@gmod/cram 1.6.3 → 1.7.0

package/esm/craiIndex.js

@@ -4,14 +4,6 @@ import { unzip } from './unzip';
 import { open } from './io';
 import { CramMalformedError } from './errors';
 const BAI_MAGIC = 21578050; // BAI\1
-class Slice {
-    constructor(args) {
-        Object.assign(this, args);
-    }
-    toString() {
-        return `${this.start}:${this.span}:${this.containerStart}:${this.sliceStart}:${this.sliceBytes}`;
-    }
-}
 function addRecordToIndex(index, record) {
     if (record.some(el => el === undefined)) {
         throw new CramMalformedError('invalid .crai index file');
@@ -20,23 +12,15 @@ function addRecordToIndex(index, record) {
     if (!index[seqId]) {
         index[seqId] = [];
     }
-    index[seqId].push(new Slice({
+    index[seqId].push({
         start,
         span,
         containerStart,
         sliceStart,
         sliceBytes,
-    }));
+    });
 }
 export default class CraiIndex {
-    // A CRAM index (.crai) is a gzipped tab delimited file containing the following columns:
-    // 1. Sequence id
-    // 2. Alignment start
-    // 3. Alignment span
-    // 4. Container start byte position in the file
-    // 5. Slice start byte position in the container data (‘blocks’)
-    // 6. Slice size in bytes
-    // Each line represents a slice in the CRAM file. Please note that all slices must be listed in index file.
     /**
      *
      * @param {object} args
@@ -45,16 +29,16 @@ export default class CraiIndex {
      * @param {FileHandle} [args.filehandle]
      */
     constructor(args) {
-        const filehandle = open(args.url, args.path, args.filehandle);
+        this.filehandle = open(args.url, args.path, args.filehandle);
         this._parseCache = new AbortablePromiseCache({
             cache: new QuickLRU({ maxSize: 1 }),
-            fill: (data, signal) => this.parseIndex({ signal }),
+            fill: (data, signal) => this.parseIndex(),
         });
-        this.readFile = filehandle.readFile.bind(filehandle);
     }
     parseIndex() {
         const index = {};
-        return this.readFile()
+        return this.filehandle
+            .readFile()
             .then(data => {
             if (data[0] === 31 && data[1] === 139) {
                 return unzip(data);
@@ -135,10 +119,10 @@ export default class CraiIndex {
         if (!seqEntries) {
             return [];
         }
-        const compare = entry => {
+        const compare = (entry) => {
             const entryStart = entry.start;
             const entryEnd = entry.start + entry.span;
-            if (entryStart >= queryEnd) {
+            if (entryStart > queryEnd) {
                 return -1;
             } // entry is ahead of query
             if (entryEnd <= queryStart) {

package/esm/craiIndex.js.map

@@ -1 +1 @@
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+{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"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;AAI7C,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAYnC,SAAS,gBAAgB,CAAC,KAAkB,EAAE,MAAgB;IAC5D,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,CAAC;QAChB,KAAK;QACL,IAAI;QACJ,cAAc;QACd,UAAU;QACV,UAAU;KACX,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,SAAS;IAY5B;;;;;;OAMG;IACH,YAAY,IAAoB;QAC9B,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QAC5D,IAAI,CAAC,WAAW,GAAG,IAAI,qBAAqB,CAAuB;YACjE,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;YACnC,IAAI,EAAE,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,EAAE;SAC1C,CAAC,CAAA;IACJ,CAAC;IAED,UAAU;QACR,MAAM,KAAK,GAAgB,EAAE,CAAA;QAC7B,OAAO,IAAI,CAAC,UAAU;aACnB,QAAQ,EAAE;aACV,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,GAAa,EAAE,CAAA;YAChC,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,OAAiC,EAAE;QAC1C,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,KAAa;QAC7C,OAAO,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;IACzC,CAAC;IAED;;;;;;;;;;OAUG;IACH,KAAK,CAAC,kBAAkB,CACtB,KAAa,EACb,UAAkB,EAClB,QAAgB;QAEhB,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,CAAC,KAAY,EAAE,EAAE;YAC/B,MAAM,UAAU,GAAG,KAAK,CAAC,KAAK,CAAA;YAC9B,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,IAAI,CAAA;YACzC,IAAI,UAAU,GAAG,QAAQ,EAAE;gBACzB,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/codecs/_base.d.ts

