@gmod/cram 1.6.3 → 1.7.0

package/esm/cramFile/file.d.ts

@@ -1,63 +1,113 @@
+/// <reference types="node" />
+import QuickLRU from 'quick-lru';
+import { BlockHeader, CompressionMethod } from './sectionParsers';
+import CramContainer from './container';
+import { Parser } from '@gmod/binary-parser';
+import CramRecord from './record';
+import { Filehandle } from './filehandle';
+export declare type CramFileSource = {
+    filehandle?: Filehandle;
+    url?: string;
+    path?: string;
+};
+export declare type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
+export declare type CramFileArgs = CramFileSource & {
+    checkSequenceMD5: boolean;
+    cacheSize?: number;
+    seqFetch: SeqFetch;
+};
+export declare type CramFileBlock = BlockHeader & {
+    _endPosition: number;
+    contentPosition: number;
+    _size: number;
+    content: Buffer;
+    crc32?: number;
+};
 export default class CramFile {
-    /**
-     * @param {object} args
-     * @param {object} [args.filehandle] - a filehandle that implements the stat() and
-     * read() methods of the Node filehandle API https://nodejs.org/api/fs.html#fs_class_filehandle
-     * @param {object} [args.path] - path to the cram file
-     * @param {object} [args.url] - url for the cram file.  also supports file:// urls for local files
-     * @param {function} [args.seqFetch] - a function with signature
-     * `(seqId, startCoordinate, endCoordinate)` that returns a promise for a string of sequence bases
-     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
-     * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
-     * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
-     */
-    constructor(args: {
-        filehandle?: object | undefined;
-        path?: object | undefined;
-        url?: object | undefined;
-        seqFetch?: Function | undefined;
-        cacheSize?: number | undefined;
-        checkSequenceMD5?: boolean | undefined;
-    });
-    file: any;
+    private file;
     validateChecksums: boolean;
-    fetchReferenceSequenceCallback: Function | undefined;
+    fetchReferenceSequenceCallback: SeqFetch;
     options: {
         checkSequenceMD5: boolean;
         cacheSize: number;
     };
-    featureCache: any;
-    toString(): any;
-    read(buffer: any, offset: any, length: any, position: any): any;
-    stat(): any;
+    featureCache: QuickLRU<string, Promise<CramRecord[]>>;
+    private header;
+    constructor(args: CramFileArgs);
+    read(buffer: Buffer, offset: number, length: number, position: number): Promise<{
+        bytesRead: number;
+        buffer: Buffer;
+    }>;
+    stat(): Promise<import("generic-filehandle").Stats>;
     getDefinition(): Promise<any>;
-    getSamHeader(): Promise<any[]>;
-    header: any;
-    getHeaderText(): Promise<any>;
+    getSamHeader(): Promise<import("../sam").HeaderDataItem[]>;
+    getHeaderText(): Promise<string | undefined>;
     getSectionParsers(): Promise<{
         cramFileDefinition: {
-            parser: any;
+            parser: Parser<{
+                magic: string;
+                majorVersion: number;
+                minorVersion: number;
+                fileId: string;
+            }>;
+            maxLength: number;
+        };
+        cramContainerHeader1: {
+            parser: Parser<{
+                length: number;
+                refSeqId: number;
+                refSeqStart: number;
+                alignmentSpan: number;
+                numRecords: number;
+                recordCounter: number;
+                numBases: number;
+                numBlocks: number;
+                numLandmarks: number;
+            }>;
             maxLength: number;
         };
+        cramContainerHeader2: {
+            parser: Parser<{
+                numLandmarks: number;
+                landmarks: number[];
+                crc32: number;
+            }>;
+            maxLength: (x: number) => number;
+        };
         cramBlockHeader: {
-            parser: any;
+            parser: Parser<BlockHeader>;
             maxLength: number;
         };
         cramBlockCrc32: {
-            parser: any;
+            parser: Parser<{
+                crc32: number;
+            }>;
             maxLength: number;
         };
+        cramCompressionHeader: {
+            parser: Parser<import("./sectionParsers").CramCompressionHeader>;
+        };
+        cramMappedSliceHeader: {
+            parser: Parser<import("./sectionParsers").MappedSliceHeader>;
+            maxLength: (numContentIds: number) => number;
+        };
+        cramUnmappedSliceHeader: {
+            parser: Parser<import("./sectionParsers").UnmappedSliceHeader>;
+            maxLength: (numContentIds: number) => number;
+        };
     }>;
-    getContainerById(containerNumber: any): Promise<CramContainer | undefined>;
-    checkCrc32(position: any, length: any, recordedCrc32: any, description: any): Promise<void>;
+    getContainerById(containerNumber: number): Promise<CramContainer | undefined>;
+    checkCrc32(position: number, length: number, recordedCrc32: number, description: string): Promise<void>;
     /**
      * @returns {Promise[number]} the number of containers in the file
      */
-    containerCount(): any;
-    getContainerAtPosition(position: any): CramContainer;
-    readBlockHeader(position: any): Promise<any>;
-    _parseSection(section: any, position: any, size: any, preReadBuffer: any): Promise<any>;
-    _uncompress(compressionMethod: any, inputBuffer: any, outputBuffer: any): void;
-    readBlock(position: any): Promise<any>;
+    containerCount(): Promise<number | undefined>;
+    getContainerAtPosition(position: number): CramContainer;
+    readBlockHeader(position: number): Promise<import("./util").ParsedItem<BlockHeader> | undefined>;
+    _parseSection<T>(section: {
+        parser: Parser<T>;
+        maxLength: number;
+    }, position: number, size?: number, preReadBuffer?: undefined): Promise<import("./util").ParsedItem<T> | undefined>;
+    _uncompress(compressionMethod: CompressionMethod, inputBuffer: Buffer, outputBuffer: Buffer): void;
+    readBlock(position: number): Promise<CramFileBlock | undefined>;
 }
-import CramContainer from "./container";

