@gmod/cram 4.0.10 → 5.0.0

package/esm/indexedCramFile.js

@@ -1,5 +1,5 @@
-import CramFile from './cramFile';
-import { CramUnimplementedError } from './errors';
+import CramFile from "./cramFile/index.js";
+import { CramUnimplementedError } from "./errors.js";
 export default class IndexedCramFile {
     /**
      *

package/esm/indexedCramFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":"AAEA,OAAO,QAAQ,MAAM,qBAAqB,CAAA;AAE1C,OAAO,EAAE,sBAAsB,EAAE,MAAM,aAAa,CAAA;AAmBpD,MAAM,CAAC,OAAO,OAAO,eAAe;IAIlC;;;;;;;;;;;;;;;OAeG;IACH,YACE,IAUC;QAED,IAAI,CAAC,IAAI;YACP,IAAI,CAAC,IAAI;gBACT,IAAI,QAAQ,CAAC;oBACX,GAAG,EAAE,IAAI,CAAC,OAAO;oBACjB,IAAI,EAAE,IAAI,CAAC,QAAQ;oBACnB,UAAU,EAAE,IAAI,CAAC,cAAc;oBAC/B,QAAQ,EAAE,IAAI,CAAC,QAAQ;oBACvB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;oBACvC,SAAS,EAAE,IAAI,CAAC,SAAS;iBAC1B,CAAC,CAAA;QAEJ,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,YAAY,QAAQ,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAA;QACnD,CAAC;QAED,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IACzB,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,KAAa,EACb,GAAW,EACX,OAII,EAAE;QAEN,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,IAAI,KAAK,CAAA;QAC5C,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,KAAK,CAAA;QAChD,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,MAAM,CAAA;QAEjD,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;YAC5B,wDAAwD;YACxD,MAAM,IAAI,sBAAsB,CAC9B,yCAAyC,CAC1C,CAAA;QACH,CAAC;QACD,MAAM,KAAK,GAAG,GAAG,CAAA;QACjB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;QAErE,kDAAkD;QAClD,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CACjB,IAAI,CAAC,iBAAiB,CACpB,KAAK,EACL,OAAO,CAAC,EAAE,CACR,OAAO,CAAC,UAAU,KAAK,GAAG;YAC1B,OAAO,CAAC,cAAc,IAAI,GAAG;YAC7B,OAAO,CAAC,WAAW,KAAK,SAAS;YACjC,OAAO,CAAC,cAAc,GAAG,OAAO,CAAC,WAAW,GAAG,CAAC,IAAI,KAAK,CAC5D,CACF,CACF,CAAA;QAED,IAAI,GAAG,GAAiB,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,YAAY,CAAC,CAAA;QAC/D,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACrB,MAAM,SAAS,GAA2B,EAAE,CAAA;YAC5C,MAAM,OAAO,GAA2B,EAAE,CAAA;YAC1C,KAAK,MAAM,IAAI,IAAI,GAAG,EAAE,CAAC;gBACvB,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,CAAA;gBAC1B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,MAAM,EAAE,GAAG,IAAI,CAAC,QAAQ,CAAA;gBACxB,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;oBACrB,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACrB,CAAC;gBACD,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,OAAO,CAAC,EAAE,CAAC,GAAG,CAAC,CAAA;YACjB,CAAC;YACD,MAAM,YAAY,GAA4B,EAAE,CAAA;YAChD,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE;gBAC3C,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;oBACZ,YAAY,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;gBACxB,CAAC;YACH,CAAC,CAAC,CAAA;YACF,MAAM,YAAY,GAAG,EAAE,CAAA;YACvB,KAAK,MAAM,UAAU,IAAI,GAAG,EAAE,CAAC;gBAC7B,MAAM,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;gBAChC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,IACE,YAAY,CAAC,IAAI,CAAC;oBAClB,UAAU,CAAC,IAAI;oBACf,CAAC,UAAU,CAAC,IAAI,CAAC,UAAU,KAAK,KAAK,IAAI,IAAI,CAAC,aAAa,CAAC;oBAC5D,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,cAAc,GAAG,UAAU,CAAC,IAAI,CAAC,cAAc,CAAC;wBAClE,IAAI,CAAC,aAAa,EACpB,CAAC;oBACD,MAAM,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAC9C,UAAU,CAAC,IAAI,CAAC,UAAU,EAC1B,UAAU,CAAC,IAAI,CAAC,cAAc,EAC9B,UAAU,CAAC,IAAI,CAAC,cAAc,GAAG,CAAC,CACnC,CAAA;oBACD,YAAY,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;gBAC/B,CAAC;YACH,CAAC;YACD,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;YAClD,IAAI,UAAU,GAAG,EAAa,CAAA;YAC9B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;gBAC/B,UAAU,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,CAAA;YAC3B,CAAC;YACD,wBAAwB;YACxB,UAAU,GAAG,UAAU;iBACpB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;iBACxD,MAAM,CACL,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CACjB,CAAC,GAAG,IAAI,IAAI,CAAC,QAAQ,EAAE,KAAK,GAAG,CAAC,GAAG,GAAG,CAAC,CAAE,CAAC,QAAQ,EAAE,CACvD,CAAA;YAEH,MAAM,kBAAkB,GAAG,EAAE,CAAA;YAC7B,MAAM,gBAAgB,GAA4B,EAAE,CAAA;YACpD,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;gBAC3B,IAAI,aAAa,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAA;gBAC5D,IAAI,CAAC,aAAa,EAAE,CAAC;oBACnB,aAAa,GAAG,IAAI,CAAC,iBAAiB,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,CAAA;oBACrD,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE,aAAa,CAAC,CAAA;gBACzD,CAAC;gBACD,kBAAkB,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;gBACtC,MAAM,WAAW,GAAG,aAAa,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE;oBAC7C,MAAM,QAAQ,GAAG,EAAE,CAAA;oBACnB,KAAK,MAAM,OAAO,IAAI,KAAK,EAAE,CAAC;wBAC5B,IAAI,OAAO,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;4BACnC,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;wBACvC,CAAC;wBACD,IAAI,YAAY,CAAC,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;4BACjE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;wBACxB,CAAC;oBACH,CAAC;oBACD,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBACF,gBAAgB,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;YACD,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAA;YACxD,IAAI,YAAY,CAAC,MAAM,EAAE,CAAC;gBACxB,MAAM,QAAQ,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CACvD,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CACvB,CAAA;gBACD,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,iBAAiB,CACf,EACE,cAAc,EACd,UAAU,EACV,UAAU,GACyD,EACrE,cAA0C;QAE1C,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,sBAAsB,CAAC,cAAc,CAAC,CAAA;QAClE,MAAM,KAAK,GAAG,SAAS,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,CAAC,CAAA;QACxD,OAAO,KAAK,CAAC,UAAU,CAAC,cAAc,CAAC,CAAA;I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package/esm/{io/index.js → io.js}