@@ -1,6 +1,27 @@
-export default class CramCodec {
-    constructor(parameters: {} | undefined, dataType: any);
-    parameters: {};
-    dataType: any;
-    _getBits(data: any, cursor: any, numBits: any): number;
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+import { DataType } from './dataSeriesTypes';
+export declare type DataTypeMapping = {
+    byte: number;
+    int: number;
+    long: number;
+    byteArray: Uint8Array;
+};
+export declare type Cursor = {
+    bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7;
+    bytePosition: number;
+};
+export declare type Cursors = {
+    lastAlignmentStart: number;
+    coreBlock: Cursor;
+    externalBlocks: {
+        map: Map<any, any>;
+        getCursor: (contentId: number) => Cursor;
+    };
+};
+export default abstract class CramCodec<TResult extends DataType = DataType, TParameters = unknown> {
+    parameters: TParameters;
+    dataType: DataType;
+    constructor(parameters: TParameters, dataType: TResult);
+    abstract decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): DataTypeMapping[TResult];
 }

package/esm/cramFile/codecs/_base.js

@@ -1,42 +1,8 @@
-import { CramBufferOverrunError } from '../../errors';
-const validDataTypes = {
-    int: true,
-    byte: true,
-    long: true,
-    byteArray: true,
-    byteArrayBlock: true,
-};
 // codec base class
 export default class CramCodec {
-    constructor(parameters = {}, dataType) {
+    constructor(parameters, dataType) {
         this.parameters = parameters;
         this.dataType = dataType;
-        if (!dataType) {
-            throw new TypeError('must provide a data type to codec constructor');
-        }
-        if (!validDataTypes[dataType]) {
-            throw new TypeError(`invalid data type ${dataType}`);
-        }
-    }
-    // decode(slice, coreDataBlock, blocksByContentId, cursors) {
-    // }
-    _getBits(data, cursor, numBits) {
-        let val = 0;
-        if (cursor.bytePosition + (7 - cursor.bitPosition + numBits) / 8 >
-            data.length) {
-            throw new CramBufferOverrunError('read error during decoding. the file seems to be truncated.');
-        }
-        for (let dlen = numBits; dlen; dlen -= 1) {
-            // get the next `dlen` bits in the input, put them in val
-            val <<= 1;
-            val |= (data[cursor.bytePosition] >> cursor.bitPosition) & 1;
-            cursor.bitPosition -= 1;
-            if (cursor.bitPosition < 0) {
-                cursor.bytePosition += 1;
-            }
-            cursor.bitPosition &= 7;
-        }
-        return val;
     }
 }
 //# sourceMappingURL=_base.js.map

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

@@ -1 +1 @@
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package/esm/cramFile/codecs/beta.d.ts

@@ -1,4 +1,8 @@
-export default class BetaCodec extends CramCodec {
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): number;
+import CramCodec, { Cursors } from './_base';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+import { BetaEncoding } from '../encoding';
+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;
 }
-import CramCodec from "./_base";

package/esm/cramFile/codecs/beta.js

@@ -1,15 +1,16 @@
 import { CramUnimplementedError } from '../../errors';
 import CramCodec from './_base';
+import { getBits } from './getBits';
 export default class BetaCodec extends CramCodec {
-    constructor(parameters = {}, dataType) {
+    constructor(parameters, dataType) {
         super(parameters, dataType);
         if (this.dataType !== 'int') {
             throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by BETA codec`);
         }
     }
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
-        const data = this._getBits(coreDataBlock.content, cursors.coreBlock, this.parameters.length) - this.parameters.offset;
-        return data;
+        const fromBits = getBits(coreDataBlock.content, cursors.coreBlock, this.parameters.length);
+        return fromBits - this.parameters.offset;
     }
 }
 //# sourceMappingURL=beta.js.map

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

@@ -1 +1 @@
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package/esm/cramFile/codecs/byteArrayLength.d.ts

@@ -1,8 +1,14 @@
-export default class ByteArrayStopCodec extends CramCodec {
-    constructor(parameters: {} | undefined, dataType: any, instantiateCodec: any);
-    instantiateCodec: any;
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): Uint8Array;
-    _getLengthCodec(): any;
-    _getDataCodec(): any;
+import CramCodec, { Cursors } from './_base';
+import { ByteArrayLengthEncoding, CramEncoding } from '../encoding';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+import { DataType } from './dataSeriesTypes';
+declare 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;
+    _getLengthCodec(): CramCodec<"int", unknown>;
+    _getDataCodec(): CramCodec<"byte", unknown>;
 }
-import CramCodec from "./_base";
+export {};

package/esm/cramFile/codecs/byteArrayLength.js

@@ -1,7 +1,7 @@
 import { tinyMemoize } from '../util';
 import CramCodec from './_base';
 export default class ByteArrayStopCodec extends CramCodec {
-    constructor(parameters = {}, dataType, instantiateCodec) {
+    constructor(parameters, dataType, instantiateCodec) {
         super(parameters, dataType);
         this.instantiateCodec = instantiateCodec;
         if (dataType !== 'byteArray') {