package/esm/cramFile/file.js

@@ -1,7 +1,7 @@
 import { unzip } from '../unzip';
 import crc32 from 'buffer-crc32';
-import LRU from 'quick-lru';
-import { CramUnimplementedError, CramMalformedError } from '../errors';
+import QuickLRU from 'quick-lru';
+import { CramMalformedError, CramUnimplementedError } from '../errors';
 import ransuncompress from '../rans';
 import { cramFileDefinition as cramFileDefinitionParser, getSectionParsers, } from './sectionParsers';
 import htscodecs from '@jkbonfield/htscodecs';
@@ -11,8 +11,8 @@ import { parseItem, tinyMemoize } from './util';
 import { parseHeaderText } from '../sam';
 //source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
 function getEndianness() {
-    let uInt32 = new Uint32Array([0x11223344]);
-    let uInt8 = new Uint8Array(uInt32.buffer);
+    const uInt32 = new Uint32Array([0x11223344]);
+    const uInt8 = new Uint8Array(uInt32.buffer);
     if (uInt8[0] === 0x44) {
         return 0; //little-endian
     }
@@ -24,46 +24,36 @@ function getEndianness() {
     }
 }
 export default class CramFile {
-    /**
-     * @param {object} args
-     * @param {object} [args.filehandle] - a filehandle that implements the stat() and
-     * read() methods of the Node filehandle API https://nodejs.org/api/fs.html#fs_class_filehandle
-     * @param {object} [args.path] - path to the cram file
-     * @param {object} [args.url] - url for the cram file.  also supports file:// urls for local files
-     * @param {function} [args.seqFetch] - a function with signature
-     * `(seqId, startCoordinate, endCoordinate)` that returns a promise for a string of sequence bases
-     * @param {number} [args.cacheSize] optional maximum number of CRAM records to cache.  default 20,000
-     * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
-     * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
-     */
     constructor(args) {
+        var _a;
         this.file = open(args.url, args.path, args.filehandle);
         this.validateChecksums = true;
         this.fetchReferenceSequenceCallback = args.seqFetch;
         this.options = {
-            checkSequenceMD5: args.checkSequenceMD5 !== false,
-            cacheSize: args.cacheSize !== undefined ? args.cacheSize : 20000,
+            checkSequenceMD5: args.checkSequenceMD5,
+            cacheSize: (_a = args.cacheSize) !== null && _a !== void 0 ? _a : 20000,
         };
         // cache of features in a slice, keyed by the
         // slice offset. caches all of the features in a slice, or none.
         // the cache is actually used by the slice object, it's just
         // kept here at the level of the file
-        this.featureCache = new LRU({
+        this.featureCache = new QuickLRU({
             maxSize: this.options.cacheSize,
         });
         if (getEndianness() > 0) {
             throw new Error('Detected big-endian machine, may be unable to run');
         }
     }
-    toString() {
-        if (this.file.filename) {
-            return this.file.filename;
-        }
-        if (this.file.url) {
-            return this.file.url;
-        }
-        return '(cram file)';
-    }
+    // toString() {
+    //   if (this.file.filename) {
+    //     return this.file.filename
+    //   }
+    //   if (this.file.url) {
+    //     return this.file.url
+    //   }
+    //
+    //   return '(cram file)'
+    // }
     // can just read this object like a filehandle
     read(buffer, offset, length, position) {
         return this.file.read(buffer, offset, length, position);
@@ -76,7 +66,8 @@ export default class CramFile {
     async getDefinition() {
         const headbytes = Buffer.allocUnsafe(cramFileDefinitionParser.maxLength);
         await this.file.read(headbytes, 0, cramFileDefinitionParser.maxLength, 0);
-        const definition = cramFileDefinitionParser.parser.parse(headbytes).result;
+        const definition = cramFileDefinitionParser.parser.parse(headbytes)
+            .result;
         if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
             throw new CramUnimplementedError(`CRAM version ${definition.majorVersion} not supported`);
         }
@@ -88,7 +79,11 @@ export default class CramFile {
         if (!firstContainer) {
             throw new CramMalformedError('file contains no containers');
         }
-        const { content } = await firstContainer.getFirstBlock();
+        const firstBlock = await firstContainer.getFirstBlock();
+        if (firstBlock === undefined) {
+            return parseHeaderText('');
+        }
+        const content = firstBlock.content;
         // find the end of the trailing zeros in the header text
         const headerLength = content.readInt32LE(0);
         const textStart = 4;
@@ -134,6 +129,9 @@ export default class CramFile {
                 position = currentHeader._endPosition;
                 for (let j = 0; j < currentHeader.numBlocks; j += 1) {
                     const block = await this.readBlock(position);
+                    if (block === undefined) {
+                        return undefined;
+                    }
                     position = block._endPosition;
                 }
             }
@@ -173,6 +171,9 @@ export default class CramFile {
                 position = currentHeader._endPosition;
                 for (let j = 0; j < currentHeader.numBlocks; j += 1) {
                     const block = await this.readBlock(position);
+                    if (block === undefined) {
+                        return undefined;
+                    }
                     position = block._endPosition;
                 }
             }
@@ -198,7 +199,7 @@ export default class CramFile {
         await this.file.read(buffer, 0, cramBlockHeader.maxLength, position);
         return parseItem(buffer, cramBlockHeader.parser, 0, position);
     }
-    async _parseSection(section, position, size = section.maxLength, preReadBuffer) {
+    async _parseSection(section, position, size = section.maxLength, preReadBuffer = undefined) {
         let buffer;
         if (preReadBuffer) {
             buffer = preReadBuffer;
@@ -223,11 +224,12 @@ export default class CramFile {
             result.copy(outputBuffer);
         }
         else if (compressionMethod === 'bzip2') {
-            var bits = bzip2.array(inputBuffer);
-            var size = bzip2.header(bits);
-            var j = 0;
+            const bits = bzip2.array(inputBuffer);
+            let size = bzip2.header(bits);
+            let j = 0;
+            let chunk;
             do {
-                var chunk = bzip2.decompress(bits, size);
+                chunk = bzip2.decompress(bits, size);
                 if (chunk != -1) {
                     Buffer.from(chunk).copy(outputBuffer, j);
                     j += chunk.length;
@@ -259,26 +261,36 @@ export default class CramFile {
     async readBlock(position) {
         const { majorVersion } = await this.getDefinition();
         const sectionParsers = await this.getSectionParsers();
-        const block = await this.readBlockHeader(position);
-        const blockContentPosition = block._endPosition;
-        block.contentPosition = block._endPosition;
-        const uncompressedData = Buffer.allocUnsafe(block.uncompressedSize);
-        if (block.compressionMethod !== 'raw') {
-            const compressedData = Buffer.allocUnsafe(block.compressedSize);
-            await this.read(compressedData, 0, block.compressedSize, blockContentPosition);
-            this._uncompress(block.compressionMethod, compressedData, uncompressedData);
+        const blockHeader = await this.readBlockHeader(position);
+        if (blockHeader === undefined) {
+            return undefined;
+        }
+        const blockContentPosition = blockHeader._endPosition;
+        const uncompressedData = Buffer.allocUnsafe(blockHeader.uncompressedSize);
+        const block = {
+            ...blockHeader,
+            _endPosition: blockContentPosition,
+            contentPosition: blockContentPosition,
+            content: uncompressedData,
+        };
+        if (blockHeader.compressionMethod !== 'raw') {
+            const compressedData = Buffer.allocUnsafe(blockHeader.compressedSize);
+            await this.read(compressedData, 0, blockHeader.compressedSize, blockContentPosition);
+            this._uncompress(blockHeader.compressionMethod, compressedData, uncompressedData);
         }
         else {
-            await this.read(uncompressedData, 0, block.uncompressedSize, blockContentPosition);
+            await this.read(uncompressedData, 0, blockHeader.uncompressedSize, blockContentPosition);
         }
-        block.content = uncompressedData;
         if (majorVersion >= 3) {
             // parse the crc32
-            const crc = await this._parseSection(sectionParsers.cramBlockCrc32, blockContentPosition + block.compressedSize);
+            const crc = await this._parseSection(sectionParsers.cramBlockCrc32, blockContentPosition + blockHeader.compressedSize);
+            if (crc === undefined) {
+                return undefined;
+            }
             block.crc32 = crc.crc32;
             // check the block data crc32
             if (this.validateChecksums) {
-                await this.checkCrc32(position, block._size + block.compressedSize, block.crc32, 'block data');
+                await this.checkCrc32(position, blockHeader._size + blockHeader.compressedSize, crc.crc32, 'block data');
             }
             // make the endposition and size reflect the whole block
             block._endPosition = crc._endPosition;

