@gmod/cram 1.6.3 → 1.7.0

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

@@ -1,2 +1,4 @@
-export function getCodecClassWithId(id: any): any;
-export function instantiateCodec(encodingData: any, dataType: any): any;
+import CramCodec from './_base';
+import { CramEncoding } from '../encoding';
+import { DataType } from './dataSeriesTypes';
+export declare function instantiateCodec<TResult extends DataType = DataType>(encodingData: CramEncoding, dataType: DataType | 'ignore'): CramCodec<TResult>;

package/esm/cramFile/codecs/index.js

@@ -17,7 +17,7 @@ const codecClasses = {
     // 8: GolombRiceCodec,
     9: GammaCodec,
 };
-export function getCodecClassWithId(id) {
+function getCodecClassWithId(id) {
     return codecClasses[id];
 }
 export function instantiateCodec(encodingData, dataType) {

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

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAErD,OAAO,eAAe,MAAM,WAAW,CAAA;AACvC,OAAO,aAAa,MAAM,YAAY,CAAA;AACtC,OAAO,kBAAkB,MAAM,iBAAiB,CAAA;AAChD,OAAO,oBAAoB,MAAM,mBAAmB,CAAA;AACpD,OAAO,SAAS,MAAM,QAAQ,CAAA;AAC9B,OAAO,UAAU,MAAM,SAAS,CAAA;AAChC,OAAO,WAAW,MAAM,UAAU,CAAA;AAElC,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,MAAM,UAAU,mBAAmB,CAAC,EAAE;IACpC,OAAO,YAAY,CAAC,EAAE,CAAC,CAAA;AACzB,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,YAAY,EAAE,QAAQ;IACrD,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;QACf,MAAM,IAAI,sBAAsB,CAC9B,qCAAqC,YAAY,CAAC,OAAO,EAAE,CAC5D,CAAA;KACF;IAED,OAAO,IAAI,UAAU,CAAC,YAAY,CAAC,UAAU,EAAE,QAAQ,EAAE,gBAAgB,CAAC,CAAA;AAC5E,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAErD,OAAO,eAAe,MAAM,WAAW,CAAA;AACvC,OAAO,aAAa,MAAM,YAAY,CAAA;AACtC,OAAO,kBAAkB,MAAM,iBAAiB,CAAA;AAChD,OAAO,oBAAoB,MAAM,mBAAmB,CAAA;AACpD,OAAO,SAAS,MAAM,QAAQ,CAAA;AAC9B,OAAO,UAAU,MAAM,SAAS,CAAA;AAChC,OAAO,WAAW,MAAM,UAAU,CAAA;AAKlC,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;QACf,MAAM,IAAI,sBAAsB,CAC9B,qCAAqC,YAAY,CAAC,OAAO,EAAE,CAC5D,CAAA;KACF;IAED,OAAO,IAAI,UAAU,CAAC,YAAY,CAAC,UAAU,EAAE,QAAQ,EAAE,gBAAgB,CAAC,CAAA;AAC5E,CAAC"}

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

@@ -1,4 +1,8 @@
-export default class SubexpCodec 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 { SubexpEncoding } from '../encoding';
+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;
 }
-import CramCodec from "./_base";

package/esm/cramFile/codecs/subexp.js

@@ -1,7 +1,8 @@
 import { CramUnimplementedError } from '../../errors';
 import CramCodec from './_base';
+import { getBits } from './getBits';
 export default class SubexpCodec 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 SUBEXP codec`);
@@ -9,18 +10,19 @@ export default class SubexpCodec extends CramCodec {
     }
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         let numLeadingOnes = 0;
-        while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
-            numLeadingOnes += 1;
+        while (getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
+            numLeadingOnes = numLeadingOnes + 1;
         }
         let b;
         let n;
         if (numLeadingOnes === 0) {
             b = this.parameters.K;
-            n = this._getBits(coreDataBlock.content, cursors.coreBlock, b);
+            n = getBits(coreDataBlock.content, cursors.coreBlock, b);
         }
         else {
             b = numLeadingOnes + this.parameters.K - 1;
-            n = (1 << b) | this._getBits(coreDataBlock.content, cursors.coreBlock, b);
+            const bits = getBits(coreDataBlock.content, cursors.coreBlock, b);
+            n = (1 << b) | bits;
         }
         return n - this.parameters.offset;
     }

