-import CramSlice from '../slice';
 import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 import { DataType } from './dataSeriesTypes';
 type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEncoding, dataType: TData | 'ignore') => CramCodec<TData>;
 export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayLengthEncoding['parameters']> {
     private instantiateCodec;
     constructor(parameters: ByteArrayLengthEncoding['parameters'], dataType: 'byteArray', instantiateCodec: CramCodecFactory);
-    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array;
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array<ArrayBuffer>;
     _getLengthCodec(): CramCodec<"int", unknown>;
     _getDataCodec(): CramCodec<"byte", unknown>;
 }

package/dist/cramFile/codecs/byteArrayStop.d.ts

@@ -1,8 +1,8 @@
 import CramCodec, { Cursor, Cursors } from './_base';
-import CramSlice from '../slice';
-import { CramFileBlock } from '../file';
 import { ByteArrayStopCramEncoding } from '../encoding';
+import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayStopCramEncoding['parameters']> {
-    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Buffer;
-    _decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor): Buffer;
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array<ArrayBufferLike>;
+    _decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor): Uint8Array<ArrayBufferLike>;
 }

package/dist/cramFile/codecs/byteArrayStop.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
+const errors_1 = require("../../errors");
 const getBits_1 = require("./getBits");
 class ByteArrayStopCodec extends _base_1.default {
     decode(slice, coreDataBlock, blocksByContentId, cursors) {

package/dist/cramFile/codecs/byteArrayStop.js.map

@@ -1 +1 @@
-{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":";;;;;AAAA,yCAAiD;AAEjD,oDAAoD;AAIpD,uCAAkD;AAElD,MAAqB,kBAAmB,SAAQ,eAG/C;IACC,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,gBAAgB,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IACpD,CAAC;IAED,gBAAgB,CAAC,YAA2B,EAAE,MAAc;QAC1D,MAAM,UAAU,GAAG,YAAY,CAAC,OAAO,CAAA;QACvC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,6BAA6B;QAC7B,MAAM,aAAa,GAAG,MAAM,CAAC,YAAY,CAAA;QACzC,IAAI,YAAY,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,OACE,UAAU,CAAC,YAAY,CAAC,KAAK,QAAQ;YACrC,YAAY,GAAG,UAAU,CAAC,MAAM,EAChC,CAAC;YACD,IAAI,YAAY,KAAK,UAAU,CAAC,MAAM,EAAE,CAAC;gBACvC,MAAM,IAAI,gCAAsB,CAC9B,qDAAqD,CACtD,CAAA;YACH,CAAC;YACD,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACjC,CAAC;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,OAAO,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;IACzD,CAAC;CACF;AAzCD,qCAyCC"}
+{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":";;;;;AAAA,oDAAoD;AACpD,yCAAiD;AAIjD,uCAAkD;AAElD,MAAqB,kBAAmB,SAAQ,eAG/C;IACC,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,gBAAgB,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IACpD,CAAC;IAED,gBAAgB,CAAC,YAA2B,EAAE,MAAc;QAC1D,MAAM,UAAU,GAAG,YAAY,CAAC,OAAO,CAAA;QACvC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,6BAA6B;QAC7B,MAAM,aAAa,GAAG,MAAM,CAAC,YAAY,CAAA;QACzC,IAAI,YAAY,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,OACE,UAAU,CAAC,YAAY,CAAC,KAAK,QAAQ;YACrC,YAAY,GAAG,UAAU,CAAC,MAAM,EAChC,CAAC;YACD,IAAI,YAAY,KAAK,UAAU,CAAC,MAAM,EAAE,CAAC;gBACvC,MAAM,IAAI,gCAAsB,CAC9B,qDAAqD,CACtD,CAAA;YACH,CAAC;YACD,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACjC,CAAC;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,OAAO,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;IACzD,CAAC;CACF;AAzCD,qCAyCC"}

package/dist/cramFile/codecs/external.d.ts

@@ -1,6 +1,6 @@
 import CramCodec, { Cursor, Cursors } from './_base';
-import CramSlice from '../slice';
 import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 import { ExternalCramEncoding } from '../encoding';
 export default class ExternalCodec extends CramCodec<'int' | 'byte', ExternalCramEncoding['parameters']> {
     private readonly _decodeData;

package/dist/cramFile/codecs/external.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
+const errors_1 = require("../../errors");
 const util_1 = require("../util");
 const getBits_1 = require("./getBits");
 class ExternalCodec extends _base_1.default {

