@gmod/cram 2.0.1 → 2.0.3

package/esm/craiIndex.js

@@ -5,9 +5,6 @@ import { open } from './io';
 import { CramMalformedError } from './errors';
 const BAI_MAGIC = 21578050; // BAI\1
 function addRecordToIndex(index, record) {
-    if (record.some(el => el === undefined)) {
-        throw new CramMalformedError('invalid .crai index file');
-    }
     const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record;
     if (!index[seqId]) {
         index[seqId] = [];
@@ -32,7 +29,7 @@ export default class CraiIndex {
         this.filehandle = open(args.url, args.path, args.filehandle);
         this._parseCache = new AbortablePromiseCache({
             cache: new QuickLRU({ maxSize: 1 }),
-            fill: (data, signal) => this.parseIndex(),
+            fill: (_data, _signal) => this.parseIndex(),
         });
     }
     parseIndex() {
@@ -56,8 +53,7 @@ export default class CraiIndex {
             // because some .crai files can be pretty large.
             let currentRecord = [];
             let currentString = '';
-            for (let i = 0; i < uncompressedBuffer.length; i += 1) {
-                const charCode = uncompressedBuffer[i];
+            for (const charCode of uncompressedBuffer) {
                 if ((charCode >= 48 && charCode <= 57) /* 0-9 */ ||
                     (!currentString && charCode === 45) /* leading - */) {
                     currentString += String.fromCharCode(charCode);
@@ -131,9 +127,9 @@ export default class CraiIndex {
             return 0; // entry overlaps query
         };
         const bins = [];
-        for (let i = 0; i < seqEntries.length; i += 1) {
-            if (compare(seqEntries[i]) === 0) {
-                bins.push(seqEntries[i]);
+        for (const entry of seqEntries) {
+            if (compare(entry) === 0) {
+                bins.push(entry);
             }
         }
         return bins;

