@gmod/cram 3.0.6 → 4.0.0

package/esm/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 & WithArrayBufferLike<ArrayBufferLike>;
-    _decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor): Buffer & WithArrayBufferLike<ArrayBufferLike>;
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array<ArrayBufferLike>;
+    _decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor): Uint8Array<ArrayBufferLike>;
 }

package/esm/cramFile/codecs/byteArrayStop.js

@@ -1,5 +1,5 @@
-import { CramMalformedError } from '../../errors';
 import CramCodec from './_base';
+import { CramMalformedError } from '../../errors';
 import { CramBufferOverrunError } from './getBits';
 export default class ByteArrayStopCodec extends CramCodec {
     decode(slice, coreDataBlock, blocksByContentId, cursors) {

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

@@ -1 +1 @@
-{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAEjD,OAAO,SAA8B,MAAM,SAAS,CAAA;AAIpD,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/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,kBAAkB,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,sBAAsB,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"}
+{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAIjD,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/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,kBAAkB,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,sBAAsB,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"}

package/esm/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/esm/cramFile/codecs/external.js

@@ -1,5 +1,5 @@
-import { CramMalformedError, CramUnimplementedError } from '../../errors';
 import CramCodec from './_base';
+import { CramMalformedError, CramUnimplementedError } from '../../errors';
 import { parseItf8 } from '../util';
 import { CramBufferOverrunError } from './getBits';
 export default class ExternalCodec extends CramCodec {

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

@@ -1 +1 @@
-{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACzE,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAGnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;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,sBAAsB,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,kBAAkB,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,SAAS,CACnC,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,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF"}
+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGzE,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;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,sBAAsB,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,kBAAkB,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,SAAS,CACnC,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,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF"}

package/esm/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/esm/cramFile/codecs/gamma.js

@@ -1,6 +1,6 @@
-import { CramUnimplementedError } from '../../errors';
 import CramCodec from './_base';
 import { getBits } from './getBits';
+import { CramUnimplementedError } from '../../errors';
 export default class GammaCodec extends CramCodec {
     constructor(parameters, dataType) {
         super(parameters, dataType);

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

@@ -1 +1 @@
-{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAKnC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAGvC;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,sBAAsB,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,OAAO,CAAC,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,OAAO,CACtB,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"}
+{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAKrD,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAGvC;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,sBAAsB,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,OAAO,CAAC,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,OAAO,CACtB,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"}

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

@@ -1 +1 @@
-{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,sBAAuB,SAAQ,KAAK;CAAG;AAEpD,MAAM,UAAU,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,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"}
+{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,sBAAuB,SAAQ,KAAK;CAAG;AAEpD,MAAM,UAAU,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/esm/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/esm/cramFile/codecs/huffman.js

@@ -1,6 +1,6 @@
-import { CramMalformedError } from '../../errors';
 import CramCodec from './_base';
 import { getBits } from './getBits';
+import { CramMalformedError } from '../../errors';
 function numberOfSetBits(ii) {
     let i = (ii - (ii >> 1)) & 0x55555555;
     i = (i & 0x33333333) + ((i >> 2) & 0x33333333);

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

@@ -1 +1 @@
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package/esm/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/esm/cramFile/codecs/index.js

@@ -1,11 +1,11 @@
-import { CramUnimplementedError } from '../../errors';
-import HuffmanIntCodec from './huffman';
-import ExternalCodec from './external';
-import ByteArrayStopCodec from './byteArrayStop';
-import ByteArrayLengthCodec from './byteArrayLength';
 import BetaCodec from './beta';
+import ByteArrayLengthCodec from './byteArrayLength';
+import ByteArrayStopCodec from './byteArrayStop';
+import ExternalCodec from './external';
 import GammaCodec from './gamma';
+import HuffmanIntCodec from './huffman';
 import SubexpCodec from './subexp';
+import { CramUnimplementedError } from '../../errors';
 const codecClasses = {
     1: ExternalCodec,
     // 2: GolombCodec,