@@ -13,4 +13,4 @@ function open(maybeUrl, maybePath, maybeFilehandle) {
 }
 export { open };
 export { LocalFile, RemoteFile } from 'generic-filehandle2';
-//# sourceMappingURL=index.js.map
+//# sourceMappingURL=io.js.map

package/esm/io.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"io.js","sourceRoot":"","sources":["../src/io.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA;AAI3D,SAAS,IAAI,CACX,QAAiB,EACjB,SAAkB,EAClB,eAAmC;IAEnC,IAAI,eAAe,EAAE,CAAC;QACpB,OAAO,eAAe,CAAA;IACxB,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,IAAI,UAAU,CAAC,QAAQ,CAAC,CAAA;IACjC,CAAC;IACD,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,IAAI,SAAS,CAAC,SAAS,CAAC,CAAA;IACjC,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAED,OAAO,EAAE,IAAI,EAAE,CAAA;AAEf,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA"}

package/esm/rans/d04.js

@@ -1,7 +1,7 @@
 // @ts-nocheck
-import { CramMalformedError } from '../errors';
-import { TF_SHIFT } from './constants';
-import Decoding from './decoding';
+import { CramMalformedError } from "../errors.js";
+import { TF_SHIFT } from "./constants.js";
+import Decoding from "./decoding.js";
 export default function uncompress(
 /* ByteBuffer */ input, 
 /* Decoding.AriDecoder */ D, 

package/esm/rans/d04.js.map

@@ -1 +1 @@
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package/esm/rans/d14.js