package/esm/craiIndex.js.map

@@ -1 +1 @@
-{"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,CAAC;QACxC,MAAM,IAAI,kBAAkB,CAAC,0BAA0B,CAAC,CAAA;IAC1D,CAAC;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,CAAC;QAClB,KAAK,CAAC,KAAK,CAAC,GAAG,EAAE,CAAA;IACnB,CAAC;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,CAAC;gBACtC,OAAO,KAAK,CAAC,IAAI,CAAC,CAAA;YACpB,CAAC;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,CAAC;gBACD,MAAM,IAAI,kBAAkB,CAC1B,+IAA+I,CAChJ,CAAA;YACH,CAAC;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,CAAC;gBACtD,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,CAAC;oBACD,aAAa,IAAI,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAA;gBAChD,CAAC;qBAAM,IAAI,QAAQ,KAAK,CAAC,CAAC,QAAQ,EAAE,CAAC;oBACnC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;oBACtD,aAAa,GAAG,EAAE,CAAA;gBACpB,CAAC;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC;oBACpC,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;gBACpB,CAAC;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,IAAI,QAAQ,KAAK,EAAE,CAAC,WAAW,EAAE,CAAC;oBACnE,oDAAoD;oBACpD,oCAAoC;oBACpC,MAAM,IAAI,kBAAkB,CAAC,0BAA0B,CAAC,CAAA;gBAC1D,CAAC;YACH,CAAC;YAED,8DAA8D;YAC9D,IAAI,aAAa,EAAE,CAAC;gBAClB,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;YACxD,CAAC;YACD,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC/B,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;YACxC,CAAC;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,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;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,CAAC;gBAC1B,OAAO,CAAC,CAAC,CAAA;YACX,CAAC,CAAC,0BAA0B;YAC5B,IAAI,QAAQ,IAAI,UAAU,EAAE,CAAC;gBAC3B,OAAO,CAAC,CAAA;YACV,CAAC,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,CAAC;YAC9C,IAAI,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;gBACjC,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA;YAC1B,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
+{"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,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,CAAC;QAClB,KAAK,CAAC,KAAK,CAAC,GAAG,EAAE,CAAA;IACnB,CAAC;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,KAAK,EAAE,OAAO,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,EAAE;SAC5C,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,CAAC;gBACtC,OAAO,KAAK,CAAC,IAAI,CAAC,CAAA;YACpB,CAAC;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,CAAC;gBACD,MAAM,IAAI,kBAAkB,CAC1B,+IAA+I,CAChJ,CAAA;YACH,CAAC;YACD,mDAAmD;YACnD,uDAAuD;YACvD,uEAAuE;YACvE,gDAAgD;YAChD,IAAI,aAAa,GAAa,EAAE,CAAA;YAChC,IAAI,aAAa,GAAG,EAAE,CAAA;YACtB,KAAK,MAAM,QAAQ,IAAI,kBAAkB,EAAE,CAAC;gBAC1C,IACE,CAAC,QAAQ,IAAI,EAAE,IAAI,QAAQ,IAAI,EAAE,CAAC,CAAC,SAAS;oBAC5C,CAAC,CAAC,aAAa,IAAI,QAAQ,KAAK,EAAE,CAAC,CAAC,eAAe,EACnD,CAAC;oBACD,aAAa,IAAI,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAA;gBAChD,CAAC;qBAAM,IAAI,QAAQ,KAAK,CAAC,CAAC,QAAQ,EAAE,CAAC;oBACnC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;oBACtD,aAAa,GAAG,EAAE,CAAA;gBACpB,CAAC;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC;oBACpC,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;gBACpB,CAAC;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,IAAI,QAAQ,KAAK,EAAE,CAAC,WAAW,EAAE,CAAC;oBACnE,oDAAoD;oBACpD,oCAAoC;oBACpC,MAAM,IAAI,kBAAkB,CAAC,0BAA0B,CAAC,CAAA;gBAC1D,CAAC;YACH,CAAC;YAED,8DAA8D;YAC9D,IAAI,aAAa,EAAE,CAAC;gBAClB,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;YACxD,CAAC;YACD,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC/B,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;YACxC,CAAC;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,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;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,CAAC;gBAC1B,OAAO,CAAC,CAAC,CAAA;YACX,CAAC,CAAC,0BAA0B;YAC5B,IAAI,QAAQ,IAAI,UAAU,EAAE,CAAC;gBAC3B,OAAO,CAAC,CAAA;YACV,CAAC,CAAC,wBAAwB;YAC1B,OAAO,CAAC,CAAA,CAAC,uBAAuB;QAClC,CAAC,CAAA;QACD,MAAM,IAAI,GAAG,EAAa,CAAA;QAC1B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;YAC/B,IAAI,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;gBACzB,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAClB,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}

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

@@ -1,24 +1,24 @@
 import CramSlice from '../slice';
 import { CramFileBlock } from '../file';
 import { DataType } from './dataSeriesTypes';
-export type DataTypeMapping = {
+export interface DataTypeMapping {
     byte: number;
     int: number;
     long: number;
     byteArray: Uint8Array;
-};
-export type Cursor = {
+}
+export interface Cursor {
     bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7;
     bytePosition: number;
-};
-export type Cursors = {
+}
+export interface 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;

package/esm/cramFile/codecs/external.js

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError, CramUnimplementedError } from '../../errors';
 import CramCodec from './_base';
 import { parseItf8 } from '../util';

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

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

@@ -5,7 +5,6 @@ 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;

package/esm/cramFile/codecs/huffman.js

@@ -1,3 +1,4 @@
+/* eslint-disable @typescript-eslint/unbound-method */
 import { CramMalformedError } from '../../errors';
 import CramCodec from './_base';
 import { getBits } from './getBits';
@@ -11,7 +12,6 @@ export default class HuffmanIntCodec extends CramCodec {
         super(parameters, dataType);
         this.codes = {};
         this.codeBook = {};
-        this.sortedByValue = [];
         this.sortedCodes = [];
         this.sortedValuesByBitCode = [];
         this.sortedBitCodes = [];
@@ -73,8 +73,6 @@ export default class HuffmanIntCodec extends CramCodec {
     }
     buildCaches() {
         this.sortedCodes = Object.values(this.codes).sort((a, b) => a.bitLength - b.bitLength || a.bitCode - b.bitCode);
-        // this.sortedValues = this.parameters.values.sort((a,b) => a-b)
-        this.sortedByValue = Object.values(this.codes).sort((a, b) => a.value - b.value);
         this.sortedValuesByBitCode = this.sortedCodes.map(c => c.value);
         this.sortedBitCodes = this.sortedCodes.map(c => c.bitCode);
         this.sortedBitLengthsByBitCode = this.sortedCodes.map(c => c.bitLength);