package/esm/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":"AACA,OAAO,SAAS,MAAM,QAAQ,CAAA;AAC9B,OAAO,oBAAoB,MAAM,mBAAmB,CAAA;AACpD,OAAO,kBAAkB,MAAM,iBAAiB,CAAA;AAEhD,OAAO,aAAa,MAAM,YAAY,CAAA;AACtC,OAAO,UAAU,MAAM,SAAS,CAAA;AAChC,OAAO,eAAe,MAAM,WAAW,CAAA;AACvC,OAAO,WAAW,MAAM,UAAU,CAAA;AAClC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGrD,MAAM,YAAY,GAAG;IACnB,CAAC,EAAE,aAAa;IAChB,kBAAkB;IAClB,CAAC,EAAE,eAAe;IAClB,CAAC,EAAE,oBAAoB;IACvB,CAAC,EAAE,kBAAkB;IACrB,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,WAAW;IACd,sBAAsB;IACtB,CAAC,EAAE,UAAU;CACd,CAAA;AAED,SAAS,mBAAmB,CAAC,EAAU;IACrC,OAAQ,YAAoB,CAAC,EAAE,CAAC,CAAA;AAClC,CAAC;AAED,MAAM,UAAU,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,sBAAsB,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/esm/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/esm/cramFile/codecs/subexp.js

@@ -1,6 +1,6 @@
-import { CramUnimplementedError } from '../../errors';
 import CramCodec from './_base';
 import { getBits } from './getBits';
+import { CramUnimplementedError } from '../../errors';
 export default class SubexpCodec extends CramCodec {
     constructor(parameters, dataType) {
         super(parameters, dataType);

package/esm/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,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAKrD,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,SAGxC;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,sBAAsB,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,OAAO,CAAC,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,OAAO,CAAC,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,OAAO,CAAC,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"}

package/esm/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/esm/cramFile/container/compressionScheme.js

@@ -1,5 +1,5 @@
-import { instantiateCodec } from '../codecs';
 import { CramMalformedError } from '../../errors';
+import { instantiateCodec } from '../codecs';
 // the hardcoded data type to be decoded for each core
 // data field
 const dataSeriesTypes = {

package/esm/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,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,WAAW,CAAA;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,MAAM,CAAC,OAAO,OAAO,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,gBAAgB,CAC1B,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,kBAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;gBACH,CAAC;gBACD,CAAC,GAAG,gBAAgB,CAAC,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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package/esm/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/esm/cramFile/container/index.js

@@ -1,8 +1,7 @@
-import { Buffer } from 'buffer';
 import { CramMalformedError } from '../../errors';
 // locals
-import { itf8Size, parseItem, tinyMemoize } from '../util';
 import CramSlice from '../slice';
+import { itf8Size, parseItem, tinyMemoize } from '../util';
 import CramContainerCompressionScheme from './compressionScheme';
 import { getSectionParsers } from '../sectionParsers';
 export default class CramContainer {
@@ -17,7 +16,7 @@ export default class CramContainer {
         const containerHeader = await 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)) {
+        if (!containerHeader?.numRecords) {
             return null;
         }
         const { majorVersion } = await this.file.getDefinition();
@@ -67,8 +66,7 @@ export default class CramContainer {
         }
         // parse the container header. do it in 2 pieces because you cannot tell
         // how much to buffer until you read numLandmarks
-        const bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength);
-        await this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position);
+        const bytes1 = await this.file.read(cramContainerHeader1.maxLength, position);
         const header1 = parseItem(bytes1, cramContainerHeader1.parser);
         const numLandmarksSize = itf8Size(header1.numLandmarks);
         if (position + header1.length >= fileSize) {
@@ -76,8 +74,7 @@ export default class CramContainer {
             console.warn(`container at ${position} is beyond fileSize:${fileSize}, skipping`);
             return undefined;
         }
-        const bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
-        await this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
+        const bytes2 = await this.file.read(cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
         const header2 = 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}`);