@@ -1,6 +1,6 @@
 // @ts-nocheck
-import { TF_SHIFT } from './constants';
-import Decoding from './decoding';
+import { TF_SHIFT } from "./constants.js";
+import Decoding from "./decoding.js";
 export default function uncompress(
 /* ByteBuffer */ input, 
 /* ByteBuffer */ output, 

package/esm/rans/d14.js.map

@@ -1 +1 @@
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package/esm/rans/decoding.js

@@ -1,6 +1,6 @@
 // @ts-nocheck
-import { CramMalformedError } from '../errors';
-import { RANS_BYTE_L } from './constants';
+import { CramMalformedError } from "../errors.js";
+import { RANS_BYTE_L } from "./constants.js";
 class FC {
     // int F, C;
     constructor() {

package/esm/rans/decoding.js.map

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package/esm/rans/frequencies.js

@@ -1,7 +1,7 @@
 // @ts-nocheck
-import { CramMalformedError } from '../errors';
-import { TOTFREQ } from './constants';
-import Decoding from './decoding';
+import { CramMalformedError } from "../errors.js";
+import { TOTFREQ } from "./constants.js";
+import Decoding from "./decoding.js";
 function assert(result) {
     if (!result) {
         throw new CramMalformedError('assertion failed');

package/esm/rans/frequencies.js.map

@@ -1 +1 @@
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package/esm/rans/index.js

@@ -1,9 +1,9 @@
 // @ts-nocheck
-import { CramMalformedError } from '../errors';
-import D04 from './d04';
-import D14 from './d14';
-import Decoding from './decoding';
-import { readStatsO0, readStatsO1 } from './frequencies';
+import { CramMalformedError } from "../errors.js";
+import D04 from "./d04.js";
+import D14 from "./d14.js";
+import Decoding from "./decoding.js";
+import { readStatsO0, readStatsO1 } from "./frequencies.js";
 // const /* int */ ORDER_BYTE_LENGTH = 1
 // const /* int */ COMPRESSED_BYTE_LENGTH = 4
 const /* int */ RAW_BYTE_LENGTH = 4;

package/esm/rans/index.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,11 +1,19 @@
 {
   "name": "@gmod/cram",
-  "version": "4.0.10",
+  "version": "5.0.0",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
-  "main": "dist/index.js",
-  "module": "esm/index.js",
+  "type": "module",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    "import": {
+      "import": "./esm/index.js"
+    },
+    "require": {
+      "require": "./dist/index.js"
+    }
+  },
   "author": {
     "name": "Robert Buels",
     "email": "rbuels@gmail.com",
@@ -41,7 +49,7 @@
   ],
   "dependencies": {
     "crc": "^4.3.2",
-    "generic-filehandle2": "^1.0.0",
+    "generic-filehandle2": "^2.0.1",
     "md5": "^2.2.1",
     "pako": "^1.0.4",
     "quick-lru": "^4.0.1",
@@ -51,21 +59,19 @@
     "@gmod/indexedfasta": "^3.0.0",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
-    "@typescript-eslint/eslint-plugin": "^8.0.0",
-    "@typescript-eslint/parser": "^8.0.0",
     "@vitest/coverage-v8": "^3.0.1",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
     "eslint": "^9.9.0",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^56.0.1",
+    "eslint-plugin-unicorn": "^59.0.0",
     "mock-fs": "^5.2.0",
     "prettier": "^3.2.5",
     "rimraf": "^6.0.1",
     "typescript": "^5.7.0",
-    "typescript-eslint": "^8.0.1",
+    "typescript-eslint": "^8.31.1",
     "vitest": "^3.0.1",
-    "webpack": "^5.90.3",
+    "webpack": "^5.99.7",
     "webpack-cli": "^6.0.1"
   },
   "publishConfig": {