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

@@ -1 +1 @@
-{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAS,MAAM,SAAS,CAAA;AAE/B,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,SAAS;IAChD,YAAY,UAAU,GAAG,EAAE,EAAE,QAAQ;QACnC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;SACF;IACH,CAAC;IAED,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QACrD,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE;YACjE,cAAc,IAAI,CAAC,CAAA;SACpB;QAED,IAAI,CAAC,CAAA;QACL,IAAI,CAAC,CAAA;QACL,IAAI,cAAc,KAAK,CAAC,EAAE;YACxB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;SAC/D;aAAM;YACL,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;SAC1E;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF"}
+{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.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,WAAY,SAAQ,SAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;SACF;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;YAC3D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;SACpC;QAED,IAAI,CAAC,CAAA;QACL,IAAI,CAAC,CAAA;QACL,IAAI,cAAc,KAAK,CAAC,EAAE;YACxB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;SACzD;aAAM;YACL,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;SACpB;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF"}

package/esm/cramFile/constants.d.ts

@@ -1,36 +1,36 @@
+declare const Constants: {
+    CRAM_FLAG_PRESERVE_QUAL_SCORES: number;
+    CRAM_FLAG_DETACHED: number;
+    CRAM_FLAG_MATE_DOWNSTREAM: number;
+    CRAM_FLAG_NO_SEQ: number;
+    CRAM_FLAG_MASK: number;
+    CRAM_M_REVERSE: number;
+    CRAM_M_UNMAP: number;
+    BAM_FPAIRED: number;
+    BAM_FPROPER_PAIR: number;
+    BAM_FUNMAP: number;
+    BAM_FMUNMAP: number;
+    BAM_FREVERSE: number;
+    BAM_FMREVERSE: number;
+    BAM_FREAD1: number;
+    BAM_FREAD2: number;
+    BAM_FSECONDARY: number;
+    BAM_FQCFAIL: number;
+    BAM_FDUP: number;
+    BAM_FSUPPLEMENTARY: number;
+    BAM_CMATCH: number;
+    BAM_CINS: number;
+    BAM_CDEL: number;
+    BAM_CREF_SKIP: number;
+    BAM_CSOFT_CLIP: number;
+    BAM_CHARD_CLIP: number;
+    BAM_CPAD: number;
+    BAM_CEQUAL: number;
+    BAM_CDIFF: number;
+    BAM_CBACK: number;
+    BAM_CIGAR_STR: string;
+    BAM_CIGAR_SHIFT: number;
+    BAM_CIGAR_MASK: number;
+    BAM_CIGAR_TYPE: number;
+};
 export default Constants;
-declare namespace Constants {
-    const CRAM_FLAG_PRESERVE_QUAL_SCORES: number;
-    const CRAM_FLAG_DETACHED: number;
-    const CRAM_FLAG_MATE_DOWNSTREAM: number;
-    const CRAM_FLAG_NO_SEQ: number;
-    const CRAM_FLAG_MASK: number;
-    const CRAM_M_REVERSE: number;
-    const CRAM_M_UNMAP: number;
-    const BAM_FPAIRED: number;
-    const BAM_FPROPER_PAIR: number;
-    const BAM_FUNMAP: number;
-    const BAM_FMUNMAP: number;
-    const BAM_FREVERSE: number;
-    const BAM_FMREVERSE: number;
-    const BAM_FREAD1: number;
-    const BAM_FREAD2: number;
-    const BAM_FSECONDARY: number;
-    const BAM_FQCFAIL: number;
-    const BAM_FDUP: number;
-    const BAM_FSUPPLEMENTARY: number;
-    const BAM_CMATCH: number;
-    const BAM_CINS: number;
-    const BAM_CDEL: number;
-    const BAM_CREF_SKIP: number;
-    const BAM_CSOFT_CLIP: number;
-    const BAM_CHARD_CLIP: number;
-    const BAM_CPAD: number;
-    const BAM_CEQUAL: number;
-    const BAM_CDIFF: number;
-    const BAM_CBACK: number;
-    const BAM_CIGAR_STR: string;
-    const BAM_CIGAR_SHIFT: number;
-    const BAM_CIGAR_MASK: number;
-    const BAM_CIGAR_TYPE: number;
-}

