@gmod/cram 2.0.4 → 3.0.0

package/esm/cramFile/sectionParsers.js.map

@@ -1 +1 @@
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package/esm/cramFile/slice/index.d.ts

@@ -10,7 +10,29 @@ export default class CramSlice {
     containerPosition: number;
     private file;
     constructor(container: CramContainer, containerPosition: number, _unused: number);
-    getHeader(): Promise<SliceHeader>;
+    getHeader(): Promise<{
+        parsedContent: {
+            recordCounter: number;
+            md5: [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number] | undefined;
+            contentIds: number[];
+            numContentIds: number;
+            numBlocks: number;
+            numRecords: number;
+        } & {
+            _endPosition: number;
+            _size: number;
+        };
+        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;
+    }>;
     getBlocks(): Promise<CramFileBlock[]>;
     getCoreDataBlock(): Promise<CramFileBlock>;
     _getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;

package/esm/cramFile/slice/index.js

@@ -3,7 +3,7 @@ import { parseItem, sequenceMD5, tinyMemoize } from '../util';
 import Constants from '../constants';
 import decodeRecord from './decodeRecord';
 import CramRecord from '../record';
-import { isMappedSliceHeader, } from '../sectionParsers';
+import { getSectionParsers, isMappedSliceHeader, } from '../sectionParsers';
 import { CramBufferOverrunError } from '../codecs/getBits';
 /**
  * @private
@@ -132,8 +132,12 @@ export default class CramSlice {
     // memoize
     async getHeader() {
         // fetch and parse the slice header
-        const sectionParsers = await this.file.getSectionParsers();
+        const { majorVersion } = await this.file.getDefinition();
+        const sectionParsers = getSectionParsers(majorVersion);
         const containerHeader = await this.container.getHeader();
+        if (!containerHeader) {
+            throw new Error('no container header detected');
+        }
         const header = await this.file.readBlock(containerHeader._endPosition + this.containerPosition);
         if (header === undefined) {
             throw new Error('block header undefined');
@@ -156,7 +160,7 @@ export default class CramSlice {
         // read all the blocks into memory and store them
         let blockPosition = header._endPosition;
         const blocks = new Array(header.parsedContent.numBlocks);
-        for (let i = 0; i < blocks.length; i += 1) {
+        for (let i = 0; i < blocks.length; i++) {
             const block = await this.file.readBlock(blockPosition);
             if (block === undefined) {
                 throw new Error('block undefined');
@@ -239,6 +243,7 @@ export default class CramSlice {
         return this.getRecords(() => true);
     }
     async _fetchRecords() {
+        var _a, _b;
         const { majorVersion } = await this.file.getDefinition();
         const compressionScheme = await this.container.getCompressionScheme();
         if (compressionScheme === undefined) {
@@ -254,14 +259,12 @@ export default class CramSlice {
             this.file.options.checkSequenceMD5 &&
             isMappedSliceHeader(sliceHeader.parsedContent) &&
             sliceHeader.parsedContent.refSeqId >= 0 &&
-            sliceHeader.parsedContent.md5.join('') !== '0000000000000000') {
+            ((_a = sliceHeader.parsedContent.md5) === null || _a === void 0 ? void 0 : _a.join('')) !== '0000000000000000') {
             const refRegion = await this.getReferenceRegion();
             if (refRegion) {
                 const { seq, start, end } = refRegion;
                 const seqMd5 = sequenceMD5(seq);
-                const storedMd5 = sliceHeader.parsedContent.md5
-                    .map(byte => (byte < 16 ? '0' : '') + byte.toString(16))
-                    .join('');
+                const storedMd5 = (_b = sliceHeader.parsedContent.md5) === null || _b === void 0 ? void 0 : _b.map(byte => (byte < 16 ? '0' : '') + byte.toString(16)).join('');
                 if (seqMd5 !== storedMd5) {
                     throw new CramMalformedError(`MD5 checksum reference mismatch for ref ${sliceHeader.parsedContent.refSeqId} pos ${start}..${end}. recorded MD5: ${storedMd5}, calculated MD5: ${seqMd5}`);
                 }