package/src/craiIndex.ts

@@ -1,7 +1,7 @@
-import { CramFileSource } from './cramFile/file'
-import { CramMalformedError } from './errors'
-import { open } from './io'
-import { unzip } from './unzip'
+import { CramFileSource } from './cramFile/file.ts'
+import { CramMalformedError } from './errors.ts'
+import { open } from './io.ts'
+import { unzip } from './unzip.ts'
 
 import type { GenericFilehandle } from 'generic-filehandle2'
 

package/src/cramFile/codecs/_base.ts

@@ -1,6 +1,6 @@
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
-import { DataType } from './dataSeriesTypes'
+import { CramFileBlock } from '../file.ts'
+import { DataType } from './dataSeriesTypes.ts'
+import CramSlice from '../slice/index.ts'
 
 export interface DataTypeMapping {
   byte: number

package/src/cramFile/codecs/beta.ts

@@ -1,9 +1,9 @@
-import CramCodec, { Cursors } from './_base'
-import { getBits } from './getBits'
-import { CramUnimplementedError } from '../../errors'
-import { BetaEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
+import CramCodec, { Cursors } from './_base.ts'
+import { getBits } from './getBits.ts'
+import { CramUnimplementedError } from '../../errors.ts'
+import { BetaEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import CramSlice from '../slice/index.ts'
 
 export default class BetaCodec extends CramCodec<
   'int',
@@ -19,9 +19,9 @@ export default class BetaCodec extends CramCodec<
   }
 
   decode(
-    slice: CramSlice,
+    _slice: CramSlice,
     coreDataBlock: CramFileBlock,
-    blocksByContentId: Record<number, CramFileBlock>,
+    _blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {
     const fromBits = getBits(

package/src/cramFile/codecs/byteArrayLength.ts

@@ -1,9 +1,9 @@
-import CramCodec, { Cursors } from './_base'
-import { ByteArrayLengthEncoding, CramEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
-import { DataType } from './dataSeriesTypes'
-import { tinyMemoize } from '../util'
+import CramCodec, { Cursors } from './_base.ts'
+import { ByteArrayLengthEncoding, CramEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import { DataType } from './dataSeriesTypes.ts'
+import CramSlice from '../slice/index.ts'
+import { tinyMemoize } from '../util.ts'
 
 type CramCodecFactory = <TData extends DataType = DataType>(
   encodingData: CramEncoding,

package/src/cramFile/codecs/byteArrayStop.ts

@@ -1,17 +1,17 @@
-import CramCodec, { Cursor, Cursors } from './_base'
-import { CramMalformedError } from '../../errors'
-import { ByteArrayStopCramEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
-import { CramBufferOverrunError } from './getBits'
+import CramCodec, { Cursor, Cursors } from './_base.ts'
+import { CramMalformedError } from '../../errors.ts'
+import { ByteArrayStopCramEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import { CramBufferOverrunError } from './getBits.ts'
+import CramSlice from '../slice/index.ts'
 
 export default class ByteArrayStopCodec extends CramCodec<
   'byteArray',
   ByteArrayStopCramEncoding['parameters']
 > {
   decode(
-    slice: CramSlice,
-    coreDataBlock: CramFileBlock,
+    _slice: CramSlice,
+    _coreDataBlock: CramFileBlock,
     blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {

package/src/cramFile/codecs/dataSeriesTypes.ts

@@ -1,4 +1,4 @@
-import { CramEncoding } from '../encoding'
+import { CramEncoding } from '../encoding.ts'
 
 export type DataType = 'int' | 'byte' | 'long' | 'byteArray'
 