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

@@ -1 +1 @@
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package/esm/cramFile/container/compressionScheme.js

@@ -121,7 +121,7 @@ export default class CramContainerCompressionScheme {
     toJSON() {
         const data = {};
         Object.keys(this).forEach(k => {
-            if (/Cache$/.test(k)) {
+            if (k.endsWith('Cache')) {
                 return;
             }
             data[k] = this[k];

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,CAAC;QAC9B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IAC1B,CAAC;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,CAAC;YACjC,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC9C,IAAI,YAAY,EAAE,CAAC;gBACjB,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,gBAAgB,CAC5C,YAAY,EACZ,WAAW,CACZ,CAAA;YACH,CAAC;QACH,CAAC;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,CAAC;YACpB,MAAM,YAAY,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAA;YAC5D,IAAI,YAAY,EAAE,CAAC;gBACjB,MAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,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,OAA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package/esm/cramFile/encoding.d.ts

@@ -1,24 +1,24 @@
-export type NullEncoding = {
+export interface NullEncoding {
     codecId: 0;
     parametersBytes: number;
     parameters: Record<string, never>;
-};
-export type ExternalCramEncoding = {
+}
+export interface ExternalCramEncoding {
     codecId: 1;
     parametersBytes: number;
     parameters: {
         blockContentId: number;
     };
-};
-export type GolombEncoding = {
+}
+export interface GolombEncoding {
     codecId: 2;
     parametersBytes: number;
     parameters: {
         offset: number;
         M: number;
     };
-};
-export type HuffmanEncoding = {
+}
+export interface HuffmanEncoding {
     codecId: 3;
     parametersBytes: number;
     parameters: {
@@ -27,52 +27,52 @@ export type HuffmanEncoding = {
         numLengths: number;
         bitLengths: number[];
     };
-};
-export type ByteArrayLengthEncoding = {
+}
+export interface ByteArrayLengthEncoding {
     codecId: 4;
     parametersBytes: number;
     parameters: {
         lengthsEncoding: CramEncoding;
         valuesEncoding: CramEncoding;
     };
-};
-export type ByteArrayStopCramEncoding = {
+}
+export interface ByteArrayStopCramEncoding {
     codecId: 5;
     parametersBytes: number;
     parameters: {
         stopByte: number;
         blockContentId: number;
     };
-};
-export type BetaEncoding = {
+}
+export interface BetaEncoding {
     codecId: 6;
     parametersBytes: number;
     parameters: {
         offset: number;
         length: number;
     };
-};
-export type SubexpEncoding = {
+}
+export interface SubexpEncoding {
     codecId: 7;
     parametersBytes: number;
     parameters: {
         offset: number;
         K: number;
     };
-};
-export type GolombRiceEncoding = {
+}
+export interface GolombRiceEncoding {
     codecId: 8;
     parametersBytes: number;
     parameters: {
         offset: number;
         log2m: number;
     };
-};
-export type GammaEncoding = {
+}
+export interface GammaEncoding {
     codecId: 9;
     parametersBytes: number;
     parameters: {
         offset: number;
     };
-};
+}
 export type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;