package/esm/cramFile/file.js.map

@@ -1 +1 @@
-{"version":3,"file":"file.js","sourceRoot":"","sources":["../../src/cramFile/file.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,UAAU,CAAA;AAChC,OAAO,KAAK,MAAM,cAAc,CAAA;AAChC,OAAO,GAAG,MAAM,WAAW,CAAA;AAE3B,OAAO,EAAE,sBAAsB,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AACtE,OAAO,cAAc,MAAM,SAAS,CAAA;AACpC,OAAO,EACL,kBAAkB,IAAI,wBAAwB,EAC9C,iBAAiB,GAClB,MAAM,kBAAkB,CAAA;AACzB,OAAO,SAAS,MAAM,uBAAuB,CAAA;AAC7C,OAAO,aAAa,MAAM,aAAa,CAAA;AAEvC,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAC5B,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,QAAQ,CAAA;AACxC,+EAA+E;AAC/E,SAAS,aAAa;IACpB,IAAI,MAAM,GAAG,IAAI,WAAW,CAAC,CAAC,UAAU,CAAC,CAAC,CAAA;IAC1C,IAAI,KAAK,GAAG,IAAI,UAAU,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;IAEzC,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;QACrB,OAAO,CAAC,CAAA,CAAC,eAAe;KACzB;SAAM,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;QAC5B,OAAO,CAAC,CAAA,CAAC,YAAY;KACtB;SAAM;QACL,OAAO,CAAC,CAAA,CAAC,eAAe;KACzB;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,QAAQ;IAC3B;;;;;;;;;;;OAWG;IACH,YAAY,IAAI;QACd,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QACtD,IAAI,CAAC,iBAAiB,GAAG,IAAI,CAAA;QAC7B,IAAI,CAAC,8BAA8B,GAAG,IAAI,CAAC,QAAQ,CAAA;QACnD,IAAI,CAAC,OAAO,GAAG;YACb,gBAAgB,EAAE,IAAI,CAAC,gBAAgB,KAAK,KAAK;YACjD,SAAS,EAAE,IAAI,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK;SACjE,CAAA;QAED,6CAA6C;QAC7C,gEAAgE;QAChE,4DAA4D;QAC5D,qCAAqC;QACrC,IAAI,CAAC,YAAY,GAAG,IAAI,GAAG,CAAC;YAC1B,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,SAAS;SAChC,CAAC,CAAA;QACF,IAAI,aAAa,EAAE,GAAG,CAAC,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;SACrE;IACH,CAAC;IAED,QAAQ;QACN,IAAI,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE;YACtB,OAAO,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAA;SAC1B;QACD,IAAI,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE;YACjB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAA;SACrB;QAED,OAAO,aAAa,CAAA;IACtB,CAAC;IAED,8CAA8C;IAC9C,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ;QACnC,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;IACzD,CAAC;IAED,8CAA8C;IAC9C,IAAI;QACF,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACzB,CAAC;IAED,WAAW;IACX,KAAK,CAAC,aAAa;QACjB,MAAM,SAAS,GAAG,MAAM,CAAC,WAAW,CAAC,wBAAwB,CAAC,SAAS,CAAC,CAAA;QACxE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,EAAE,wBAAwB,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QACzE,MAAM,UAAU,GAAG,wBAAwB,CAAC,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAA;QAC1E,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,EAAE;YAClE,MAAM,IAAI,sBAAsB,CAC9B,gBAAgB,UAAU,CAAC,YAAY,gBAAgB,CACxD,CAAA;SACF;QACD,OAAO,UAAU,CAAA;IACnB,CAAC;IAED,UAAU;IACV,KAAK,CAAC,YAAY;QAChB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAA;QACrD,IAAI,CAAC,cAAc,EAAE;YACnB,MAAM,IAAI,kBAAkB,CAAC,6BAA6B,CAAC,CAAA;SAC5D;QAED,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,cAAc,CAAC,aAAa,EAAE,CAAA;QACxD,wDAAwD;QACxD,MAAM,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3C,MAAM,SAAS,GAAG,CAAC,CAAA;QACnB,mCAAmC;QACnC,iEAAiE;QACjE,8BAA8B;QAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,MAAM,EAAE,SAAS,EAAE,SAAS,GAAG,YAAY,CAAC,CAAA;QAC1E,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;QAClB,OAAO,eAAe,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,IAAI,CAAC,YAAY,EAAE,CAAA;QACzB,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,UAAU;IACV,KAAK,CAAC,iBAAiB;QACrB,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACnD,OAAO,iBAAiB,CAAC,YAAY,CAAC,CAAA;IACxC,CAAC;IAED,KAAK,CAAC,gBAAgB,CAAC,eAAe;QACpC,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,IAAI,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;QAC1D,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QACjD,MAAM,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QAE/C,sDAAsD;QACtD,IAAI,gBAAgB,CAAA;QACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,eAAe,EAAE,CAAC,IAAI,CAAC,EAAE;YAC5C,gDAAgD;YAChD,uDAAuD;YACvD,IAAI,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,IAAI,QAAQ,EAAE;gBAC7D,OAAO,SAAS,CAAA;aACjB;YAED,gBAAgB,GAAG,IAAI,CAAC,sBAAsB,CAAC,QAAQ,CAAC,CAAA;YACxD,MAAM,aAAa,GAAG,MAAM,gBAAgB,CAAC,SAAS,EAAE,CAAA;YACxD,IAAI,CAAC,aAAa,EAAE;gBAClB,MAAM,IAAI,kBAAkB,CAC1B,aAAa,eAAe,oBAAoB,CACjD,CAAA;aACF;YACD,6DAA6D;YAC7D,6DAA6D;YAC7D,6DAA6D;YAC7D,YAAY;YACZ,IAAI,CAAC,KAAK,CAAC,EAAE;gBACX,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;gBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;oBACnD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;oBAC5C,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;iBAC9B;aACF;iBAAM;gBACL,8EAA8E;gBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;aACvD;SACF;QAED,OAAO,gBAAgB,CAAA;IACzB,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,aAAa,EAAE,WAAW;QAC3D,MAAM,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QACpC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;QAC5C,MAAM,eAAe,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACzC,IAAI,eAAe,KAAK,aAAa,EAAE;YACrC,MAAM,IAAI,kBAAkB,CAC1B,mBAAmB,WAAW,sBAAsB,aAAa,4BAA4B,eAAe,EAAE,CAC/G,CAAA;SACF;IACH,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,cAAc;QAClB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QACjD,MAAM,