package/esm/cramFile/constants.js.map

@@ -1 +1 @@
-{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/cramFile/constants.js"],"names":[],"mappings":"AAAA,MAAM,SAAS,GAAG;IAChB,8BAA8B,EAAE,CAAC,IAAI,CAAC;IACtC,kBAAkB,EAAE,CAAC,IAAI,CAAC;IAC1B,yBAAyB,EAAE,CAAC,IAAI,CAAC;IACjC,gBAAgB,EAAE,CAAC,IAAI,CAAC;IACxB,cAAc,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC;IAE5B,wBAAwB;IACxB,cAAc,EAAE,CAAC;IACjB,yBAAyB;IACzB,YAAY,EAAE,CAAC;IAEf,8EAA8E;IAC9E,WAAW,EAAE,CAAC;IACd,uCAAuC;IACvC,gBAAgB,EAAE,CAAC;IACnB,kEAAkE;IAClE,UAAU,EAAE,CAAC;IACb,wBAAwB;IACxB,WAAW,EAAE,CAAC;IACd,4CAA4C;IAC5C,YAAY,EAAE,EAAE;IAChB,4CAA4C;IAC5C,aAAa,EAAE,EAAE;IACjB,iBAAiB;IACjB,UAAU,EAAE,EAAE;IACd,iBAAiB;IACjB,UAAU,EAAE,GAAG;IACf,yBAAyB;IACzB,cAAc,EAAE,GAAG;IACnB,cAAc;IACd,WAAW,EAAE,GAAG;IAChB,4BAA4B;IAC5B,QAAQ,EAAE,IAAI;IACd,2BAA2B;IAC3B,kBAAkB,EAAE,IAAI;IAExB,UAAU,EAAE,CAAC;IACb,QAAQ,EAAE,CAAC;IACX,QAAQ,EAAE,CAAC;IACX,aAAa,EAAE,CAAC;IAChB,cAAc,EAAE,CAAC;IACjB,cAAc,EAAE,CAAC;IACjB,QAAQ,EAAE,CAAC;IACX,UAAU,EAAE,CAAC;IACb,SAAS,EAAE,CAAC;IACZ,SAAS,EAAE,CAAC;IAEZ,aAAa,EAAE,YAAY;IAC3B,eAAe,EAAE,CAAC;IAClB,cAAc,EAAE,GAAG;IACnB,cAAc,EAAE,OAAO;CACxB,CAAA;AAED,eAAe,SAAS,CAAA"}
+{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/cramFile/constants.ts"],"names":[],"mappings":"AAAA,MAAM,SAAS,GAAG;IAChB,8BAA8B,EAAE,CAAC,IAAI,CAAC;IACtC,kBAAkB,EAAE,CAAC,IAAI,CAAC;IAC1B,yBAAyB,EAAE,CAAC,IAAI,CAAC;IACjC,gBAAgB,EAAE,CAAC,IAAI,CAAC;IACxB,cAAc,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC;IAE5B,wBAAwB;IACxB,cAAc,EAAE,CAAC;IACjB,yBAAyB;IACzB,YAAY,EAAE,CAAC;IAEf,8EAA8E;IAC9E,WAAW,EAAE,CAAC;IACd,uCAAuC;IACvC,gBAAgB,EAAE,CAAC;IACnB,kEAAkE;IAClE,UAAU,EAAE,CAAC;IACb,wBAAwB;IACxB,WAAW,EAAE,CAAC;IACd,4CAA4C;IAC5C,YAAY,EAAE,EAAE;IAChB,4CAA4C;IAC5C,aAAa,EAAE,EAAE;IACjB,iBAAiB;IACjB,UAAU,EAAE,EAAE;IACd,iBAAiB;IACjB,UAAU,EAAE,GAAG;IACf,yBAAyB;IACzB,cAAc,EAAE,GAAG;IACnB,cAAc;IACd,WAAW,EAAE,GAAG;IAChB,4BAA4B;IAC5B,QAAQ,EAAE,IAAI;IACd,2BAA2B;IAC3B,kBAAkB,EAAE,IAAI;IAExB,UAAU,EAAE,CAAC;IACb,QAAQ,EAAE,CAAC;IACX,QAAQ,EAAE,CAAC;IACX,aAAa,EAAE,CAAC;IAChB,cAAc,EAAE,CAAC;IACjB,cAAc,EAAE,CAAC;IACjB,QAAQ,EAAE,CAAC;IACX,UAAU,EAAE,CAAC;IACb,SAAS,EAAE,CAAC;IACZ,SAAS,EAAE,CAAC;IAEZ,aAAa,EAAE,YAAY;IAC3B,eAAe,EAAE,CAAC;IAClB,cAAc,EAAE,GAAG;IACnB,cAAc,EAAE,OAAO;CACxB,CAAA;AAED,eAAe,SAAS,CAAA"}