package/dist/cramFile/codecs/external.js.map

@@ -1 +1 @@
-{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,yCAAyE;AACzE,oDAAoD;AACpD,kCAAmC;AAGnC,uCAAkD;AAGlD,MAAqB,aAAc,SAAQ,eAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,GAAG,CACpD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC/C,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAS,EACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,GAAG,MAAM,CAAC,YAAY,GAAG,SAAS,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAA2B,EAAE,MAAc;QACrD,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACvD,MAAM,IAAI,gCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF;AA3DD,gCA2DC"}
+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,oDAAoD;AACpD,yCAAyE;AAGzE,kCAAmC;AACnC,uCAAkD;AAGlD,MAAqB,aAAc,SAAQ,eAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,GAAG,CACpD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC/C,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAS,EACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,GAAG,MAAM,CAAC,YAAY,GAAG,SAAS,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAA2B,EAAE,MAAc;QACrD,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACvD,MAAM,IAAI,gCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF;AA3DD,gCA2DC"}

package/dist/cramFile/codecs/gamma.d.ts

@@ -1,7 +1,7 @@
 import CramCodec, { Cursors } from './_base';
 import { GammaEncoding } from '../encoding';
-import CramSlice from '../slice';
 import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 export default class GammaCodec extends CramCodec<'int', GammaEncoding['parameters']> {
     constructor(parameters: GammaEncoding['parameters'], dataType: 'int');
     decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;

package/dist/cramFile/codecs/gamma.js

@@ -3,9 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
 const getBits_1 = require("./getBits");
+const errors_1 = require("../../errors");
 class GammaCodec extends _base_1.default {
     constructor(parameters, dataType) {
         super(parameters, dataType);

package/dist/cramFile/codecs/gamma.js.map

@@ -1 +1 @@
-{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,UAAW,SAAQ,eAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,8CAA8C,CAC/D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,MAAM,GAAG,CAAC,CAAA;QAEd,OAAO,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAClE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QACrB,CAAC;QAED,MAAM,QAAQ,GAAG,IAAA,iBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,MAAM,GAAG,CAAC,CACX,CAAA;QAED,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAC5C,OAAO,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACvC,CAAC;CACF;AAlCD,6BAkCC"}
+{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":";;;;;AAAA,oDAA4C;AAC5C,uCAAmC;AACnC,yCAAqD;AAKrD,MAAqB,UAAW,SAAQ,eAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,8CAA8C,CAC/D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,MAAM,GAAG,CAAC,CAAA;QAEd,OAAO,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAClE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QACrB,CAAC;QAED,MAAM,QAAQ,GAAG,IAAA,iBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,MAAM,GAAG,CAAC,CACX,CAAA;QAED,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAC5C,OAAO,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACvC,CAAC;CACF;AAlCD,6BAkCC"}

package/dist/cramFile/codecs/getBits.d.ts

@@ -1,6 +1,6 @@
 export declare class CramBufferOverrunError extends Error {
 }
-export declare function getBits(data: Buffer, cursor: {
+export declare function getBits(data: Uint8Array, cursor: {
     bytePosition: number;
     bitPosition: number;
 }, numBits: number): number;

package/dist/cramFile/codecs/getBits.js.map

@@ -1 +1 @@
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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,IAAgB,EAChB,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,CAAE,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QAC7D,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"}

package/dist/cramFile/codecs/huffman.d.ts

@@ -1,7 +1,7 @@
 import CramCodec, { Cursor, Cursors } from './_base';
 import { HuffmanEncoding } from '../encoding';
-import CramSlice from '../slice';
 import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 export default class HuffmanIntCodec extends CramCodec<'byte' | 'int', HuffmanEncoding['parameters']> {
     private codes;
     private codeBook;

package/dist/cramFile/codecs/huffman.js

@@ -3,9 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
 const getBits_1 = require("./getBits");
+const errors_1 = require("../../errors");
 function numberOfSetBits(ii) {
     let i = (ii - (ii >> 1)) & 0x55555555;
     i = (i & 0x33333333) + ((i >> 2) & 0x33333333);

package/dist/cramFile/codecs/huffman.js.map

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package/dist/cramFile/codecs/index.d.ts