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

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

@@ -1,10 +1,12 @@
-import { Parser } from '@gmod/binary-parser';
 export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
-export declare function parseItf8(buffer: Uint8Array, initialOffset: number): [number, number];
-export type ParsedItem<T> = T & {
+export declare function parseItf8(buffer: Uint8Array, initialOffset: number): readonly [number, number];
+export declare function parseLtf8(buffer: Buffer, initialOffset: number): readonly [number, number];
+export declare function parseItem<T>(buffer: Buffer, parser: (buffer: Buffer, offset: number) => {
+    offset: number;
+    value: T;
+}, startBufferPosition?: number, startFilePosition?: number): T & {
     _endPosition: number;
     _size: number;
 };
-export declare function parseItem<T>(buffer: Buffer, parser: Parser<T>, startBufferPosition?: number, startFilePosition?: number): ParsedItem<T>;
 export declare function tinyMemoize(_class: any, methodName: any): void;
 export declare function sequenceMD5(seq: string): string;

package/esm/cramFile/util.js

@@ -1,4 +1,5 @@
 import md5 from 'md5';
+import Long from 'long';
 import { CramBufferOverrunError } from './codecs/getBits';
 export function itf8Size(v) {
     if (!(v & ~0x7f)) {
@@ -58,18 +59,98 @@ export function parseItf8(buffer, initialOffset) {
     }
     return [result, offset - initialOffset];
 }
+export function parseLtf8(buffer, initialOffset) {
+    let offset = initialOffset;
+    const countFlags = buffer[offset];
+    let n;
+    if (countFlags < 0x80) {
+        n = countFlags;
+        offset += 1;
+    }
+    else if (countFlags < 0xc0) {
+        n = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff;
+        offset += 2;
+    }
+    else if (countFlags < 0xe0) {
+        n =
+            ((buffer[offset] << 16) |
+                (buffer[offset + 1] << 8) |
+                buffer[offset + 2]) &
+                0x1fffff;
+        n = ((countFlags & 63) << 16) | buffer.readUInt16LE(offset + 1);
+        offset += 3;
+    }
+    else if (countFlags < 0xf0) {
+        n =
+            ((buffer[offset] << 24) |
+                (buffer[offset + 1] << 16) |
+                (buffer[offset + 2] << 8) |
+                buffer[offset + 3]) &
+                0x0fffffff;
+        offset += 4;
+    }
+    else if (countFlags < 0xf8) {
+        n =
+            ((buffer[offset] & 15) * Math.pow(2, 32) + (buffer[offset + 1] << 24)) |
+                ((buffer[offset + 2] << 16) |
+                    (buffer[offset + 3] << 8) |
+                    buffer[offset + 4]);
+        // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
+        offset += 5;
+    }
+    else if (countFlags < 0xfc) {
+        n =
+            ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2, 32) +
+                (buffer[offset + 2] << 24)) |
+                ((buffer[offset + 3] << 16) |
+                    (buffer[offset + 4] << 8) |
+                    buffer[offset + 5]);
+        offset += 6;
+    }
+    else if (countFlags < 0xfe) {
+        n =
+            ((((buffer[offset] & 3) << 16) |
+                (buffer[offset + 1] << 8) |
+                buffer[offset + 2]) *
+                Math.pow(2, 32) +
+                (buffer[offset + 3] << 24)) |
+                ((buffer[offset + 4] << 16) |
+                    (buffer[offset + 5] << 8) |
+                    buffer[offset + 6]);
+        offset += 7;
+    }
+    else if (countFlags < 0xff) {
+        n = Long.fromBytesBE(buffer.slice(offset + 1, offset + 8));
+        if (n.greaterThan(Number.MAX_SAFE_INTEGER) ||
+            n.lessThan(Number.MIN_SAFE_INTEGER)) {
+            throw new Error('integer overflow');
+        }
+        n = n.toNumber();
+        offset += 8;
+    }
+    else {
+        n = Long.fromBytesBE(buffer.slice(offset + 1, offset + 9));
+        if (n.greaterThan(Number.MAX_SAFE_INTEGER) ||
+            n.lessThan(Number.MIN_SAFE_INTEGER)) {
+            throw new Error('integer overflow');
+        }
+        n = n.toNumber();
+        offset += 9;
+    }
+    return [n, offset - initialOffset];
+}
 export function parseItem(buffer, parser, startBufferPosition = 0, startFilePosition = 0) {
-    const { offset, result } = parser.parse(buffer);
+    const { offset, value } = parser(buffer, startBufferPosition);
     return {
-        ...result,
+        ...value,
         _endPosition: offset + startFilePosition,
         _size: offset - startBufferPosition,
     };
 }
-// this would be nice as a decorator, but i'm a little worried about
-// babel support for it going away or changing.
-// memoizes a method in the stupidest possible way, with no regard for the
-// arguments.  actually, this only works on methods that take no arguments
+// this would be nice as a decorator, but i'm a little worried about babel
+// support for it going away or changing. memoizes a method in the stupidest
+// possible way, with no regard for the arguments.  actually, this only works
+// on methods that take no arguments
 export function tinyMemoize(_class, methodName) {
     const method = _class.prototype[methodName];
     const memoAttrName = `_memo_${methodName}`;