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

@@ -1,23 +1,69 @@
+import CramCodec from '../codecs/_base';
+import { CramCompressionHeader } from '../sectionParsers';
+import { CramEncoding } from '../encoding';
+import { DataSeriesEncodingKey, DataSeriesEncodingMap } from '../codecs/dataSeriesTypes';
+declare const dataSeriesTypes: {
+    readonly BF: "int";
+    readonly CF: "int";
+    readonly RI: "int";
+    readonly RL: "int";
+    readonly AP: "int";
+    readonly RG: "int";
+    readonly MF: "int";
+    readonly NS: "int";
+    readonly NP: "int";
+    readonly TS: "int";
+    readonly NF: "int";
+    readonly TC: "byte";
+    readonly TN: "int";
+    readonly FN: "int";
+    readonly FC: "byte";
+    readonly FP: "int";
+    readonly BS: "byte";
+    readonly IN: "byteArray";
+    readonly SC: "byteArray";
+    readonly DL: "int";
+    readonly BA: "byte";
+    readonly BB: "byteArray";
+    readonly RS: "int";
+    readonly PD: "int";
+    readonly HC: "int";
+    readonly MQ: "int";
+    readonly RN: "byteArray";
+    readonly QS: "byte";
+    readonly QQ: "byteArray";
+    readonly TL: "int";
+};
+export declare type DataSeriesTypes = typeof dataSeriesTypes;
+declare type DataSeriesCache = {
+    [K in DataSeriesEncodingKey]?: CramCodec<DataSeriesTypes[K]>;
+};
 export default class CramContainerCompressionScheme {
-    constructor(content: any);
-    readNamesIncluded: any;
-    APdelta: any;
+    readNamesIncluded: boolean;
+    APdelta: boolean;
     referenceRequired: boolean;
-    tagIdsDictionary: any;
-    substitutionMatrix: any[];
-    dataSeriesCodecCache: Map<any, any>;
-    tagCodecCache: {};
+    tagIdsDictionary: Record<number, string[]>;
+    substitutionMatrix: string[][];
+    dataSeriesCodecCache: DataSeriesCache;
+    tagCodecCache: Record<string, CramCodec>;
+    tagEncoding: Record<string, CramEncoding>;
+    dataSeriesEncoding: DataSeriesEncodingMap;
+    private preservation;
+    private _endPosition;
+    private _size;
+    constructor(content: CramCompressionHeader);
     /**
      * @param {string} tagName three-character tag name
      * @private
      */
-    private getCodecForTag;
+    getCodecForTag(tagName: string): CramCodec;
     /**
      *
      * @param {number} tagListId ID of the tag list to fetch from the tag dictionary
      * @private
      */
-    private getTagNames;
-    getCodecForDataSeries(dataSeriesName: any): any;
-    toJSON(): {};
+    getTagNames(tagListId: number): string[];
+    getCodecForDataSeries<TDataSeries extends DataSeriesEncodingKey>(dataSeriesName: TDataSeries): CramCodec<DataSeriesTypes[TDataSeries]> | undefined;
+    toJSON(): any;
 }
+export {};