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QAE/C,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,IAAI,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;QAC1D,OAAO,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,GAAG,QAAQ,EAAE;YAC/D,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,sBAAsB,CACrD,QAAQ,CACT,CAAC,SAAS,EAAE,CAAA;YACb,IAAI,CAAC,aAAa,EAAE;gBAClB,MAAK;aACN;YACD,6DAA6D;YAC7D,mDAAmD;YACnD,yDAAyD;YACzD,IAAI,cAAc,KAAK,CAAC,EAAE;gBACxB,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;gBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;oBACnD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;oBAC5C,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;iBAC9B;aACF;iBAAM;gBACL,8EAA8E;gBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;aACvD;YACD,cAAc,IAAI,CAAC,CAAA;SACpB;QAED,OAAO,cAAc,CAAA;IACvB,CAAC;IAED,sBAAsB,CAAC,QAAQ;QAC7B,OAAO,IAAI,aAAa,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;IAC1C,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,QAAQ;QAC5B,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,EAAE,eAAe,EAAE,GAAG,cAAc,CAAA;QAC1C,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QAEjD,IAAI,QAAQ,GAAG,eAAe,CAAC,SAAS,IAAI,QAAQ,EAAE;YACpD,OAAO,SAAS,CAAA;SACjB;QAED,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,eAAe,CAAC,SAAS,CAAC,CAAA;QAC5D,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,eAAe,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;QACpE,OAAO,SAAS,CAAC,MAAM,EAAE,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;IAC/D,CAAC;IAED,KAAK,CAAC,aAAa,CACjB,OAAO,EACP,QAAQ,EACR,IAAI,GAAG,OAAO,CAAC,SAAS,EACxB,aAAa;QAEb,IAAI,MAAM,CAAA;QACV,IAAI,aAAa,EAAE;YACjB,MAAM,GAAG,aAAa,CAAA;SACvB;aAAM;YACL,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;YACjD,IAAI,QAAQ,GAAG,IAAI,IAAI,QAAQ,EAAE;gBAC/B,OAAO,SAAS,CAAA;aACjB;YACD,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;YACjC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,IAAI,EAAE,QAAQ,CAAC,CAAA;SAChD;QACD,MAAM,IAAI,GAAG,SAAS,CAAC,MAAM,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QAC3D,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,MAAM,IAAI,kBAAkB,CAC1B,sCAAsC,IAAI,+BAA+B,IAAI,CAAC,KAAK,EAAE,CACtF,CAAA;SACF;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,WAAW,CAAC,iBAAiB,EAAE,WAAW,EAAE,YAAY;QACtD,IAAI,iBAAiB,KAAK,MAAM,EAAE;YAChC,MAAM,MAAM,GAAG,KAAK,CAAC,WAAW,CAAC,CAAA;YACjC,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;SAC1B;aAAM,IAAI,iBAAiB,KAAK,OAAO,EAAE;YACxC,IAAI,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;YACnC,IAAI,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YAC7B,IAAI,CAAC,GAAG,CAAC,CAAA;YACT,GAAG;gBACD,IAAI,KAAK,GAAG,KAAK,CAAC,UAAU,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBACxC,IAAI,KAAK,IAAI,CAAC,CAAC,EAAE;oBACf,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC,CAAA;oBACxC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAA;oBACjB,IAAI,IAAI,KAAK,CAAC,MAAM,CAAA;iBACrB;aACF,QAAQ,KAAK,IAAI,CAAC,CAAC,EAAC;SACtB;aAAM,IAAI,iBAAiB,KAAK,MAAM,EAAE;YACvC,cAAc,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;YACzC,2CAA2C;YAC3C,uDAAuD;SACxD;aAAM,IAAI,iBAAiB,KAAK,UAAU,EAAE;YAC3C,SAAS,CAAC,gBAAgB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACtD;aAAM,IAAI,iBAAiB,KAAK,OAAO,EAAE;YACxC,SAAS,CAAC,gBAAgB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACtD;aAAM,IAAI,iBAAiB,KAAK,SAAS,EAAE;YAC1C,SAAS,CAAC,kBAAkB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACxD;aAAM,IAAI,iBAAiB,KAAK,MAAM,EAAE;YACvC,SAAS,CAAC,eAAe,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACrD;aAAM;YACL,MAAM,IAAI,sBAAsB,CAC9B,GAAG,iBAAiB,oCAAoC,CACzD,CAAA;SACF;IACH,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,QAAQ;QACtB,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACnD,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,QAAQ,CAAC,CAAA;QAClD,MAAM,oBAAoB,GAAG,KAAK,CAAC,YAAY,CAAA;QAC/C,KAAK,CAAC,eAAe,GAAG,KAAK,CAAC,YAAY,CAAA;QAE1C,MAAM,gBAAgB,GAAG,MAAM,CAAC,WAAW,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAA;QAEnE,IAAI,KAAK,CAAC,iBAAiB,KAAK,KAAK,EAAE;YACrC,MAAM,cAAc,GAAG,MAAM,CAAC,WAAW,CAAC,KAAK,CAAC,cAAc,CAAC,CAAA;YAC/D,MAAM,IAAI,CAAC,IAAI,CACb,cAAc,EACd,CAAC,EACD,KAAK,CAAC,cAAc,EACpB,oBAAoB,CACrB,CAAA;YAED,IAAI,CAAC,WAAW,CACd,KAAK,CAAC,iBAAiB,EACvB,cAAc,EACd,gBAAgB,CACjB,CAAA;SACF;aAAM;YACL,MAAM,IAAI,CAAC,IAAI,CACb,gBAAgB,EAChB,CAAC,EACD,KAAK,CAAC,gBAAgB,EACtB,oBAAoB,CACrB,CAAA;SACF;QAED,KAAK,CAAC,OAAO,GAAG,gBAAgB,CAAA;QAEhC,IAAI,YAAY,IAAI,CAAC,EAAE;YACrB,kBAAkB;YAClB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,aAAa,CAClC,cAAc,CAAC,cAAc,EAC7B,oBAAoB,GAAG,KAAK,CAAC,cAAc,CAC5C,CAAA;YACD,KAAK,CAAC,KAAK,GAAG,GAAG,CAAC,KAAK,CAAA;YAEvB,6BAA6B;YAC7B,IAAI,IAAI,CAAC,iBAAiB,EAAE;gBAC1B,MAAM,IAAI,CAAC,UAAU,CACnB,QAAQ,EACR,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,cAAc,EAClC,KAAK,CAAC,KAAK,EACX,YAAY,CACb,CAAA;aACF;YAED,wDAAwD;YACxD,KAAK,CAAC,YAAY,GAAG,GAAG,CAAC,YAAY,CAAA;YACrC,KAAK,CAAC,KAAK;gBACT,KAAK,CAAC,cAAc,GAAG,cAAc,CAAC,cAAc,CAAC,SAAS,CAAA;SACjE;aAAM;YACL,KAAK,CAAC,YAAY,GAAG,oBAAoB,GAAG,KAAK,CAAC,cAAc,CAAA;YAChE,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,cAAc,CAAA;SACnC;QAED,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AAED,8CAA8C;KAC3C,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAAA"}