@@ -1,4 +1,4 @@
 import CramCodec from './_base';
-import { CramEncoding } from '../encoding';
 import { DataType } from './dataSeriesTypes';
+import { CramEncoding } from '../encoding';
 export declare function instantiateCodec<TResult extends DataType = DataType>(encodingData: CramEncoding, dataType: DataType | 'ignore'): CramCodec<TResult>;

package/dist/cramFile/codecs/index.js

@@ -4,14 +4,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.instantiateCodec = instantiateCodec;
-const errors_1 = require("../../errors");
-const huffman_1 = __importDefault(require("./huffman"));
-const external_1 = __importDefault(require("./external"));
-const byteArrayStop_1 = __importDefault(require("./byteArrayStop"));
-const byteArrayLength_1 = __importDefault(require("./byteArrayLength"));
 const beta_1 = __importDefault(require("./beta"));
+const byteArrayLength_1 = __importDefault(require("./byteArrayLength"));
+const byteArrayStop_1 = __importDefault(require("./byteArrayStop"));
+const external_1 = __importDefault(require("./external"));
 const gamma_1 = __importDefault(require("./gamma"));
+const huffman_1 = __importDefault(require("./huffman"));
 const subexp_1 = __importDefault(require("./subexp"));
+const errors_1 = require("../../errors");
 const codecClasses = {
     1: external_1.default,
     // 2: GolombCodec,

package/dist/cramFile/codecs/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.ts"],"names":[],"mappings":";;;;;AA4BA,4CAcC;AAzCD,kDAA8B;AAC9B,wEAAoD;AACpD,oEAAgD;AAEhD,0DAAsC;AACtC,oDAAgC;AAChC,wDAAuC;AACvC,sDAAkC;AAClC,yCAAqD;AAGrD,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"}

package/dist/cramFile/codecs/subexp.d.ts

@@ -1,7 +1,7 @@
 import CramCodec, { Cursors } from './_base';
-import CramSlice from '../slice';
-import { CramFileBlock } from '../file';
 import { SubexpEncoding } from '../encoding';
+import { CramFileBlock } from '../file';
+import CramSlice from '../slice';
 export default class SubexpCodec extends CramCodec<'int', SubexpEncoding['parameters']> {
     constructor(parameters: SubexpEncoding['parameters'], dataType: 'int');
     decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;

package/dist/cramFile/codecs/subexp.js

@@ -3,9 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
 const getBits_1 = require("./getBits");
+const errors_1 = require("../../errors");
 class SubexpCodec extends _base_1.default {
     constructor(parameters, dataType) {
         super(parameters, dataType);

package/dist/cramFile/codecs/subexp.js.map

@@ -1 +1 @@
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+{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":";;;;;AAAA,oDAA4C;AAC5C,uCAAmC;AACnC,yCAAqD;AAKrD,MAAqB,WAAY,SAAQ,eAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC;YAC5D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;QACrC,CAAC;QAED,IAAI,CAAS,CAAA;QACb,IAAI,CAAS,CAAA;QACb,IAAI,cAAc,KAAK,CAAC,EAAE,CAAC;YACzB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QAC1D,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACjE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;QACrB,CAAC;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF;AArCD,8BAqCC"}

package/dist/cramFile/container/compressionScheme.d.ts

@@ -1,7 +1,7 @@
 import CramCodec from '../codecs/_base';
-import { CramCompressionHeader } from '../sectionParsers';
-import { CramEncoding } from '../encoding';
 import { DataSeriesEncodingKey, DataSeriesEncodingMap } from '../codecs/dataSeriesTypes';
+import { CramEncoding } from '../encoding';
+import { CramCompressionHeader } from '../sectionParsers';
 declare const dataSeriesTypes: {
     readonly BF: "int";
     readonly CF: "int";

package/dist/cramFile/container/compressionScheme.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const codecs_1 = require("../codecs");
 const errors_1 = require("../../errors");
+const codecs_1 = require("../codecs");
 // the hardcoded data type to be decoded for each core
 // data field
 const dataSeriesTypes = {