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

@@ -1 +1 @@
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package/esm/cramFile/codecs/byteArrayStop.d.ts

@@ -1,6 +1,10 @@
-export default class ByteArrayStopCodec extends CramCodec {
-    _decode: (contentBlock: any, cursor: any) => any;
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): any;
-    _decodeByteArray(contentBlock: any, cursor: any): any;
+/// <reference types="node" />
+import CramCodec, { Cursor, Cursors } from './_base';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+import { ByteArrayStopCramEncoding } from '../encoding';
+export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayStopCramEncoding['parameters']> {
+    constructor(parameters: ByteArrayStopCramEncoding['parameters'], dataType: 'byteArray');
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Buffer;
+    _decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor): Buffer;
 }
-import CramCodec from "./_base";

package/esm/cramFile/codecs/byteArrayStop.js

@@ -1,12 +1,10 @@
-import { CramBufferOverrunError, CramMalformedError } from '../../errors';
+import { CramMalformedError } from '../../errors';
 import CramCodec from './_base';
+import { CramBufferOverrunError } from './getBits';
 export default class ByteArrayStopCodec extends CramCodec {
-    constructor(parameters = {}, dataType) {
+    constructor(parameters, dataType) {
         super(parameters, dataType);
-        if (dataType === 'byteArray') {
-            this._decode = this._decodeByteArray;
-        }
-        else {
+        if (dataType !== 'byteArray') {
             throw new TypeError(`byteArrayStop codec does not support data type ${dataType}`);
         }
     }
@@ -17,7 +15,7 @@ export default class ByteArrayStopCodec extends CramCodec {
             throw new CramMalformedError(`no block found with content ID ${blockContentId}`);
         }
         const cursor = cursors.externalBlocks.getCursor(blockContentId);
-        return this._decode(contentBlock, cursor);
+        return this._decodeByteArray(contentBlock, cursor);
     }
     _decodeByteArray(contentBlock, cursor) {
         const dataBuffer = contentBlock.content;
@@ -30,10 +28,10 @@ export default class ByteArrayStopCodec extends CramCodec {
             if (stopPosition === dataBuffer.length) {
                 throw new CramBufferOverrunError(`byteArrayStop reading beyond length of data buffer?`);
             }
-            stopPosition += 1;
+            stopPosition = stopPosition + 1;
         }
         cursor.bytePosition = stopPosition + 1;
-        return dataBuffer.slice(startPosition, stopPosition);
+        return dataBuffer.subarray(startPosition, stopPosition);
     }
 }
 //# sourceMappingURL=byteArrayStop.js.map

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

@@ -1 +1 @@
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package/esm/cramFile/codecs/dataSeriesTypes.d.ts

@@ -0,0 +1,4 @@
+import { CramEncoding } from '../encoding';
+export declare type DataType = 'int' | 'byte' | 'long' | 'byteArray';
+export declare type DataSeriesEncodingKey = 'BF' | 'CF' | 'RI' | 'RL' | 'AP' | 'RG' | 'RN' | 'MF' | 'NS' | 'NP' | 'TS' | 'NF' | 'TL' | 'FN' | 'FC' | 'FP' | 'DL' | 'BB' | 'QQ' | 'BS' | 'IN' | 'RS' | 'PD' | 'HC' | 'SC' | 'MQ' | 'BA' | 'QS' | 'TC' | 'TN';
+export declare type DataSeriesEncodingMap = Record<DataSeriesEncodingKey, CramEncoding>;

package/esm/cramFile/codecs/dataSeriesTypes.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=dataSeriesTypes.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"dataSeriesTypes.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/dataSeriesTypes.ts"],"names":[],"mappings":""}