+{"version":3,"file":"file.js","sourceRoot":"","sources":["../../src/cramFile/file.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,UAAU,CAAA;AAChC,OAAO,KAAK,MAAM,cAAc,CAAA;AAChC,OAAO,QAAQ,MAAM,WAAW,CAAA;AAEhC,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AACtE,OAAO,cAAc,MAAM,SAAS,CAAA;AACpC,OAAO,EAGL,kBAAkB,IAAI,wBAAwB,EAC9C,iBAAiB,GAClB,MAAM,kBAAkB,CAAA;AACzB,OAAO,SAAS,MAAM,uBAAuB,CAAA;AAC7C,OAAO,aAAa,MAAM,aAAa,CAAA;AAEvC,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAC5B,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,QAAQ,CAAA;AAKxC,+EAA+E;AAC/E,SAAS,aAAa;IACpB,MAAM,MAAM,GAAG,IAAI,WAAW,CAAC,CAAC,UAAU,CAAC,CAAC,CAAA;IAC5C,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;IAE3C,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;QACrB,OAAO,CAAC,CAAA,CAAC,eAAe;KACzB;SAAM,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;QAC5B,OAAO,CAAC,CAAA,CAAC,YAAY;KACtB;SAAM;QACL,OAAO,CAAC,CAAA,CAAC,eAAe;KACzB;AACH,CAAC;AAiCD,MAAM,CAAC,OAAO,OAAO,QAAQ;IAW3B,YAAY,IAAkB;;QAC5B,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QACtD,IAAI,CAAC,iBAAiB,GAAG,IAAI,CAAA;QAC7B,IAAI,CAAC,8BAA8B,GAAG,IAAI,CAAC,QAAQ,CAAA;QACnD,IAAI,CAAC,OAAO,GAAG;YACb,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;YACvC,SAAS,EAAE,MAAA,IAAI,CAAC,SAAS,mCAAI,KAAK;SACnC,CAAA;QAED,6CAA6C;QAC7C,gEAAgE;QAChE,4DAA4D;QAC5D,qCAAqC;QACrC,IAAI,CAAC,YAAY,GAAG,IAAI,QAAQ,CAAC;YAC/B,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,SAAS;SAChC,CAAC,CAAA;QACF,IAAI,aAAa,EAAE,GAAG,CAAC,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;SACrE;IACH,CAAC;IAED,eAAe;IACf,8BAA8B;IAC9B,gCAAgC;IAChC,MAAM;IACN,yBAAyB;IACzB,2BAA2B;IAC3B,MAAM;IACN,EAAE;IACF,yBAAyB;IACzB,IAAI;IAEJ,8CAA8C;IAC9C,IAAI,CACF,MAAc,EACd,MAAc,EACd,MAAc,EACd,QAAgB;QAKhB,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;IACzD,CAAC;IAED,8CAA8C;IAC9C,IAAI;QACF,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACzB,CAAC;IAED,WAAW;IACX,KAAK,CAAC,aAAa;QACjB,MAAM,SAAS,GAAG,MAAM,CAAC,WAAW,CAAC,wBAAwB,CAAC,SAAS,CAAC,CAAA;QACxE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,EAAE,wBAAwB,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QACzE,MAAM,UAAU,GAAG,wBAAwB,CAAC,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC;aAChE,MAAa,CAAA;QAChB,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,EAAE;YAClE,MAAM,IAAI,sBAAsB,CAC9B,gBAAgB,UAAU,CAAC,YAAY,gBAAgB,CACxD,CAAA;SACF;QACD,OAAO,UAAU,CAAA;IACnB,CAAC;IAED,UAAU;IACV,KAAK,CAAC,YAAY;QAChB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAA;QACrD,IAAI,CAAC,cAAc,EAAE;YACnB,MAAM,IAAI,kBAAkB,CAAC,6BAA6B,CAAC,CAAA;SAC5D;QAED,MAAM,UAAU,GAAG,MAAM,cAAc,CAAC,aAAa,EAAE,CAAA;QACvD,IAAI,UAAU,KAAK,SAAS,EAAE;YAC5B,OAAO,eAAe,CAAC,EAAE,CAAC,CAAA;SAC3B;QACD,MAAM,OAAO,GAAG,UAAU,CAAC,OAAO,CAAA;QAClC,wDAAwD;QACxD,MAAM,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3C,MAAM,SAAS,GAAG,CAAC,CAAA;QACnB,mCAAmC;QACnC,iEAAiE;QACjE,8BAA8B;QAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,MAAM,EAAE,SAAS,EAAE,SAAS,GAAG,YAAY,CAAC,CAAA;QAC1E,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;QAClB,OAAO,eAAe,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,IAAI,CAAC,YAAY,EAAE,CAAA;QACzB,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,UAAU;IACV,KAAK,CAAC,iBAAiB;QACrB,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACnD,OAAO,iBAAiB,CAAC,YAAY,CAAC,CAAA;IACxC,CAAC;IAED,KAAK,CAAC,gBAAgB,CAAC,eAAuB;QAC5C,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,IAAI,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;QAC1D,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QACjD,MAAM,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QAE/C,sDAAsD;QACtD,IAAI,gBAAgB,CAAA;QACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,eAAe,EAAE,CAAC,IAAI,CAAC,EAAE;YAC5C,gDAAgD;YAChD,uDAAuD;YACvD,IAAI,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,IAAI,QAAQ,EAAE;gBAC7D,OAAO,SAAS,CAAA;aACjB;YAED,gBAAgB,GAAG,IAAI,CAAC,sBAAsB,CAAC,QAAQ,CAAC,CAAA;YACxD,MAAM,aAAa,GAAG,MAAM,gBAAgB,CAAC,SAAS,EAAE,CAAA;YACxD,IAAI,CAAC,aAAa,EAAE;gBAClB,MAAM,IAAI,kBAAkB,CAC1B,aAAa,eAAe,oBAAoB,CACjD,CAAA;aACF;YACD,6DAA6D;YAC7D,6DAA6D;YAC7D,6DAA6D;YAC7D,YAAY;YACZ,IAAI,CAAC,KAAK,CAAC,EAAE;gBACX,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;gBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;oBACnD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;oBAC5C,IAAI,KAAK,KAAK,SAAS,EAAE;wBACvB,OAAO,SAAS,CAAA;qBACjB;oBACD,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;iBAC9B;aACF;iBAAM;gBACL,8EAA8E;gBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;aACvD;SACF;QAED,OAAO,gBAAgB,CAAA;IACzB,CAAC;IAED,KAAK,CAAC,UAAU,CACd,QAAgB,EAChB,MAAc,EACd,aAAqB,EACrB,WAAmB;QAEnB,MAAM,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QACpC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;QAC5C,MAAM,eAAe,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACzC,IAAI,eAAe,KAAK,aAAa,EAAE;YACrC,MAAM,IAAI,kBAAkB,CAC1B,mBAAmB,WAAW,sBAAsB,aAAa,4BAA4B,eAAe,EAAE,CAC/G,CAAA;SACF;IACH,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,cAAc;QAClB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QACjD,MAAM,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QAE/C,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,IAAI,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;QAC1D,OAAO,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