package/dist/cramFile/container/compressionScheme.js.map

@@ -1 +1 @@
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+{"version":3,"file":"compressionScheme.js","sourceRoot":"","sources":["../../../src/cramFile/container/compressionScheme.ts"],"names":[],"mappings":";;AAAA,yCAAiD;AACjD,sCAA4C;AAS5C,sDAAsD;AACtD,aAAa;AACb,MAAM,eAAe,GAAG;IACtB,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,gBAAgB;IAChB,gBAAgB;CACR,CAAA;AAIV,SAAS,uBAAuB,CAAC,SAAmB;IAClD,MAAM,MAAM,GAAe,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IAC1B,CAAC;IAED,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,CAAC,CAAC,CAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAE1C,OAAO,MAAM,CAAA;AACf,CAAC;AAMD,MAAqB,8BAA8B;IAWjD,YAAY,OAA8B;QALnC,yBAAoB,GAAoB,EAAE,CAAA;QAC1C,kBAAa,GAA8B,EAAE,CAAA;QAC7C,gBAAW,GAAiC,EAAE,CAAA;QAInD,iEAAiE;QACjE,IAAI,CAAC,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAChD,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QACtC,IAAI,CAAC,iBAAiB,GAAG,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAClD,IAAI,CAAC,gBAAgB,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAC/C,IAAI,CAAC,kBAAkB,GAAG,uBAAuB,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;QAC1E,IAAI,CAAC,kBAAkB,GAAG,OAAO,CAAC,kBAAkB,CAAA;QACpD,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,WAAW,CAAA;IACxC,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,OAAe;QAC5B,MAAM,IAAI,GAAG,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QACxC,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC9C,IAAI,CAAC,YAAY,EAAE,CAAC;gBAClB,MAAM,IAAI,KAAK,CAAC,wBAAwB,CAAC,CAAA;YAC3C,CAAC;YACD,MAAM,GAAG,GAAG,IAAA,yBAAgB,EAC1B,YAAY,EACZ,WAAW,CACZ,CAAA;YACD,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,GAAG,CAAA;YACjC,OAAO,GAAG,CAAA;QACZ,CAAC;aAAM,CAAC;YACN,OAAO,IAAI,CAAA;QACb,CAAC;IACH,CAAC;IAED;;;;OAIG;IACH,WAAW,CAAC,SAAiB;QAC3B,OAAO,IAAI,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;IACzC,CAAC;IAED,qBAAqB,CACnB,cAA2B;QAE3B,IAAI,CAAC,GACH,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,CAAA;QAC3C,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YACpB,MAAM,YAAY,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAA;YAC5D,uEAAuE;YACvE,IAAI,YAAY,EAAE,CAAC;gBACjB,MAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,uEAAuE;gBACvE,IAAI,CAAC,QAAQ,EAAE,CAAC;oBACd,MAAM,IAAI,2BAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;gBACH,CAAC;gBACD,CAAC,GAAG,IAAA,yBAAgB,EAAC,YAAY,EAAE,QAAQ,CAAC,CAAA;gBAC5C,+CAA+C;gBAC/C,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,GAAG,CAAmB,CAAA;YACjE,CAAC;QACH,CAAC;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAAQ,EAAE,CAAA;QACpB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAC5B,IAAI,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE,CAAC;gBACxB,OAAM;YACR,CAAC;YACD,IAAI,CAAC,CAAC,CAAC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package/dist/cramFile/container/index.d.ts

@@ -1,4 +1,3 @@
-import { Buffer } from 'buffer';
 import CramSlice from '../slice';
 import CramContainerCompressionScheme from './compressionScheme';
 import CramFile from '../file';
@@ -47,7 +46,7 @@ export default class CramContainer {
         _endPosition: number;
         contentPosition: number;
         _size: number;
-        content: Buffer;
+        content: Uint8Array;
         crc32?: number;
     } | null | undefined>;
     getFirstBlock(): Promise<import("../file").CramFileBlock | undefined>;

