@gmod/cram 2.0.4 → 3.0.1

package/dist/cramFile/file.js

@@ -12,14 +12,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const unzip_1 = require("../unzip");
+const buffer_1 = require("buffer");
 const buffer_crc32_1 = __importDefault(require("buffer-crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
 const htscodecs_1 = __importDefault(require("@jkbonfield/htscodecs"));
-// @ts-expect-error
 const bzip2_1 = __importDefault(require("bzip2"));
 const xz_decompress_1 = require("xz-decompress");
 const errors_1 = require("../errors");
+// locals
+const unzip_1 = require("../unzip");
 const rans_1 = __importDefault(require("../rans"));
 const sectionParsers_1 = require("./sectionParsers");
 const container_1 = __importDefault(require("./container"));
@@ -34,18 +35,18 @@ function bufferToStream(buf) {
         },
     });
 }
-//source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
+// source: https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
 function getEndianness() {
     const uInt32 = new Uint32Array([0x11223344]);
     const uInt8 = new Uint8Array(uInt32.buffer);
     if (uInt8[0] === 0x44) {
-        return 0; //little-endian
+        return 0; // little-endian
     }
     else if (uInt8[0] === 0x11) {
-        return 1; //big-endian
+        return 1; // big-endian
     }
     else {
-        return 2; //mixed-endian?
+        return 2; // mixed-endian?
     }
 }
 class CramFile {
@@ -80,10 +81,10 @@ class CramFile {
     // memoized
     getDefinition() {
         return __awaiter(this, void 0, void 0, function* () {
-            const headbytes = Buffer.allocUnsafe(sectionParsers_1.cramFileDefinition.maxLength);
-            yield this.file.read(headbytes, 0, sectionParsers_1.cramFileDefinition.maxLength, 0);
-            const definition = sectionParsers_1.cramFileDefinition.parser.parse(headbytes)
-                .result;
+            const { maxLength, parser } = (0, sectionParsers_1.cramFileDefinition)();
+            const headbytes = buffer_1.Buffer.allocUnsafe(maxLength);
+            yield this.file.read(headbytes, 0, maxLength, 0);
+            const definition = parser(headbytes).value;
             if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
                 throw new errors_1.CramUnimplementedError(`CRAM version ${definition.majorVersion} not supported`);
             }
@@ -119,22 +120,16 @@ class CramFile {
             return this.header;
         });
     }
-    // memoize
-    getSectionParsers() {
-        return __awaiter(this, void 0, void 0, function* () {
-            const { majorVersion } = yield this.getDefinition();
-            return (0, sectionParsers_1.getSectionParsers)(majorVersion);
-        });
-    }
     getContainerById(containerNumber) {
         return __awaiter(this, void 0, void 0, function* () {
-            const sectionParsers = yield this.getSectionParsers();
+            const { majorVersion } = yield this.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             let position = sectionParsers.cramFileDefinition.maxLength;
             const { size: fileSize } = yield this.file.stat();
             const { cramContainerHeader1 } = sectionParsers;
             // skip with a series of reads to the proper container
             let currentContainer;
-            for (let i = 0; i <= containerNumber; i += 1) {
+            for (let i = 0; i <= containerNumber; i++) {
                 // if we are about to go off the end of the file
                 // and have not found that container, it does not exist
                 if (position + cramContainerHeader1.maxLength + 8 >= fileSize) {
@@ -145,13 +140,12 @@ class CramFile {
                 if (!currentHeader) {
                     throw new errors_1.CramMalformedError(`container ${containerNumber} not found in file`);
                 }
-                // if this is the first container, read all the blocks in the
-                // container to determine its length, because we cannot trust
-                // the container header's given length due to a bug somewhere
-                // in htslib
+                // if this is the first container, read all the blocks in the container
+                // to determine its length, because we cannot trust the container
+                // header's given length due to a bug somewhere in htslib
                 if (i === 0) {
                     position = currentHeader._endPosition;
-                    for (let j = 0; j < currentHeader.numBlocks; j += 1) {
+                    for (let j = 0; j < currentHeader.numBlocks; j++) {
                         const block = yield this.readBlock(position);
                         if (block === undefined) {
                             return undefined;
@@ -169,7 +163,7 @@ class CramFile {
     }
     checkCrc32(position, length, recordedCrc32, description) {
         return __awaiter(this, void 0, void 0, function* () {
-            const b = Buffer.allocUnsafe(length);