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

@@ -1,7 +1,11 @@
-export default class ExternalCodec extends CramCodec {
-    _decodeData: (contentBlock: any, cursor: any) => any;
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): any;
-    _decodeInt(contentBlock: any, cursor: any): any;
-    _decodeByte(contentBlock: any, cursor: any): any;
+import CramCodec, { Cursor, Cursors } from './_base';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+import { ExternalCramEncoding } from '../encoding';
+export default class ExternalCodec extends CramCodec<'int' | 'byte', ExternalCramEncoding['parameters']> {
+    private readonly _decodeData;
+    constructor(parameters: ExternalCramEncoding['parameters'], dataType: 'int' | 'byte');
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
+    _decodeInt(contentBlock: CramFileBlock, cursor: Cursor): number;
+    _decodeByte(contentBlock: CramFileBlock, cursor: Cursor): number;
 }
-import CramCodec from "./_base";

package/esm/cramFile/codecs/external.js

@@ -1,8 +1,9 @@
-import { CramUnimplementedError, CramMalformedError, CramBufferOverrunError, } from '../../errors';
+import { CramMalformedError, CramUnimplementedError } from '../../errors';
 import CramCodec from './_base';
 import { parseItf8 } from '../util';
+import { CramBufferOverrunError } from './getBits';
 export default class ExternalCodec extends CramCodec {
-    constructor(parameters = {}, dataType) {
+    constructor(parameters, dataType) {
         super(parameters, dataType);
         if (this.dataType === 'int') {
             this._decodeData = this._decodeInt;
@@ -25,7 +26,7 @@ export default class ExternalCodec extends CramCodec {
     }
     _decodeInt(contentBlock, cursor) {
         const [result, bytesRead] = parseItf8(contentBlock.content, cursor.bytePosition);
-        cursor.bytePosition += bytesRead;
+        cursor.bytePosition = cursor.bytePosition + bytesRead;
         return result;
     }
     _decodeByte(contentBlock, cursor) {

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

@@ -1 +1 @@
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+{"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;YAC3B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;SACnC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE;YACnC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;SACpC;aAAM;YACL,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;SACF;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;YACjB,MAAM,IAAI,kBAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;SACF;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;YACtD,MAAM,IAAI,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;SACF;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF"}

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

@@ -1,4 +1,8 @@
-export default class GammaCodec extends CramCodec {
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): number;
+import CramCodec, { Cursors } from './_base';
+import { GammaEncoding } from '../encoding';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+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;
 }
-import CramCodec from "./_base";

package/esm/cramFile/codecs/gamma.js

@@ -1,7 +1,8 @@
 import { CramUnimplementedError } from '../../errors';
 import CramCodec from './_base';
+import { getBits } from './getBits';
 export default class GammaCodec extends CramCodec {
-    constructor(parameters = {}, dataType) {
+    constructor(parameters, dataType) {
         super(parameters, dataType);
         if (this.dataType !== 'int') {
             throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`);
@@ -9,10 +10,10 @@ export default class GammaCodec extends CramCodec {
     }
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         let length = 1;
-        while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
-            length += 1;
+        while (getBits(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
+            length = length + 1;
         }
-        const readBits = this._getBits(coreDataBlock.content, cursors.coreBlock, length - 1);
+        const readBits = getBits(coreDataBlock.content, cursors.coreBlock, length - 1);
         const value = readBits | (1 << (length - 1));
         return value - this.parameters.offset;
     }

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

@@ -1 +1 @@
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+{"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;YAC3B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,8CAA8C,CAC/D,CAAA;SACF;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;YACjE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;SACpB;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

@@ -0,0 +1,7 @@
+/// <reference types="node" />
+export declare class CramBufferOverrunError extends Error {
+}
+export declare function getBits(data: Buffer, cursor: {
+    bytePosition: number;
+    bitPosition: number;
+}, numBits: number): number;

package/esm/cramFile/codecs/getBits.js

@@ -0,0 +1,21 @@
+export class CramBufferOverrunError extends Error {
+}
+export function getBits(data, cursor, numBits) {
+    let val = 0;
+    if (cursor.bytePosition + (7 - cursor.bitPosition + numBits) / 8 >
+        data.length) {
+        throw new CramBufferOverrunError('read error during decoding. the file seems to be truncated.');
+    }
+    for (let dlen = numBits; dlen; dlen--) {
+        // get the next `dlen` bits in the input, put them in val
+        val <<= 1;
+        val |= (data[cursor.bytePosition] >> cursor.bitPosition) & 1;
+        cursor.bitPosition -= 1;
+        if (cursor.bitPosition < 0) {
+            cursor.bytePosition += 1;
+        }
+        cursor.bitPosition &= 7;
+    }
+    return val;
+}
+//# sourceMappingURL=getBits.js.map

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

@@ -0,0 +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;QACA,MAAM,IAAI,sBAAsB,CAC9B,6DAA6D,CAC9D,CAAA;KACF;IACD,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;QACrC,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;YAC1B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;SACzB;QACD,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;KACxB;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}