,GAAG,QAAQ,EAAE;YAC/D,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,sBAAsB,CACrD,QAAQ,CACT,CAAC,SAAS,EAAE,CAAA;YACb,IAAI,CAAC,aAAa,EAAE;gBAClB,MAAK;aACN;YACD,6DAA6D;YAC7D,mDAAmD;YACnD,yDAAyD;YACzD,IAAI,cAAc,KAAK,CAAC,EAAE;gBACxB,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;gBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;oBACnD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;oBAC5C,IAAI,KAAK,KAAK,SAAS,EAAE;wBACvB,OAAO,SAAS,CAAA;qBACjB;oBACD,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;iBAC9B;aACF;iBAAM;gBACL,8EAA8E;gBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;aACvD;YACD,cAAc,IAAI,CAAC,CAAA;SACpB;QAED,OAAO,cAAc,CAAA;IACvB,CAAC;IAED,sBAAsB,CAAC,QAAgB;QACrC,OAAO,IAAI,aAAa,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;IAC1C,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,QAAgB;QACpC,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,EAAE,eAAe,EAAE,GAAG,cAAc,CAAA;QAC1C,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QAEjD,IAAI,QAAQ,GAAG,eAAe,CAAC,SAAS,IAAI,QAAQ,EAAE;YACpD,OAAO,SAAS,CAAA;SACjB;QAED,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,eAAe,CAAC,SAAS,CAAC,CAAA;QAC5D,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,eAAe,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;QACpE,OAAO,SAAS,CAAC,MAAM,EAAE,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;IAC/D,CAAC;IAED,KAAK,CAAC,aAAa,CACjB,OAAiD,EACjD,QAAgB,EAChB,IAAI,GAAG,OAAO,CAAC,SAAS,EACxB,aAAa,GAAG,SAAS;QAEzB,IAAI,MAAM,CAAA;QACV,IAAI,aAAa,EAAE;YACjB,MAAM,GAAG,aAAa,CAAA;SACvB;aAAM;YACL,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;YACjD,IAAI,QAAQ,GAAG,IAAI,IAAI,QAAQ,EAAE;gBAC/B,OAAO,SAAS,CAAA;aACjB;YACD,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;YACjC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,IAAI,EAAE,QAAQ,CAAC,CAAA;SAChD;QACD,MAAM,IAAI,GAAG,SAAS,CAAC,MAAM,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QAC3D,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,MAAM,IAAI,kBAAkB,CAC1B,sCAAsC,IAAI,+BAA+B,IAAI,CAAC,KAAK,EAAE,CACtF,CAAA;SACF;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,WAAW,CACT,iBAAoC,EACpC,WAAmB,EACnB,YAAoB;QAEpB,IAAI,iBAAiB,KAAK,MAAM,EAAE;YAChC,MAAM,MAAM,GAAG,KAAK,CAAC,WAAW,CAAC,CAAA;YACjC,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;SAC1B;aAAM,IAAI,iBAAiB,KAAK,OAAO,EAAE;YACxC,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;YACrC,IAAI,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YAC7B,IAAI,CAAC,GAAG,CAAC,CAAA;YACT,IAAI,KAAK,CAAA;YACT,GAAG;gBACD,KAAK,GAAG,KAAK,CAAC,UAAU,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBACpC,IAAI,KAAK,IAAI,CAAC,CAAC,EAAE;oBACf,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC,CAAA;oBACxC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAA;oBACjB,IAAI,IAAI,KAAK,CAAC,MAAM,CAAA;iBACrB;aACF,QAAQ,KAAK,IAAI,CAAC,CAAC,EAAC;SACtB;aAAM,IAAI,iBAAiB,KAAK,MAAM,EAAE;YACvC,cAAc,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;YACzC,2CAA2C;YAC3C,uDAAuD;SACxD;aAAM,IAAI,iBAAiB,KAAK,UAAU,EAAE;YAC3C,SAAS,CAAC,gBAAgB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACtD;aAAM,IAAI,iBAAiB,KAAK,OAAO,EAAE;YACxC,SAAS,CAAC,gBAAgB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACtD;aAAM,IAAI,iBAAiB,KAAK,SAAS,EAAE;YAC1C,SAAS,CAAC,kBAAkB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACxD;aAAM,IAAI,iBAAiB,KAAK,MAAM,EAAE;YACvC,SAAS,CAAC,eAAe,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACrD;aAAM;YACL,MAAM,IAAI,sBAAsB,CAC9B,GAAG,iBAAiB,oCAAoC,CACzD,CAAA;SACF;IACH,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,QAAgB;QAC9B,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACnD,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,QAAQ,CAAC,CAAA;QACxD,IAAI,WAAW,KAAK,SAAS,EAAE;YAC7B,OAAO,SAAS,CAAA;SACjB;QACD,MAAM,oBAAoB,GAAG,WAAW,CAAC,YAAY,CAAA;QAErD,MAAM,gBAAgB,GAAG,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,gBAAgB,CAAC,CAAA;QAEzE,MAAM,KAAK,GAAkB;YAC3B,GAAG,WAAW;YACd,YAAY,EAAE,oBAAoB;YAClC,eAAe,EAAE,oBAAoB;YACrC,OAAO,EAAE,gBAAgB;SAC1B,CAAA;QAED,IAAI,WAAW,CAAC,iBAAiB,KAAK,KAAK,EAAE;YAC3C,MAAM,cAAc,GAAG,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,cAAc,CAAC,CAAA;YACrE,MAAM,IAAI,CAAC,IAAI,CACb,cAAc,EACd,CAAC,EACD,WAAW,CAAC,cAAc,EAC1B,oBAAoB,CACrB,CAAA;YAED,IAAI,CAAC,WAAW,CACd,WAAW,CAAC,iBAAiB,EAC7B,cAAc,EACd,gBAAgB,CACjB,CAAA;SACF;aAAM;YACL,MAAM,IAAI,CAAC,IAAI,CACb,gBAAgB,EAChB,CAAC,EACD,WAAW,CAAC,gBAAgB,EAC5B,oBAAoB,CACrB,CAAA;SACF;QAED,IAAI,YAAY,IAAI,CAAC,EAAE;YACrB,kBAAkB;YAClB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,aAAa,CAClC,cAAc,CAAC,cAAc,EAC7B,oBAAoB,GAAG,WAAW,CAAC,cAAc,CAClD,CAAA;YACD,IAAI,GAAG,KAAK,SAAS,EAAE;gBACrB,OAAO,SAAS,CAAA;aACjB;YACD,KAAK,CAAC,KAAK,GAAG,GAAG,CAAC,KAAK,CAAA;YAEvB,6BAA6B;YAC7B,IAAI,IAAI,CAAC,iBAAiB,EAAE;gBAC1B,MAAM,IAAI,CAAC,UAAU,CACnB,QAAQ,EACR,WAAW,CAAC,KAAK,GAAG,WAAW,CAAC,cAAc,EAC9C,GAAG,CAAC,KAAK,EACT,YAAY,CACb,CAAA;aACF;YAED,wDAAwD;YACxD,KAAK,CAAC,YAAY,GAAG,GAAG,CAAC,YAAY,CAAA;YACrC,KAAK,CAAC,KAAK;gBACT,KAAK,CAAC,cAAc,GAAG,cAAc,CAAC,cAAc,CAAC,SAAS,CAAA;SACjE;aAAM;YACL,KAAK,CAAC,YAAY,GAAG,oBAAoB,GAAG,KAAK,CAAC,cAAc,CAAA;YAChE,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,cAAc,CAAA;SACnC;QAED,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AAED,8CAA8C;KAC3C,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAAA"}