package/esm/cramFile/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/cramFile/util.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,KAAK,CAAA;AACrB,OAAO,IAAI,MAAM,MAAM,CAAA;AACvB,OAAO,EAAE,sBAAsB,EAAE,MAAM,kBAAkB,CAAA;AAEzD,MAAM,UAAU,QAAQ,CAAC,CAAS;IAChC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC;QACjB,OAAO,CAAC,CAAA;IACV,CAAC;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC;QACnB,OAAO,CAAC,CAAA;IACV,CAAC;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC;QACrB,OAAO,CAAC,CAAA;IACV,CAAC;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC;QACtB,OAAO,CAAC,CAAA;IACV,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,MAAkB,EAAE,aAAqB;IACjE,IAAI,MAAM,GAAG,aAAa,CAAA;IAC1B,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,CAAC,CAAA;IACjC,IAAI,MAAM,CAAA;IACV,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QACtB,MAAM,GAAG,UAAU,CAAA;QACnB,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;IACrB,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,MAAM,GAAG,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;QAC1D,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;IACrB,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,MAAM;YACJ,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACrE,QAAQ,CAAA;QACV,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;IACrB,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,MAAM;YACJ,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC;gBACjB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACrB,UAAU,CAAA;QACZ,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;IACrB,CAAC;SAAM,CAAC;QACN,MAAM;YACJ,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC;gBAC3B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,CAAA;QAC7B,+EAA+E;QAC/E,+EAA+E;QAC/E,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;IACrB,CAAC;IACD,IAAI,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC;QAC3B,MAAM,IAAI,sBAAsB,CAC9B,oEAAoE,CACrE,CAAA;IACH,CAAC;IACD,OAAO,CAAC,MAAM,EAAE,MAAM,GAAG,aAAa,CAAU,CAAA;AAClD,CAAC;AAED,MAAM,UAAU,SAAS,CAAC,MAAc,EAAE,aAAqB;IAC7D,IAAI,MAAM,GAAG,aAAa,CAAA;IAC1B,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,CAAC,CAAA;IACjC,IAAI,CAAC,CAAA;IACL,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QACtB,CAAC,GAAG,UAAU,CAAA;QACd,MAAM,IAAI,CAAC,CAAA;IACb,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;QACzD,MAAM,IAAI,CAAC,CAAA;IACb,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,CAAC;YACC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC;gBACrB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACrB,QAAQ,CAAA;QACV,CAAC,GAAG,CAAC,CAAC,UAAU,GAAG,EAAE,CAAC,IAAI,EAAE,CAAC,GAAG,MAAM,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QAC/D,MAAM,IAAI,CAAC,CAAA;IACb,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,CAAC;YACC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC;gBACrB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACrB,UAAU,CAAA;QACZ,MAAM,IAAI,CAAC,CAAA;IACb,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,CAAC;YACC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,EAAE,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;gBACtE,CAAC,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;oBACzB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;oBACzB,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QACvB,+EAA+E;QAC/E,MAAM,IAAI,CAAC,CAAA;IACb,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,CAAC;YACC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,CAAC;gBACnE,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;gBAC7B,CAAC,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;oBACzB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;oBACzB,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QACvB,MAAM,IAAI,CAAC,CAAA;IACb,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,CAAC;YACC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC5B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACnB,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,CAAC;gBACf,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;gBAC7B,CAAC,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;oBACzB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;oBACzB,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QACvB,MAAM,IAAI,CAAC,CAAA;IACb,CAAC;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QAC7B,CAAC,GAAG,IAAI,CAAC,WAAW,CAClB,MAAM,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,MAAM,GAAG,CAAC,CAAwB,CAC5D,CAAA;QACD,IACE,CAAC,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;YACtC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACnC,CAAC;YACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;QACrC,CAAC;QACD,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,CAAA;QAChB,MAAM,IAAI,CAAC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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "2.0.4",
+  "version": "3.0.0",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -22,7 +22,7 @@
   ],
   "scripts": {
     "test": "jest",
-    "lint": "eslint src test",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0 src test",
     "docs": "documentation readme --shallow src/indexedCramFile.ts --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/craiIndex.ts --section=CraiIndex;  documentation readme --shallow errors.ts '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/cramFile/record.ts --section=CramRecord",
     "prebuild": "npm run clean",
     "clean": "rimraf dist esm",
@@ -43,7 +43,6 @@
   ],
   "dependencies": {
     "@gmod/abortable-promise-cache": "^2.0.0",
-    "@gmod/binary-parser": "^1.3.5",
     "@jkbonfield/htscodecs": "^0.5.1",
     "buffer-crc32": "^1.0.0",
     "bzip2": "^0.1.1",
@@ -59,18 +58,18 @@
     "@types/long": "^4.0.0",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
-    "@typescript-eslint/eslint-plugin": "^7.0.2",
-    "@typescript-eslint/parser": "^7.0.2",
+    "@typescript-eslint/eslint-plugin": "^8.0.0",
+    "@typescript-eslint/parser": "^8.0.0",
     "buffer": "^6.0.3",
     "documentation": "^14.0.3",
-    "eslint": "^9.0.0",
+    "eslint": "^9.8.0",
     "eslint-config-prettier": "^9.0.0",
     "eslint-plugin-prettier": "^5.1.3",
-    "eslint-plugin-unicorn": "^54.0.0",
+    "eslint-plugin-unicorn": "^55.0.0",
     "jest": "^29.3.1",
     "mock-fs": "^5.2.0",
     "prettier": "^3.2.5",
-    "rimraf": "^5.0.1",
+    "rimraf": "^6.0.1",
     "ts-jest": "^29.1.2",
     "typescript": "^5.0.3",
     "webpack": "^5.90.3",