+            const b = buffer_1.Buffer.allocUnsafe(length);
             yield this.file.read(b, 0, length, position);
             const calculatedCrc32 = buffer_crc32_1.default.unsigned(b);
             if (calculatedCrc32 !== recordedCrc32) {
@@ -182,7 +176,8 @@ class CramFile {
      */
     containerCount() {
         return __awaiter(this, void 0, void 0, function* () {
-            const sectionParsers = yield this.getSectionParsers();
+            const { majorVersion } = yield this.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const { size: fileSize } = yield this.file.stat();
             const { cramContainerHeader1 } = sectionParsers;
             let containerCount = 0;
@@ -197,7 +192,7 @@ class CramFile {
                 // header's given length due to a bug somewhere in htslib
                 if (containerCount === 0) {
                     position = currentHeader._endPosition;
-                    for (let j = 0; j < currentHeader.numBlocks; j += 1) {
+                    for (let j = 0; j < currentHeader.numBlocks; j++) {
                         const block = yield this.readBlock(position);
                         if (block === undefined) {
                             return undefined;
@@ -219,13 +214,14 @@ class CramFile {
     }
     readBlockHeader(position) {
         return __awaiter(this, void 0, void 0, function* () {
-            const sectionParsers = yield this.getSectionParsers();
+            const { majorVersion } = yield this.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const { cramBlockHeader } = sectionParsers;
             const { size: fileSize } = yield this.file.stat();
             if (position + cramBlockHeader.maxLength >= fileSize) {
                 return undefined;
             }
-            const buffer = Buffer.allocUnsafe(cramBlockHeader.maxLength);
+            const buffer = buffer_1.Buffer.allocUnsafe(cramBlockHeader.maxLength);
             yield this.file.read(buffer, 0, cramBlockHeader.maxLength, position);
             return (0, util_1.parseItem)(buffer, cramBlockHeader.parser, 0, position);
         });
@@ -241,7 +237,7 @@ class CramFile {
                 if (position + size >= fileSize) {
                     return undefined;
                 }
-                buffer = Buffer.allocUnsafe(size);
+                buffer = buffer_1.Buffer.allocUnsafe(size);
                 yield this.file.read(buffer, 0, size, position);
             }
             const data = (0, util_1.parseItem)(buffer, section.parser, 0, position);
@@ -264,16 +260,16 @@ class CramFile {
                 let chunk;
                 do {
                     chunk = bzip2_1.default.decompress(bits, size);
-                    if (chunk != -1) {
-                        Buffer.from(chunk).copy(outputBuffer, j);
+                    if (chunk !== -1) {
+                        buffer_1.Buffer.from(chunk).copy(outputBuffer, j);
                         j += chunk.length;
                         size -= chunk.length;
                     }
-                } while (chunk != -1);
+                } while (chunk !== -1);
             }
             else if (compressionMethod === 'lzma') {
                 const decompressedResponse = new Response(new xz_decompress_1.XzReadableStream(bufferToStream(inputBuffer)));
-                const ret = Buffer.from(yield decompressedResponse.arrayBuffer());
+                const ret = buffer_1.Buffer.from(yield decompressedResponse.arrayBuffer());
                 ret.copy(outputBuffer);
             }
             else if (compressionMethod === 'rans') {
@@ -301,16 +297,16 @@ class CramFile {
     readBlock(position) {
         return __awaiter(this, void 0, void 0, function* () {
             const { majorVersion } = yield this.getDefinition();
-            const sectionParsers = yield this.getSectionParsers();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const blockHeader = yield this.readBlockHeader(position);
             if (blockHeader === undefined) {
                 return undefined;
             }
             const blockContentPosition = blockHeader._endPosition;
-            const uncompressedData = Buffer.allocUnsafe(blockHeader.uncompressedSize);
+            const uncompressedData = buffer_1.Buffer.allocUnsafe(blockHeader.uncompressedSize);
             const block = Object.assign(Object.assign({}, blockHeader), { _endPosition: blockContentPosition, contentPosition: blockContentPosition, content: uncompressedData });
             if (blockHeader.compressionMethod !== 'raw') {
-                const compressedData = Buffer.allocUnsafe(blockHeader.compressedSize);
+                const compressedData = buffer_1.Buffer.allocUnsafe(blockHeader.compressedSize);
                 yield this.read(compressedData, 0, blockHeader.compressedSize, blockContentPosition);
                 yield this._uncompress(blockHeader.compressionMethod, compressedData, uncompressedData);
             }