package/esm/cramFile/filehandle.d.ts

@@ -0,0 +1,2 @@
+import { GenericFilehandle } from 'generic-filehandle';
+export { GenericFilehandle as Filehandle };

package/esm/cramFile/filehandle.js

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

package/esm/cramFile/filehandle.js.map

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

package/esm/cramFile/index.d.ts

@@ -1,2 +1,2 @@
+import CramFile from './file';
 export default CramFile;
-import CramFile from "./file";

package/esm/cramFile/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.js"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,QAAQ,CAAA;AAE7B,eAAe,QAAQ,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,QAAQ,CAAA;AAE7B,eAAe,QAAQ,CAAA"}

package/esm/cramFile/record.d.ts

@@ -1,8 +1,63 @@
+import CramContainerCompressionScheme from './container/compressionScheme';
+import decodeRecord from './slice/decodeRecord';
+export declare type RefRegion = {
+    start: number;
+    end: number;
+    seq: string;
+};
+export declare type ReadFeature = {
+    code: string;
+    pos: number;
+    refPos: number;
+    data: any;
+    ref?: string;
+    sub?: string;
+};
+export declare type 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"]];
+declare type FlagsDecoder<Type> = {
+    [Property in Type as `is${Capitalize<string & Property>}`]: (flags: number) => boolean;
+};
+declare type FlagsEncoder<Type> = {
+    [Property in Type as `set${Capitalize<string & Property>}`]: (flags: number) => number;
+};
+export declare const BamFlagsDecoder: FlagsDecoder<"Paired" | "ProperlyPaired" | "SegmentUnmapped" | "MateUnmapped" | "ReverseComplemented" | "MateReverseComplemented" | "Read1" | "Read2" | "Secondary" | "FailedQc" | "Duplicate" | "Supplementary"> & FlagsEncoder<"Paired" | "ProperlyPaired" | "SegmentUnmapped" | "MateUnmapped" | "ReverseComplemented" | "MateReverseComplemented" | "Read1" | "Read2" | "Secondary" | "FailedQc" | "Duplicate" | "Supplementary">;
+export declare const CramFlagsDecoder: FlagsDecoder<"PreservingQualityScores" | "Detached" | "WithMateDownstream" | "DecodeSequenceAsStar"> & FlagsEncoder<"PreservingQualityScores" | "Detached" | "WithMateDownstream" | "DecodeSequenceAsStar">;
+export declare const MateFlagsDecoder: FlagsDecoder<"OnNegativeStrand" | "Unmapped"> & FlagsEncoder<"OnNegativeStrand" | "Unmapped">;
 /**
  * Class of each CRAM record returned by this API.
  */
 export default class CramRecord {
-    tags: {};
+    tags: Record<string, string>;
+    flags: number;
+    cramFlags: number;
+    readBases?: string | null;
+    _refRegion?: RefRegion;
+    readFeatures?: ReadFeature[];
+    alignmentStart: number;
+    lengthOnRef: number | undefined;
+    readLength: number;
+    templateLength?: number;
+    templateSize?: number;
+    readName?: string;
+    mateRecordNumber?: number;
+    mate?: MateRecord;
+    uniqueId: number;
+    sequenceId: number;
+    readGroupId: number;
+    mappingQuality: number | undefined;
+    qualityScores: number[] | null | undefined;
+    constructor({ flags, cramFlags, readLength, mappingQuality, lengthOnRef, qualityScores, mateRecordNumber, readBases, readFeatures, mateToUse, readGroupId, readName, sequenceId, uniqueId, templateSize, alignmentStart, tags, }: ReturnType<typeof decodeRecord> & {
+        uniqueId: number;
+    });
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
      */
@@ -43,13 +98,12 @@ export default class CramRecord {
      * Get the original sequence of this read.
      * @returns {String} sequence basepairs
      */
-    getReadBases(): string;
-    readBases: any;
+    getReadBases(): string | null | undefined;
     /**
      * Get the pair orientation of a paired read. Adapted from igv.js
      * @returns {String} of paired orientatin
      */
-    getPairOrientation(): string;
+    getPairOrientation(): string | null;
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base
@@ -63,17 +117,7 @@ export default class CramRecord {
      * @param {CramContainerCompressionScheme} compressionScheme
      * @returns {undefined} nothing
      */
-    addReferenceSequence(refRegion: {
-        start: number;
-        end: number;
-        seq: string;
-    }, compressionScheme: CramContainerCompressionScheme): undefined;
-    _refRegion: {
-        start: number;
-        end: number;
-        seq: string;
-    } | undefined;
-    toJSON(): {
-        readBases: string;
-    };