package/esm/cramFile/container/compressionScheme.js

@@ -1,5 +1,5 @@
-import { CramMalformedError } from '../../errors';
 import { instantiateCodec } from '../codecs';
+import { CramMalformedError } from '../../errors';
 // the hardcoded data type to be decoded for each core
 // data field
 const dataSeriesTypes = {
@@ -33,8 +33,8 @@ const dataSeriesTypes = {
     QS: 'byte',
     QQ: 'byteArray',
     TL: 'int',
-    TM: 'ignore',
-    TV: 'ignore',
+    // TM: 'ignore',
+    // TV: 'ignore',
 };
 function parseSubstitutionMatrix(byteArray) {
     const matrix = new Array(5);
@@ -65,15 +65,21 @@ function parseSubstitutionMatrix(byteArray) {
 }
 export default class CramContainerCompressionScheme {
     constructor(content) {
-        Object.assign(this, content);
+        this.dataSeriesCodecCache = {};
+        this.tagCodecCache = {};
+        this.tagEncoding = {};
+        // Object.assign(this, content)
         // interpret some of the preservation map tags for convenient use
         this.readNamesIncluded = content.preservation.RN;
         this.APdelta = content.preservation.AP;
         this.referenceRequired = !!content.preservation.RR;
         this.tagIdsDictionary = content.preservation.TD;
         this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
-        this.dataSeriesCodecCache = new Map();
-        this.tagCodecCache = {};
+        this.dataSeriesEncoding = content.dataSeriesEncoding;
+        this.tagEncoding = content.tagEncoding;
+        this.preservation = content.preservation;
+        this._size = content._size;
+        this._endPosition = content._endPosition;
     }
     /**
      * @param {string} tagName three-character tag name
@@ -97,7 +103,7 @@ export default class CramContainerCompressionScheme {
         return this.tagIdsDictionary[tagListId];
     }
     getCodecForDataSeries(dataSeriesName) {
-        let r = this.dataSeriesCodecCache.get(dataSeriesName);
+        let r = this.dataSeriesCodecCache[dataSeriesName];
         if (r === undefined) {
             const encodingData = this.dataSeriesEncoding[dataSeriesName];
             if (encodingData) {
@@ -106,7 +112,8 @@ export default class CramContainerCompressionScheme {
                     throw new CramMalformedError(`data series name ${dataSeriesName} not defined in file compression header`);
                 }
                 r = instantiateCodec(encodingData, dataType);
-                this.dataSeriesCodecCache.set(dataSeriesName, r);
+                // didn't find a way to make TS understand this
+                this.dataSeriesCodecCache[dataSeriesName] = r;
             }
         }
         return r;

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,gBAAgB,EAAE,MAAM,WAAW,CAAA;AAI5C,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAMjD,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;QAC7B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;KACzB;IAED,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,OAAO,MAAM,CAAA;AACf,CAAC;AAMD,MAAM,CAAC,OAAO,OAAO,8BAA8B;IAcjD,YAAY,OAA8B;QARnC,yBAAoB,GAAoB,EAAE,CAAA;QAC1C,kBAAa,GAA8B,EAAE,CAAA;QAC7C,gBAAW,GAAiC,EAAE,CAAA;QAOnD,+BAA+B;QAC/B,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;QACtC,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,YAAY,CAAA;QACxC,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,CAAA;QAC1B,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,YAAY,CAAA;IAC1C,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,OAAe;QAC5B,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE;YAChC,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC9C,IAAI,YAAY,EAAE;gBAChB,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,gBAAgB,CAC5C,YAAY,EACZ,WAAW,CACZ,CAAA;aACF;SACF;QACD,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IACpC,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;YACnB,MAAM,YAAY,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAA;YAC5D,IAAI,YAAY,EAAE;gBAChB,MAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,IAAI,CAAC,QAAQ,EAAE;oBACb,MAAM,IAAI,kBAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;iBACF;gBACD,CAAC,GAAG,gBAAgB,CAAC,YAAY,EAAE,QAAQ,CAAC,CAAA;gBAC5C,+CAA+C;gBAC/C,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,GAAG,CAAmB,CAAA;aAChE;SACF;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,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE;gBACpB,OAAM;aACP;YACD,IAAI,CAAC,CAAC,CAAC,GAAI,I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package/esm/cramFile/container/index.d.ts

@@ -1,13 +1,27 @@
+/// <reference types="node" />
+import CramSlice from '../slice';
+import CramContainerCompressionScheme from './compressionScheme';
+import CramFile from '../file';
 export default class CramContainer {
-    constructor(cramFile: any, position: any);
-    file: any;
-    filePosition: any;
+    file: CramFile;
+    filePosition: number;
+    constructor(file: CramFile, filePosition: number);
     getHeader(): Promise<any>;
-    getCompressionHeaderBlock(): Promise<any>;
-    getFirstBlock(): Promise<any>;
+    getCompressionHeaderBlock(): Promise<{
+        parsedContent: import("../util").ParsedItem<import("../sectionParsers").CramCompressionHeader>;
+        compressionMethod: import("../sectionParsers").CompressionMethod;
+        contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
+        contentId: number;
+        compressedSize: number;
+        uncompressedSize: number;
+        _endPosition: number;
+        contentPosition: number;
+        _size: number;
+        content: Buffer;
+        crc32?: number | undefined;
+    } | null | undefined>;
+    getFirstBlock(): Promise<import("../file").CramFileBlock | undefined>;
     getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
-    getSlice(slicePosition: any, sliceSize: any): CramSlice;
-    _readContainerHeader(position: any): Promise<any>;
+    getSlice(slicePosition: number, sliceSize: number): CramSlice;
+    _readContainerHeader(position: number): Promise<any>;
 }
-import CramContainerCompressionScheme from "./compressionScheme";
-import CramSlice from "../slice";

