@gmod/cram 1.7.0 → 1.7.2

package/esm/cramFile/sectionParsers.d.ts

@@ -7,8 +7,8 @@ declare const cramFileDefinition: {
     parser: Parser<unknown>;
     maxLength: number;
 };
-export declare type CramTagDictionary = string[][];
-export declare type CramPreservationMap = {
+export type CramTagDictionary = string[][];
+export type CramPreservationMap = {
     MI: boolean;
     UI: boolean;
     PI: boolean;
@@ -18,7 +18,7 @@ export declare type CramPreservationMap = {
     SM: [number, number, number, number, number];
     TD: CramTagDictionary;
 };
-export declare type MappedSliceHeader = {
+export type MappedSliceHeader = {
     refSeqId: number;
     refSeqStart: number;
     refSeqSpan: number;
@@ -30,7 +30,7 @@ export declare type MappedSliceHeader = {
     refBaseBlockId: number;
     md5: TupleOf<number, 16>;
 };
-export declare type UnmappedSliceHeader = {
+export type UnmappedSliceHeader = {
     numRecords: number;
     recordCounter: number;
     numBlocks: number;
@@ -39,15 +39,15 @@ export declare type UnmappedSliceHeader = {
     md5: TupleOf<number, 16>;
 };
 export declare function isMappedSliceHeader(header: MappedSliceHeader | UnmappedSliceHeader): header is MappedSliceHeader;
-export declare type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
-export declare type BlockHeader = {
+export type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
+export type 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 declare type CramCompressionHeader = ParsedItem<{
+export type CramCompressionHeader = ParsedItem<{
     preservation: CramPreservationMap;
     dataSeriesEncoding: DataSeriesEncodingMap;
     tagEncoding: Record<string, CramEncoding>;

package/esm/cramFile/slice/decodeRecord.d.ts

@@ -4,7 +4,7 @@ import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/co
 import { CramFileBlock } from '../file';
 import { Cursors, DataTypeMapping } from '../codecs/_base';
 import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes';
-export declare type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]];
+export type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]];
 export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSeriesDecoder, compressionScheme: CramContainerCompressionScheme, sliceHeader: SliceHeader, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors, majorVersion: number, recordNumber: number): {
     readLength: number;
     sequenceId: number;

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

@@ -2,7 +2,7 @@ import CramRecord from '../record';
 import CramContainer from '../container';
 import { CramFileBlock } from '../file';
 import { MappedSliceHeader, UnmappedSliceHeader } from '../sectionParsers';
-export declare type SliceHeader = CramFileBlock & {
+export type SliceHeader = CramFileBlock & {
     parsedContent: MappedSliceHeader | UnmappedSliceHeader;
 };
 export default class CramSlice {

package/esm/cramFile/util.d.ts

@@ -2,7 +2,7 @@
 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 declare type ParsedItem<T> = T & {
+export type ParsedItem<T> = T & {
     _endPosition: number;
     _size: number;
 };

package/esm/index.d.ts

@@ -1,4 +1,4 @@
-import CramFile from './cramFile';
+import CramFile, { CramRecord } from './cramFile';
 import IndexedCramFile from './indexedCramFile';
 import CraiIndex from './craiIndex';
-export { CramFile, IndexedCramFile, CraiIndex };
+export { CramFile, IndexedCramFile, CraiIndex, CramRecord };

package/esm/index.js

@@ -1,5 +1,5 @@
-import CramFile from './cramFile';
+import CramFile, { CramRecord } from './cramFile';
 import IndexedCramFile from './indexedCramFile';
 import CraiIndex from './craiIndex';
-export { CramFile, IndexedCramFile, CraiIndex };
+export { CramFile, IndexedCramFile, CraiIndex, CramRecord };
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,QAAQ,EAAE,eAAe,EAAE,SAAS,EAAE,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,EAAE,EAAE,UAAU,EAAE,MAAM,YAAY,CAAA;AACjD,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,QAAQ,EAAE,eAAe,EAAE,SAAS,EAAE,UAAU,EAAE,CAAA"}

package/esm/indexedCramFile.d.ts

@@ -3,12 +3,12 @@ import CramRecord from './cramFile/record';
 import { SeqFetch } from './cramFile/file';
 import { Filehandle } from './cramFile/filehandle';
 import { Slice } from './craiIndex';
-export declare type CramFileSource = {
+export type CramFileSource = {
     cramFilehandle?: Filehandle;
     cramUrl?: string;
     cramPath?: string;
 };
-export declare type CramIndexLike = {
+export type CramIndexLike = {
     getEntriesForRange: (seqId: number, start: number, end: number) => Promise<Slice[]>;
     hasDataForReferenceSequence: (seqId: number) => Promise<boolean>;
 };

package/esm/sam.d.ts

@@ -1,4 +1,4 @@
-export declare type HeaderDataItem = {
+export type HeaderDataItem = {
     tag: string;
     data: Array<{
         tag: string;

package/esm/typescript.d.ts

@@ -1,3 +1,3 @@
 export declare function ensureNotNullish<T>(x: T | null | undefined): T;
-export declare type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
-export declare type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;
+export type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
+export type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "1.7.0",
+  "version": "1.7.2",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
@@ -57,29 +57,29 @@
     "@babel/plugin-transform-modules-commonjs": "^7.18.2",
     "@babel/preset-typescript": "^7.17.12",
     "@gmod/indexedfasta": "^2.0.2",
-    "@types/buffer-crc32": "^0.2.0",
-    "@types/jest": "^27.4.0",
+    "@types/buffer-crc32": "^0.2.2",
+    "@types/jest": "^29.2.4",
     "@types/long": "^4.0.2",
     "@types/md5": "^2.3.2",
     "@types/pako": "^1.0.3",
-    "@typescript-eslint/eslint-plugin": "^5.9.1",
-    "@typescript-eslint/parser": "^5.9.1",
+    "@typescript-eslint/eslint-plugin": "^5.46.1",
+    "@typescript-eslint/parser": "^5.46.1",
     "buffer": "^6.0.3",
-    "documentation": "^13.2.5",
-    "eslint": "^8.15.0",
+    "documentation": "^14.0.1",
+    "eslint": "^8.30.0",
     "eslint-config-prettier": "^8.5.0",
     "eslint-plugin-import": "^2.25.4",
     "eslint-plugin-prettier": "^4.0.0",
     "glob": "^8.0.3",
-    "jest": "^28.1.0",
-    "mock-fs": "^5.1.2",
-    "prettier": "^2.5.1",
+    "jest": "^29.3.1",
+    "mock-fs": "^5.2.0",
+    "prettier": "^2.8.1",
     "rimraf": "^3.0.2",
-    "ts-jest": "^28.0.2",
-    "typescript": "^4.5.4",
+    "ts-jest": "^29.0.3",
+    "typescript": "^4.9.4",
     "url": "^0.11.0",
-    "webpack": "5.72.1",
-    "webpack-cli": "^4.9.2"
+    "webpack": "5.75.0",
+    "webpack-cli": "^5.0.1"
   },
   "publishConfig": {
     "access": "public"

package/src/cramFile/index.ts

@@ -1,3 +1,4 @@
 import CramFile from './file'
+export { default as CramRecord } from './record'
 
 export default CramFile

package/src/index.ts

@@ -1,5 +1,5 @@
-import CramFile from './cramFile'
+import CramFile, { CramRecord } from './cramFile'
 import IndexedCramFile from './indexedCramFile'
 import CraiIndex from './craiIndex'
 
-export { CramFile, IndexedCramFile, CraiIndex }
+export { CramFile, IndexedCramFile, CraiIndex, CramRecord }