+    addReferenceSequence(refRegion: RefRegion, compressionScheme: CramContainerCompressionScheme): void;
+    toJSON(): any;
 }
+export {};

package/esm/cramFile/record.js

@@ -2,10 +2,10 @@ import Constants from './constants';
 function decodeReadSequence(cramRecord, refRegion) {
     // if it has no length, it has no sequence
     if (!cramRecord.lengthOnRef && !cramRecord.readLength) {
-        return undefined;
+        return null;
     }
     if (cramRecord.isUnknownBases()) {
-        return undefined;
+        return null;
     }
     // remember: all coordinates are 1-based closed
     const regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
@@ -122,12 +122,84 @@ function decodeBaseSubstitution(cramRecord, refRegion, compressionScheme, readFe
         readFeature.sub = base;
     }
 }
+export const BamFlags = [
+    [0x1, 'Paired'],
+    [0x2, 'ProperlyPaired'],
+    [0x4, 'SegmentUnmapped'],
+    [0x8, 'MateUnmapped'],
+    [0x10, 'ReverseComplemented'],
+    //  the mate is mapped to the reverse strand
+    [0x20, 'MateReverseComplemented'],
+    //  this is read1
+    [0x40, 'Read1'],
+    //  this is read2
+    [0x80, 'Read2'],
+    //  not primary alignment
+    [0x100, 'Secondary'],
+    //  QC failure
+    [0x200, 'FailedQc'],
+    //  optical or PCR duplicate
+    [0x400, 'Duplicate'],
+    //  supplementary alignment
+    [0x800, 'Supplementary'],
+];
+export const CramFlags = [
+    [0x1, 'PreservingQualityScores'],
+    [0x2, 'Detached'],
+    [0x4, 'WithMateDownstream'],
+    [0x8, 'DecodeSequenceAsStar'],
+];
+export const MateFlags = [
+    [0x1, 'OnNegativeStrand'],
+    [0x2, 'Unmapped'],
+];
+function makeFlagsHelper(x) {
+    const r = {};
+    for (const [code, name] of x) {
+        r['is' + name] = (flags) => !!(flags & code);
+        r['set' + name] = (flags) => flags | code;
+    }
+    return r;
+}
+export const BamFlagsDecoder = makeFlagsHelper(BamFlags);
+export const CramFlagsDecoder = makeFlagsHelper(CramFlags);
+export const MateFlagsDecoder = makeFlagsHelper(MateFlags);
 /**
  * Class of each CRAM record returned by this API.
  */
 export default class CramRecord {
-    constructor() {
-        this.tags = {};
+    constructor({ flags, cramFlags, readLength, mappingQuality, lengthOnRef, qualityScores, mateRecordNumber, readBases, readFeatures, mateToUse, readGroupId, readName, sequenceId, uniqueId, templateSize, alignmentStart, tags, }) {
+        this.flags = flags;
+        this.cramFlags = cramFlags;
+        this.readLength = readLength;
+        this.mappingQuality = mappingQuality;
+        this.lengthOnRef = lengthOnRef;
+        this.qualityScores = qualityScores;
+        if (readBases) {
+            this.readBases = readBases;
+        }
+        this.readGroupId = readGroupId;
+        this.readName = readName;
+        this.sequenceId = sequenceId;
+        this.uniqueId = uniqueId;
+        this.templateSize = templateSize;
+        this.alignmentStart = alignmentStart;
+        this.tags = tags;
+        // backwards compatibility
+        if (readFeatures) {
+            this.readFeatures = readFeatures;
+        }
+        if (mateToUse) {
+            this.mate = {
+                flags: mateToUse.mateFlags,
+                readName: mateToUse.mateReadName,
+                sequenceId: mateToUse.mateSequenceId,
+                alignmentStart: mateToUse.mateAlignmentStart,
+            };
+        }
+        if (mateRecordNumber) {
+            this.mateRecordNumber = mateRecordNumber;
+        }
     }
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
@@ -203,7 +275,10 @@ export default class CramRecord {
      */
     getReadBases() {
         if (!this.readBases && this._refRegion) {
-            this.readBases = decodeReadSequence(this, this._refRegion);
+            const decoded = decodeReadSequence(this, this._refRegion);
+            if (decoded) {
+                this.readBases = decoded;
+            }
         }
         return this.readBases;
     }
@@ -231,6 +306,9 @@ export default class CramRecord {
             }
             const tmp = [];
             let isize = this.templateLength || this.templateSize;
+            if (isize === undefined) {
+                throw new Error('One of templateSize and templateLength must be set');
+            }
             if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
                 isize = -isize;
             }