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

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AACjD,SAAS;AACT,OAAO,SAAS,MAAM,UAAU,CAAA;AAChC,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAC1D,OAAO,8BAA8B,MAAM,qBAAqB,CAAA;AAEhE,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAA;AAErD,MAAM,CAAC,OAAO,OAAO,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAED,KAAK,CAAC,yBAAyB;QAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAE9C,yEAAyE;QACzE,SAAS;QACT,IAAI,CAAC,eAAe,EAAE,UAAU,EAAE,CAAC;YACjC,OAAO,IAAI,CAAA;QACb,CAAC;QACD,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QAEtD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACxC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;YAC/C,MAAM,IAAI,kBAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,8BAA8B,CACxE,CAAA;QACH,CAAC;QAED,MAAM,OAAO,GAAG,SAAS,CACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;QACD,OAAO;YACL,GAAG,KAAK;YACR,aAAa,EAAE,OAAO;SACvB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC9C,IAAI,CAAC,eAAe,EAAE,CAAC;YACrB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED,2EAA2E;IAC3E,SAAS;IACT,KAAK,CAAC,oBAAoB;QACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;QACrD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,OAAO,IAAI,8BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;IACjE,CAAC;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,SAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,QAAgB;QACzC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QACtD,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QACrE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QAEjD,IAAI,QAAQ,IAAI,QAAQ,EAAE,CAAC;YACzB,OAAO,CAAC,IAAI,CAAC,OAAO,QAAQ,cAAc,QAAQ,oBAAoB,CAAC,CAAA;YACvE,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,wEAAwE;QACxE,iDAAiD;QACjD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CACjC,oBAAoB,CAAC,SAAS,EAC9B,QAAQ,CACT,CAAA;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAC9D,MAAM,gBAAgB,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACvD,IAAI,QAAQ,GAAG,OAAO,CAAC,MAAM,IAAI,QAAQ,EAAE,CAAC;YAC1C,kDAAkD;YAClD,OAAO,CAAC,IAAI,CACV,gBAAgB,QAAQ,uBAAuB,QAAQ,YAAY,CACpE,CAAA;YACD,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CACjC,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,EACpD,QAAQ,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,CAC5C,CAAA;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;YAC/D,MAAM,IAAI,CAAC,IAAI,CAAC,UAAU,CACxB,QAAQ,EACR,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,CAAC,EACpD,OAAO,CAAC,KAAK,EACb,0CAA0C,QAAQ,EAAE,CACrD,CAAA;QACH,CAAC;QAED,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE;YACrD,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;YACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;SAC1E,CAAC,CAAA;QAEF,OAAO,cAAc,CAAA;IACvB,CAAC;CACF;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE;IAChB,WAAW,CAAC,aAAa,EAAE,MAAM,CAAC,CAAA;AACpC,CAAC,CAAC,CAAA"}

package/esm/cramFile/file.d.ts

@@ -1,11 +1,10 @@
-import { Buffer } from 'buffer';
 import QuickLRU from 'quick-lru';
-import { BlockHeader, CompressionMethod } from './sectionParsers';
 import CramContainer from './container';
 import CramRecord from './record';
-import { Filehandle } from './filehandle';
+import { BlockHeader, CompressionMethod } from './sectionParsers';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export interface CramFileSource {
-    filehandle?: Filehandle;
+    filehandle?: GenericFilehandle;
     url?: string;
     path?: string;
 }
@@ -19,7 +18,7 @@ export type CramFileBlock = BlockHeader & {
     _endPosition: number;
     contentPosition: number;
     _size: number;
-    content: Buffer;
+    content: Uint8Array;
     crc32?: number;
 };
 export default class CramFile {
@@ -33,11 +32,8 @@ export default class CramFile {
     featureCache: QuickLRU<string, Promise<CramRecord[]>>;
     private header;
     constructor(args: CramFileArgs);
-    read(buffer: Buffer, offset: number, length: number, position: number): Promise<{
-        bytesRead: number;
-        buffer: Buffer;
-    }>;
-    stat(): Promise<import("generic-filehandle").Stats>;
+    stat(): Promise<import("generic-filehandle2").Stats>;
+    read(length: number, position: number): Promise<Uint8Array<ArrayBuffer>>;
     getDefinition(): Promise<{
         magic: string;
         majorVersion: number;
@@ -71,14 +67,14 @@ export default class CramFile {
     }) | undefined>;
     _parseSection<T>(section: {
         maxLength: number;
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             offset: number;
             value: T;
         };
-    }, position: number, size?: number, preReadBuffer?: Buffer): Promise<(T & {
+    }, position: number, size?: number, preReadBuffer?: Uint8Array): Promise<(T & {
         _endPosition: number;
         _size: number;
     }) | undefined>;
-    _uncompress(compressionMethod: CompressionMethod, inputBuffer: Buffer, outputBuffer: Buffer): Promise<void>;
+    _uncompress(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<any>;
     readBlock(position: number): Promise<CramFileBlock | undefined>;
 }