package/esm/cramFile/file.d.ts

@@ -6,16 +6,16 @@ import { BlockHeader, CompressionMethod } from './sectionParsers';
 import CramContainer from './container';
 import CramRecord from './record';
 import { Filehandle } from './filehandle';
-export type CramFileSource = {
+export interface CramFileSource {
     filehandle?: Filehandle;
     url?: string;
     path?: string;
-};
+}
 export type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
 export type CramFileArgs = CramFileSource & {
-    checkSequenceMD5: boolean;
+    checkSequenceMD5?: boolean;
     cacheSize?: number;
-    seqFetch: SeqFetch;
+    seqFetch?: SeqFetch;
 };
 export type CramFileBlock = BlockHeader & {
     _endPosition: number;
@@ -27,9 +27,9 @@ export type CramFileBlock = BlockHeader & {
 export default class CramFile {
     private file;
     validateChecksums: boolean;
-    fetchReferenceSequenceCallback: SeqFetch;
+    fetchReferenceSequenceCallback?: SeqFetch;
     options: {
-        checkSequenceMD5: boolean;
+        checkSequenceMD5?: boolean;
         cacheSize: number;
     };
     featureCache: QuickLRU<string, Promise<CramRecord[]>>;
@@ -45,7 +45,7 @@ export default class CramFile {
         tag: string;
         data: {
             tag: string;
-            value: string | undefined;
+            value: string;
         }[];
     }[]>;
     getHeaderText(): Promise<string | undefined>;

package/esm/cramFile/filehandle.d.ts

@@ -1,2 +1 @@
-import { GenericFilehandle } from 'generic-filehandle';
-export { GenericFilehandle as Filehandle };
+export { GenericFilehandle as Filehandle } from 'generic-filehandle';

package/esm/cramFile/index.d.ts

@@ -1,3 +1,2 @@
-import CramFile from './file';
 export { default as CramRecord } from './record';
-export default CramFile;
+export { default } from './file';

package/esm/cramFile/index.js

@@ -1,4 +1,3 @@
-import CramFile from './file';
 export { default as CramRecord } from './record';
-export default CramFile;
+export { default } from './file';
 //# sourceMappingURL=index.js.map

package/esm/cramFile/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,QAAQ,CAAA;AAC7B,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,UAAU,CAAA;AAEhD,eAAe,QAAQ,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,UAAU,CAAA;AAEhD,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA"}

package/esm/cramFile/record.d.ts

@@ -1,25 +1,25 @@
 import CramContainerCompressionScheme from './container/compressionScheme';
 import decodeRecord from './slice/decodeRecord';
-export type RefRegion = {
+export interface RefRegion {
     start: number;
     end: number;
     seq: string;
-};
-export type ReadFeature = {
+}
+export interface ReadFeature {
     code: string;
     pos: number;
     refPos: number;
     data: any;
     ref?: string;
     sub?: string;
-};
-export type MateRecord = {
+}
+export interface MateRecord {
     readName?: string;
     sequenceId: number;
     alignmentStart: number;
     flags?: number;
     uniqueId?: number;
-};
+}
 export declare const BamFlags: readonly [readonly [1, "Paired"], readonly [2, "ProperlyPaired"], readonly [4, "SegmentUnmapped"], readonly [8, "MateUnmapped"], readonly [16, "ReverseComplemented"], readonly [32, "MateReverseComplemented"], readonly [64, "Read1"], readonly [128, "Read2"], readonly [256, "Secondary"], readonly [512, "FailedQc"], readonly [1024, "Duplicate"], readonly [2048, "Supplementary"]];
 export declare const CramFlags: readonly [readonly [1, "PreservingQualityScores"], readonly [2, "Detached"], readonly [4, "WithMateDownstream"], readonly [8, "DecodeSequenceAsStar"]];
 export declare const MateFlags: readonly [readonly [1, "OnNegativeStrand"], readonly [2, "Unmapped"]];