package/dist/cramFile/container/index.js

@@ -1,22 +1,12 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const buffer_1 = require("buffer");
 const errors_1 = require("../../errors");
 // locals
-const util_1 = require("../util");
 const slice_1 = __importDefault(require("../slice"));
+const util_1 = require("../util");
 const compressionScheme_1 = __importDefault(require("./compressionScheme"));
 const sectionParsers_1 = require("../sectionParsers");
 class CramContainer {
@@ -27,85 +17,78 @@ class CramContainer {
     getHeader() {
         return this._readContainerHeader(this.filePosition);
     }
-    getCompressionHeaderBlock() {
-        return __awaiter(this, void 0, void 0, function* () {
-            const containerHeader = yield this.getHeader();
-            // if there are no records in the container, there will be no compression
-            // header
-            if (!(containerHeader === null || containerHeader === void 0 ? void 0 : containerHeader.numRecords)) {
-                return null;
-            }
-            const { majorVersion } = yield this.file.getDefinition();
-            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
-            const block = yield this.getFirstBlock();
-            if (block === undefined) {
-                return undefined;
-            }
-            if (block.contentType !== 'COMPRESSION_HEADER') {
-                throw new errors_1.CramMalformedError(`invalid content type ${block.contentType} in compression header block`);
-            }
-            const content = (0, util_1.parseItem)(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
-            return Object.assign(Object.assign({}, block), { parsedContent: content });
-        });
+    async getCompressionHeaderBlock() {
+        const containerHeader = await this.getHeader();
+        // if there are no records in the container, there will be no compression
+        // header
+        if (!containerHeader?.numRecords) {
+            return null;
+        }
+        const { majorVersion } = await this.file.getDefinition();
+        const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
+        const block = await this.getFirstBlock();
+        if (block === undefined) {
+            return undefined;
+        }
+        if (block.contentType !== 'COMPRESSION_HEADER') {
+            throw new errors_1.CramMalformedError(`invalid content type ${block.contentType} in compression header block`);
+        }
+        const content = (0, util_1.parseItem)(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
+        return {
+            ...block,
+            parsedContent: content,
+        };
     }
-    getFirstBlock() {
-        return __awaiter(this, void 0, void 0, function* () {
-            const containerHeader = yield this.getHeader();
-            if (!containerHeader) {
-                return undefined;
-            }
-            return this.file.readBlock(containerHeader._endPosition);
-        });
+    async getFirstBlock() {
+        const containerHeader = await this.getHeader();
+        if (!containerHeader) {
+            return undefined;
+        }
+        return this.file.readBlock(containerHeader._endPosition);
     }
     // parses the compression header data into a CramContainerCompressionScheme
     // object
-    getCompressionScheme() {
-        return __awaiter(this, void 0, void 0, function* () {
-            const header = yield this.getCompressionHeaderBlock();
-            if (!header) {
-                return undefined;
-            }
-            return new compressionScheme_1.default(header.parsedContent);
-        });
+    async getCompressionScheme() {
+        const header = await this.getCompressionHeaderBlock();
+        if (!header) {
+            return undefined;
+        }
+        return new compressionScheme_1.default(header.parsedContent);
     }
     getSlice(slicePosition, sliceSize) {
         // note: slicePosition is relative to the end of the container header
         // TODO: perhaps we should cache slices?
         return new slice_1.default(this, slicePosition, sliceSize);
     }
-    _readContainerHeader(position) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const { majorVersion } = yield this.file.getDefinition();
-            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
-            const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
-            const { size: fileSize } = yield this.file.stat();
-            if (position >= fileSize) {
-                console.warn(`pos:${position}>=fileSize:${fileSize} in cram container`);
-                return undefined;
-            }
-            // parse the container header. do it in 2 pieces because you cannot tell
-            // how much to buffer until you read numLandmarks
-            const bytes1 = buffer_1.Buffer.allocUnsafe(cramContainerHeader1.maxLength);
-            yield this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position);
-            const header1 = (0, util_1.parseItem)(bytes1, cramContainerHeader1.parser);
-            const numLandmarksSize = (0, util_1.itf8Size)(header1.numLandmarks);
-            if (position + header1.length >= fileSize) {
-                // header indicates container goes beyond fileSize
-                console.warn(`container at ${position} is beyond fileSize:${fileSize}, skipping`);
-                return undefined;
-            }
-            const bytes2 = buffer_1.Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
-            yield this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
-            const header2 = (0, util_1.parseItem)(bytes2, cramContainerHeader2.parser);
-            if (this.file.validateChecksums && header2.crc32 !== undefined) {
-                yield this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, `container header beginning at position ${position}`);
-            }
-            const completeHeader = Object.assign(header1, header2, {
-                _size: header1._size + header2._size - numLandmarksSize,
-                _endPosition: header1._size + header2._size - numLandmarksSize + position,
-            });
-            return completeHeader;
+    async _readContainerHeader(position) {
+        const { majorVersion } = await this.file.getDefinition();
+        const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
+        const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
+        const { size: fileSize } = await this.file.stat();
+        if (position >= fileSize) {
+            console.warn(`pos:${position}>=fileSize:${fileSize} in cram container`);
+            return undefined;
+        }
+        // parse the container header. do it in 2 pieces because you cannot tell
+        // how much to buffer until you read numLandmarks
+        const bytes1 = await this.file.read(cramContainerHeader1.maxLength, position);
+        const header1 = (0, util_1.parseItem)(bytes1, cramContainerHeader1.parser);
+        const numLandmarksSize = (0, util_1.itf8Size)(header1.numLandmarks);
+        if (position + header1.length >= fileSize) {
+            // header indicates container goes beyond fileSize
+            console.warn(`container at ${position} is beyond fileSize:${fileSize}, skipping`);
+            return undefined;
+        }
+        const bytes2 = await this.file.read(cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
+        const header2 = (0, util_1.parseItem)(bytes2, cramContainerHeader2.parser);
+        if (this.file.validateChecksums && header2.crc32 !== undefined) {
+            await this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, `container header beginning at position ${position}`);
+        }
+        const completeHeader = Object.assign(header1, header2, {
+            _size: header1._size + header2._size - numLandmarksSize,
+            _endPosition: header1._size + header2._size - numLandmarksSize + position,
         });
+        return completeHeader;
     }
 }
 exports.default = CramContainer;

package/dist/cramFile/container/index.js.map

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