package/src/cramFile/codecs/byteArrayLength.ts

@@ -1,10 +1,9 @@
-import { tinyMemoize } from '../util'
-
 import CramCodec, { Cursors } from './_base'
 import { ByteArrayLengthEncoding, CramEncoding } from '../encoding'
 import CramSlice from '../slice'
 import { CramFileBlock } from '../file'
 import { DataType } from './dataSeriesTypes'
+import { tinyMemoize } from '../util'
 
 type CramCodecFactory = <TData extends DataType = DataType>(
   encodingData: CramEncoding,

package/src/cramFile/codecs/external.ts

@@ -42,7 +42,7 @@ export default class ExternalCodec extends CramCodec<
     const contentBlock = blocksByContentId[blockContentId]
     if (!contentBlock) {
       throw new CramMalformedError(
-        `no block found with content ID ${blockContentId}`,
+        `no block found with content ID ${blockContentId}}`,
       )
     }
     const cursor = cursors.externalBlocks.getCursor(blockContentId)

package/src/cramFile/codecs/huffman.ts

@@ -46,7 +46,8 @@ export default class HuffmanIntCodec extends CramCodec<
     this.buildCodes()
     this.buildCaches()
 
-    // if this is a degenerate zero-length huffman code, special-case the decoding
+    // if this is a degenerate zero-length huffman code, special-case the
+    // decoding
     if (this.sortedCodes[0].bitLength === 0) {
       this._decode = this._decodeZeroLengthCode
     }

package/src/cramFile/container/compressionScheme.ts

@@ -1,6 +1,6 @@
 import { instantiateCodec } from '../codecs'
 import CramCodec from '../codecs/_base'
-import { CramCompressionHeader, CramPreservationMap } from '../sectionParsers'
+import { CramCompressionHeader } from '../sectionParsers'
 import { CramEncoding } from '../encoding'
 import { CramMalformedError } from '../../errors'
 import {
@@ -95,12 +95,8 @@ export default class CramContainerCompressionScheme {
   public tagCodecCache: Record<string, CramCodec> = {}
   public tagEncoding: Record<string, CramEncoding> = {}
   public dataSeriesEncoding: DataSeriesEncodingMap
-  private preservation: CramPreservationMap
-  private _endPosition: number
-  private _size: number
 
   constructor(content: CramCompressionHeader) {
-    // Object.assign(this, content)
     // interpret some of the preservation map tags for convenient use
     this.readNamesIncluded = content.preservation.RN
     this.APdelta = content.preservation.AP
@@ -109,9 +105,6 @@ export default class CramContainerCompressionScheme {
     this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM)
     this.dataSeriesEncoding = content.dataSeriesEncoding
     this.tagEncoding = content.tagEncoding
-    this.preservation = content.preservation
-    this._size = content._size
-    this._endPosition = content._endPosition
   }
 
   /**

package/src/cramFile/container/index.ts

@@ -4,6 +4,7 @@ import { itf8Size, parseItem, tinyMemoize } from '../util'
 import CramSlice from '../slice'
 import CramContainerCompressionScheme from './compressionScheme'
 import CramFile from '../file'
+import { getSectionParsers } from '../sectionParsers'
 
 export default class CramContainer {
   constructor(
@@ -11,20 +12,21 @@ export default class CramContainer {