package/esm/cramFile/record.js

@@ -11,7 +11,7 @@ function decodeReadSequence(cramRecord, refRegion) {
     const regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
     if (!cramRecord.readFeatures) {
         return refRegion.seq
-            .substr(regionSeqOffset, cramRecord.lengthOnRef)
+            .slice(regionSeqOffset, regionSeqOffset + (cramRecord.lengthOnRef || 0))
             .toUpperCase();
     }
     let bases = '';
@@ -75,14 +75,17 @@ function decodeReadSequence(cramRecord, refRegion) {
             }
             else if (currentReadFeature < cramRecord.readFeatures.length) {
                 // put down a chunk of sequence up to the next read feature
-                const chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
+                const chunk = refRegion.seq.slice(regionPos, regionPos +
+                    cramRecord.readFeatures[currentReadFeature].pos -
+                    bases.length -
+                    1);
                 bases += chunk;
                 regionPos += chunk.length;
             }
         }
         else {
             // put down a chunk of reference up to the full read length
-            const chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
+            const chunk = refRegion.seq.slice(regionPos, regionPos + cramRecord.readLength - bases.length);
             bases += chunk;
             regionPos += chunk.length;
         }
@@ -362,7 +365,7 @@ export default class CramRecord {
     toJSON() {
         const data = {};
         Object.keys(this).forEach(k => {
-            if (k.charAt(0) === '_') {
+            if (k.startsWith('_')) {
                 return;
             }
             data[k] = this[k];

package/esm/cramFile/record.js.map

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package/esm/cramFile/sectionParsers.d.ts

@@ -9,7 +9,7 @@ declare const cramFileDefinition: {
     maxLength: number;
 };
 export type CramTagDictionary = string[][];
-export type CramPreservationMap = {
+export interface CramPreservationMap {
     MI: boolean;
     UI: boolean;
     PI: boolean;
@@ -18,8 +18,8 @@ export type CramPreservationMap = {
     RR: boolean;
     SM: [number, number, number, number, number];
     TD: CramTagDictionary;
-};
-export type MappedSliceHeader = {
+}
+export interface MappedSliceHeader {
     refSeqId: number;
     refSeqStart: number;
     refSeqSpan: number;
@@ -30,24 +30,24 @@ export type MappedSliceHeader = {
     contentIds: number[];
     refBaseBlockId: number;
     md5: TupleOf<number, 16>;
-};
-export type UnmappedSliceHeader = {
+}
+export interface UnmappedSliceHeader {
     numRecords: number;
     recordCounter: number;
     numBlocks: number;
     numContentIds: number;
     contentIds: number[];
     md5: TupleOf<number, 16>;
-};
+}
 export declare function isMappedSliceHeader(header: MappedSliceHeader | UnmappedSliceHeader): header is MappedSliceHeader;
 export type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
-export type BlockHeader = {
+export interface BlockHeader {
     compressionMethod: CompressionMethod;
     contentType: 'FILE_HEADER' | 'COMPRESSION_HEADER' | 'MAPPED_SLICE_HEADER' | 'UNMAPPED_SLICE_HEADER' | 'EXTERNAL_DATA' | 'CORE_DATA';
     contentId: number;
     compressedSize: number;
     uncompressedSize: number;
-};
+}
 export type CramCompressionHeader = ParsedItem<{
     preservation: CramPreservationMap;
     dataSeriesEncoding: DataSeriesEncodingMap;

package/esm/cramFile/sectionParsers.js

@@ -61,7 +61,7 @@ const cramTagDictionary = new Parser().itf8('size').buffer('ents', {
             const str = buffer.toString('utf8', stringStart, stringEnd);
             const tags = [];
             for (let i = 0; i < str.length; i += 3) {
-                tags.push(str.substr(i, 3));
+                tags.push(str.slice(i, i + 3));
             }
             return tags;
         }
@@ -117,8 +117,7 @@ const cramPreservationMap = new Parser()
 /* istanbul ignore next */
 function formatMap(data) {
     const map = {};
-    for (let i = 0; i < data.ents.length; i += 1) {
-        const { key, value } = data.ents[i];
+    for (const { key, value } of data.ents) {
         if (map[key]) {
             console.warn(`duplicate key ${key} in map`);
         }
@@ -201,7 +200,7 @@ const versionedParsers = {
         const maxLengthFunc = (numContentIds) => maxLength + numContentIds * 5;
         return { parser, maxLength: maxLengthFunc };
     },
-    cramEncoding(majorVersion) {
+    cramEncoding(_majorVersion) {
         const parser = new Parser()
             .namely('cramEncoding')
             .itf8('codecId')

package/esm/cramFile/sectionParsers.js.map

@@ -1 +1 @@
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