package/src/cramFile/codecs/external.ts

@@ -1,10 +1,10 @@
-import CramCodec, { Cursor, Cursors } from './_base'
-import { CramUnimplementedError } from '../../errors'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
-import { parseItf8 } from '../util'
-import { CramBufferOverrunError } from './getBits'
-import { ExternalCramEncoding } from '../encoding'
+import CramCodec, { Cursor, Cursors } from './_base.ts'
+import { CramUnimplementedError } from '../../errors.ts'
+import { CramFileBlock } from '../file.ts'
+import CramSlice from '../slice/index.ts'
+import { parseItf8 } from '../util.ts'
+import { CramBufferOverrunError } from './getBits.ts'
+import { ExternalCramEncoding } from '../encoding.ts'
 
 export default class ExternalCodec extends CramCodec<
   'int' | 'byte',
@@ -32,16 +32,19 @@ export default class ExternalCodec extends CramCodec<
   }
 
   decode(
-    slice: CramSlice,
-    coreDataBlock: CramFileBlock,
+    _slice: CramSlice,
+    _coreDataBlock: CramFileBlock,
     blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {
     const { blockContentId } = this.parameters
     const contentBlock = blocksByContentId[blockContentId]
-
-    const cursor = cursors.externalBlocks.getCursor(blockContentId)
-    return contentBlock ? this._decodeData(contentBlock, cursor) : undefined
+    return contentBlock
+      ? this._decodeData(
+          contentBlock,
+          cursors.externalBlocks.getCursor(blockContentId),
+        )
+      : undefined
   }
 
   _decodeInt(contentBlock: CramFileBlock, cursor: Cursor) {

package/src/cramFile/codecs/gamma.ts

@@ -1,9 +1,9 @@
-import CramCodec, { Cursors } from './_base'
-import { getBits } from './getBits'
-import { CramUnimplementedError } from '../../errors'
-import { GammaEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
+import CramCodec, { Cursors } from './_base.ts'
+import { getBits } from './getBits.ts'
+import { CramUnimplementedError } from '../../errors.ts'
+import { GammaEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import CramSlice from '../slice/index.ts'
 
 export default class GammaCodec extends CramCodec<
   'int',
@@ -19,9 +19,9 @@ export default class GammaCodec extends CramCodec<
   }
 
   decode(
-    slice: CramSlice,
+    _slice: CramSlice,
     coreDataBlock: CramFileBlock,
-    blocksByContentId: Record<number, CramFileBlock>,
+    _blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {
     let length = 1

package/src/cramFile/codecs/huffman.ts

@@ -1,9 +1,9 @@
-import CramCodec, { Cursor, Cursors } from './_base'
-import { getBits } from './getBits'
-import { CramMalformedError } from '../../errors'
-import { HuffmanEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
+import CramCodec, { Cursor, Cursors } from './_base.ts'
+import { getBits } from './getBits.ts'
+import { CramMalformedError } from '../../errors.ts'
+import { HuffmanEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import CramSlice from '../slice/index.ts'
 
 function numberOfSetBits(ii: number) {
   let i = (ii - (ii >> 1)) & 0x55555555
@@ -122,7 +122,7 @@ export default class HuffmanIntCodec extends CramCodec<
   decode(
     slice: CramSlice,
     coreDataBlock: CramFileBlock,
-    blocksByContentId: Record<number, CramFileBlock>,
+    _blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {
     return this._decode(slice, coreDataBlock, cursors.coreBlock)
@@ -137,7 +137,7 @@ export default class HuffmanIntCodec extends CramCodec<
     return this.sortedCodes[0]!.value
   }
 