     public filePosition: number,
   ) {}
 
-  // memoize
   getHeader() {
     return this._readContainerHeader(this.filePosition)
   }
 
-  // memoize
   async getCompressionHeaderBlock() {
     const containerHeader = await this.getHeader()
 
-    // if there are no records in the container, there will be no compression header
-    if (!containerHeader.numRecords) {
+    // if there are no records in the container, there will be no compression
+    // header
+    if (!containerHeader?.numRecords) {
       return null
     }
-    const sectionParsers = await this.file.getSectionParsers()
+    const { majorVersion } = await this.file.getDefinition()
+    const sectionParsers = getSectionParsers(majorVersion)
+
     const block = await this.getFirstBlock()
     if (block === undefined) {
       return undefined
@@ -34,6 +36,7 @@ export default class CramContainer {
         `invalid content type ${block.contentType} in what is supposed to be the compression header block`,
       )
     }
+
     const content = parseItem(
       block.content,
       sectionParsers.cramCompressionHeader.parser,
@@ -48,16 +51,20 @@ export default class CramContainer {
 
   async getFirstBlock() {
     const containerHeader = await this.getHeader()
+    if (!containerHeader) {
+      return undefined
+    }
     return this.file.readBlock(containerHeader._endPosition)
   }
 
-  // parses the compression header data into a CramContainerCompressionScheme object
-  // memoize
+  // parses the compression header data into a CramContainerCompressionScheme
+  // object
   async getCompressionScheme() {
     const header = await this.getCompressionHeaderBlock()
     if (!header) {
       return undefined
     }
+
     return new CramContainerCompressionScheme(header.parsedContent)
   }
 
@@ -68,11 +75,15 @@ export default class CramContainer {
   }
 
   async _readContainerHeader(position: number) {
-    const sectionParsers = await this.file.getSectionParsers()
+    const { majorVersion } = await this.file.getDefinition()
+    const sectionParsers = getSectionParsers(majorVersion)
     const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers
     const { size: fileSize } = await this.file.stat()
 
     if (position >= fileSize) {
+      console.warn(
+        `position:${position}>=fileSize:${fileSize} in cram container`,
+      )
       return undefined
     }
 
@@ -80,11 +91,11 @@ export default class CramContainer {
     // how much to buffer until you read numLandmarks
     const bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength)
     await this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position)
-    const header1 = parseItem(bytes1, cramContainerHeader1.parser) as any
+    const header1 = parseItem(bytes1, cramContainerHeader1.parser)
     const numLandmarksSize = itf8Size(header1.numLandmarks)
     if (position + header1.length >= fileSize) {
       console.warn(
-        `${this.file}: container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`,
+        `container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`,
       )
       return undefined
     }