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

@@ -1,17 +1,21 @@
-export default class HuffmanIntCodec extends CramCodec {
-    _decode(slice: any, coreDataBlock: any, coreCursor: any): any;
+import CramCodec, { Cursor, Cursors } from './_base';
+import { HuffmanEncoding } from '../encoding';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+export default class HuffmanIntCodec extends CramCodec<'byte' | 'int', HuffmanEncoding['parameters']> {
+    private codes;
+    private codeBook;
+    private sortedByValue;
+    private sortedCodes;
+    private sortedValuesByBitCode;
+    private sortedBitCodes;
+    private sortedBitLengthsByBitCode;
+    private bitCodeToValue;
+    constructor(parameters: HuffmanEncoding['parameters'], dataType: 'byte' | 'int');
     buildCodeBook(): void;
-    codeBook: {} | undefined;
     buildCodes(): void;
-    codes: {} | undefined;
     buildCaches(): void;
-    sortedCodes: any[] | undefined;
-    sortedByValue: any[] | undefined;
-    sortedValuesByBitCode: any[] | undefined;
-    sortedBitCodes: any[] | undefined;
-    sortedBitLengthsByBitCode: any[] | undefined;
-    bitCodeToValue: any[] | undefined;
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): any;
-    _decodeZeroLengthCode(): any;
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
+    _decodeZeroLengthCode(): number;
+    _decode(slice: CramSlice, coreDataBlock: CramFileBlock, coreCursor: Cursor): number;
 }
-import CramCodec from "./_base";

package/esm/cramFile/codecs/huffman.js

@@ -1,13 +1,22 @@
 import { CramMalformedError } from '../../errors';
 import CramCodec from './_base';
+import { getBits } from './getBits';
 function numberOfSetBits(ii) {
     let i = (ii - (ii >> 1)) & 0x55555555;
     i = (i & 0x33333333) + ((i >> 2) & 0x33333333);
     return (((i + (i >> 4)) & 0x0f0f0f0f) * 0x01010101) >> 24;
 }
 export default class HuffmanIntCodec extends CramCodec {
-    constructor(parameters = {}, dataType) {
+    constructor(parameters, dataType) {
         super(parameters, dataType);
+        this.codes = {};
+        this.codeBook = {};
+        this.sortedByValue = [];
+        this.sortedCodes = [];
+        this.sortedValuesByBitCode = [];
+        this.sortedBitCodes = [];
+        this.sortedBitLengthsByBitCode = [];
+        this.bitCodeToValue = [];
         if (!['byte', 'int'].includes(this.dataType)) {
             throw new TypeError(`${this.dataType} decoding not yet implemented by HUFFMAN_INT codec`);
         }
@@ -43,15 +52,19 @@ export default class HuffmanIntCodec extends CramCodec {
         let codeLength = 0;
         let codeValue = -1;
         Object.entries(this.codeBook).forEach(([bitLength, symbols]) => {
-            bitLength = parseInt(bitLength, 10);
+            const bitLengthInt = parseInt(bitLength, 10);
             symbols.forEach(symbol => {
-                const code = { bitLength, value: symbol };
-                codeValue += 1;
-                const delta = bitLength - codeLength; // new length?
-                codeValue <<= delta; // pad with 0's
+                const code = {
+                    bitLength: bitLengthInt,
+                    value: symbol,
+                    bitCode: 0,
+                };
+                codeValue = codeValue + 1;
+                const delta = bitLengthInt - codeLength; // new length?
+                codeValue = codeValue << delta; // pad with 0's
                 code.bitCode = codeValue; // calculated: huffman code
-                codeLength += delta; // adjust current code length
-                if (numberOfSetBits(codeValue) > bitLength) {
+                codeLength = codeLength + delta; // adjust current code length
+                if (numberOfSetBits(codeValue) > bitLengthInt) {
                     throw new CramMalformedError('Symbol out of range');
                 }
                 this.codes[symbol] = code;
@@ -88,7 +101,7 @@ export default class HuffmanIntCodec extends CramCodec {
         for (let i = 0; i < this.sortedCodes.length; i += 1) {
             const length = this.sortedCodes[i].bitLength;
             bits <<= length - prevLen;
-            bits |= this._getBits(input, coreCursor, length - prevLen);
+            bits |= getBits(input, coreCursor, length - prevLen);
             prevLen = length;
             {
                 const index = this.bitCodeToValue[bits];

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

@@ -1 +1 @@
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