-  _decode(slice: CramSlice, coreDataBlock: CramFileBlock, coreCursor: Cursor) {
+  _decode(_slice: CramSlice, coreDataBlock: CramFileBlock, coreCursor: Cursor) {
     const input = coreDataBlock.content
 
     let prevLen = 0

package/src/cramFile/codecs/index.ts

@@ -1,14 +1,14 @@
-import CramCodec from './_base'
-import BetaCodec from './beta'
-import ByteArrayLengthCodec from './byteArrayLength'
-import ByteArrayStopCodec from './byteArrayStop'
-import { DataType } from './dataSeriesTypes'
-import ExternalCodec from './external'
-import GammaCodec from './gamma'
-import HuffmanIntCodec from './huffman'
-import SubexpCodec from './subexp'
-import { CramUnimplementedError } from '../../errors'
-import { CramEncoding } from '../encoding'
+import CramCodec from './_base.ts'
+import BetaCodec from './beta.ts'
+import ByteArrayLengthCodec from './byteArrayLength.ts'
+import ByteArrayStopCodec from './byteArrayStop.ts'
+import { DataType } from './dataSeriesTypes.ts'
+import ExternalCodec from './external.ts'
+import GammaCodec from './gamma.ts'
+import HuffmanIntCodec from './huffman.ts'
+import SubexpCodec from './subexp.ts'
+import { CramUnimplementedError } from '../../errors.ts'
+import { CramEncoding } from '../encoding.ts'
 
 const codecClasses = {
   1: ExternalCodec,

package/src/cramFile/codecs/subexp.ts

@@ -1,9 +1,9 @@
-import CramCodec, { Cursors } from './_base'
-import { getBits } from './getBits'
-import { CramUnimplementedError } from '../../errors'
-import { SubexpEncoding } from '../encoding'
-import { CramFileBlock } from '../file'
-import CramSlice from '../slice'
+import CramCodec, { Cursors } from './_base.ts'
+import { getBits } from './getBits.ts'
+import { CramUnimplementedError } from '../../errors.ts'
+import { SubexpEncoding } from '../encoding.ts'
+import { CramFileBlock } from '../file.ts'
+import CramSlice from '../slice/index.ts'
 
 export default class SubexpCodec extends CramCodec<
   'int',
@@ -19,9 +19,9 @@ export default class SubexpCodec extends CramCodec<
   }
 
   decode(
-    slice: CramSlice,
+    _slice: CramSlice,
     coreDataBlock: CramFileBlock,
-    blocksByContentId: Record<number, CramFileBlock>,
+    _blocksByContentId: Record<number, CramFileBlock>,
     cursors: Cursors,
   ) {
     let numLeadingOnes = 0

package/src/cramFile/container/compressionScheme.ts

@@ -1,12 +1,12 @@
-import { CramMalformedError } from '../../errors'
-import { instantiateCodec } from '../codecs'
-import CramCodec from '../codecs/_base'
+import { CramMalformedError } from '../../errors.ts'
+import CramCodec from '../codecs/_base.ts'
 import {
   DataSeriesEncodingKey,
   DataSeriesEncodingMap,
-} from '../codecs/dataSeriesTypes'
-import { CramEncoding } from '../encoding'
-import { CramCompressionHeader } from '../sectionParsers'
+} from '../codecs/dataSeriesTypes.ts'
+import { instantiateCodec } from '../codecs/index.ts'
+import { CramEncoding } from '../encoding.ts'
+import { CramCompressionHeader } from '../sectionParsers.ts'
 
 // the hardcoded data type to be decoded for each core
 // data field

package/src/cramFile/container/index.ts

@@ -1,10 +1,9 @@
-import { CramMalformedError } from '../../errors'
-// locals
-import CramSlice from '../slice'
-import { itf8Size, parseItem, tinyMemoize } from '../util'
-import CramContainerCompressionScheme from './compressionScheme'
-import CramFile from '../file'
-import { getSectionParsers } from '../sectionParsers'
+import { CramMalformedError } from '../../errors.ts'
+import CramSlice from '../slice/index.ts'
+import { itf8Size, parseItem, tinyMemoize } from '../util.ts'
+import CramContainerCompressionScheme from './compressionScheme.ts'
+import CramFile from '../file.ts'
+import { getSectionParsers } from '../sectionParsers.ts'
 
 export default class CramContainer {
   constructor(