package/esm/cramFile/container/index.js

@@ -3,12 +3,9 @@ import { itf8Size, parseItem, tinyMemoize } from '../util';
 import CramSlice from '../slice';
 import CramContainerCompressionScheme from './compressionScheme';
 export default class CramContainer {
-    constructor(cramFile, position) {
-        // cram file this container comes from
-        this.file = cramFile;
-        // position of this container in the file
-        this.filePosition = position;
-        // console.log(`container: ${this.filePosition}`)
+    constructor(file, filePosition) {
+        this.file = file;
+        this.filePosition = filePosition;
     }
     // memoize
     getHeader() {
@@ -23,12 +20,17 @@ export default class CramContainer {
         }
         const sectionParsers = await this.file.getSectionParsers();
         const block = await this.getFirstBlock();
+        if (block === undefined) {
+            return undefined;
+        }
         if (block.contentType !== 'COMPRESSION_HEADER') {
             throw new CramMalformedError(`invalid content type ${block.contentType} in what is supposed to be the compression header block`);
         }
         const content = parseItem(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
-        block.content = content;
-        return block;
+        return {
+            ...block,
+            parsedContent: content,
+        };
     }
     async getFirstBlock() {
         const containerHeader = await this.getHeader();
@@ -41,7 +43,7 @@ export default class CramContainer {
         if (!header) {
             return undefined;
         }
-        return new CramContainerCompressionScheme(header.content);
+        return new CramContainerCompressionScheme(header.parsedContent);
     }
     getSlice(slicePosition, sliceSize) {
         // note: slicePosition is relative to the end of the container header

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

@@ -1 +1 @@
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package/esm/cramFile/encoding.d.ts

@@ -0,0 +1,78 @@
+export declare type NullEncoding = {
+    codecId: 0;
+    parametersBytes: number;
+    parameters: Record<string, never>;
+};
+export declare type ExternalCramEncoding = {
+    codecId: 1;
+    parametersBytes: number;
+    parameters: {
+        blockContentId: number;
+    };
+};
+export declare type GolombEncoding = {
+    codecId: 2;
+    parametersBytes: number;
+    parameters: {
+        offset: number;
+        M: number;
+    };
+};
+export declare type HuffmanEncoding = {
+    codecId: 3;
+    parametersBytes: number;
+    parameters: {
+        numCodes: number;
+        symbols: number[];
+        numLengths: number;
+        bitLengths: number[];
+    };
+};
+export declare type ByteArrayLengthEncoding = {
+    codecId: 4;
+    parametersBytes: number;
+    parameters: {
+        lengthsEncoding: CramEncoding;
+        valuesEncoding: CramEncoding;
+    };
+};
+export declare type ByteArrayStopCramEncoding = {
+    codecId: 5;
+    parametersBytes: number;
+    parameters: {
+        stopByte: number;
+        blockContentId: number;
+    };
+};
+export declare type BetaEncoding = {
+    codecId: 6;
+    parametersBytes: number;
+    parameters: {
+        offset: number;
+        length: number;
+    };
+};
+export declare type SubexpEncoding = {
+    codecId: 7;
+    parametersBytes: number;
+    parameters: {
+        offset: number;
+        K: number;
+    };
+};
+export declare type GolombRiceEncoding = {
+    codecId: 8;
+    parametersBytes: number;
+    parameters: {
+        offset: number;
+        log2m: number;
+    };
+};
+export declare type GammaEncoding = {
+    codecId: 9;
+    parametersBytes: number;
+    parameters: {
+        offset: number;
+    };
+};
+export declare type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;

package/esm/cramFile/encoding.js

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

package/esm/cramFile/encoding.js.map

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