package/dist/cramFile/file.js.map

@@ -1 +1 @@
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package/dist/cramFile/record.d.ts

@@ -1,5 +1,5 @@
 import CramContainerCompressionScheme from './container/compressionScheme';
-import decodeRecord from './slice/decodeRecord';
+import type decodeRecord from './slice/decodeRecord';
 export interface RefRegion {
     start: number;
     end: number;

package/dist/cramFile/record.js

@@ -164,8 +164,8 @@ exports.MateFlags = [
 function makeFlagsHelper(x) {
     const r = {};
     for (const [code, name] of x) {
-        r['is' + name] = (flags) => !!(flags & code);
-        r['set' + name] = (flags) => flags | code;
+        r[`is${name}`] = (flags) => !!(flags & code);
+        r[`set${name}`] = (flags) => flags | code;
     }
     return r;
 }

package/dist/cramFile/record.js.map

@@ -1 +1 @@
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package/dist/cramFile/sectionParsers.d.ts

@@ -1,13 +1,50 @@
-import { Parser } from '@gmod/binary-parser';
 import { TupleOf } from '../typescript';
-import { ParsedItem } from './util';
 import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes';
 import { CramEncoding } from './encoding';
-declare const cramFileDefinition: {
-    parser: Parser<unknown>;
+export declare function cramFileDefinition(): {
+    parser: (buffer: Buffer, _startOffset?: number) => {
+        value: {
+            magic: string;
+            majorVersion: number;
+            minorVersion: number;
+            fileId: string;
+        };
+        offset: number;
+    };
+    maxLength: number;
+};
+export declare function cramBlockHeader(): {
+    parser: (buffer: Buffer, _startOffset?: number) => {
+        offset: number;
+        value: {
+            uncompressedSize: number;
+            compressedSize: number;
+            contentId: number;
+            contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
+            compressionMethod: CompressionMethod;
+        };
+    };
+    maxLength: number;
+};
+export declare function cramBlockCrc32(): {
+    parser: (buffer: Buffer, offset: number) => {
+        offset: number;
+        value: {
+            crc32: number;
+        };
+    };
     maxLength: number;
 };
 export type CramTagDictionary = string[][];
+export declare function cramTagDictionary(): {
+    parser: (buffer: Buffer, offset: number) => {
+        value: {
+            size: number;
+            ents: string[][];
+        };
+        offset: number;
+    };
+};
 export interface CramPreservationMap {
     MI: boolean;
     UI: boolean;
@@ -18,6 +55,25 @@ export interface CramPreservationMap {
     SM: [number, number, number, number, number];
     TD: CramTagDictionary;
 }
+export declare function cramPreservationMap(): {
+    parser: (buffer: Buffer, offset: number) => {
+        value: {
+            mapSize: number;
+            mapCount: number;
+            ents: ({
+                key: string;
+                value: boolean;
+            } | {
+                key: string;
+                value: number[];
+            } | {
+                key: string;
+                value: string[][];
+            })[];
+        };
+        offset: number;
+    };
+};
 export interface MappedSliceHeader {
     refSeqId: number;
     refSeqStart: number;
@@ -28,7 +84,7 @@ export interface MappedSliceHeader {
     numContentIds: number;
     contentIds: number[];
     refBaseBlockId: number;
-    md5: TupleOf<number, 16>;
+    md5?: TupleOf<number, 16>;
 }
 export interface UnmappedSliceHeader {
     numRecords: number;
@@ -36,9 +92,14 @@ export interface UnmappedSliceHeader {
     numBlocks: number;
     numContentIds: number;
     contentIds: number[];
-    md5: TupleOf<number, 16>;
+    md5?: TupleOf<number, 16>;
+}
+export declare function isMappedSliceHeader(header: unknown): header is MappedSliceHeader;
+interface Value {
+    codecId: number;
+    parametersBytes: number;
+    parameters: Record<string, unknown>;
 }
-export declare function isMappedSliceHeader(header: MappedSliceHeader | UnmappedSliceHeader): header is MappedSliceHeader;
 export type CompressionMethod = 'raw' | 'gzip' | 'bzip2' | 'lzma' | 'rans' | 'rans4x16' | 'arith' | 'fqzcomp' | 'tok3';
 export interface BlockHeader {
     compressionMethod: CompressionMethod;
@@ -47,63 +108,149 @@ export interface BlockHeader {
     compressedSize: number;
     uncompressedSize: number;
 }
-export type CramCompressionHeader = ParsedItem<{
+export interface CramCompressionHeader {
     preservation: CramPreservationMap;
     dataSeriesEncoding: DataSeriesEncodingMap;
     tagEncoding: Record<string, CramEncoding>;
-}>;
-declare function getSectionParsers(majorVersion: number): {
+    _size: number;
+    _endPosition: number;
+}
+export declare function getSectionParsers(majorVersion: number): {
     cramFileDefinition: {
-        parser: Parser<{
-            magic: string;
-            majorVersion: number;
-            minorVersion: number;
-            fileId: string;
-        }>;
+        parser: (buffer: Buffer, _startOffset?: number) => {
+            value: {
+                magic: string;
+                majorVersion: number;
+                minorVersion: number;
+                fileId: string;
+            };
+            offset: number;
+        };
         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: Parser<BlockHeader>;
+        parser: (buffer: Buffer, _startOffset?: number) => {
+            offset: number;
+            value: {
+                uncompressedSize: number;
+                compressedSize: number;
+                contentId: number;
+                contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
+                compressionMethod: CompressionMethod;
+            };
+        };
         maxLength: number;
     };
     cramBlockCrc32: {
-        parser: Parser<{
-            crc32: number;
-        }>;
+        parser: (buffer: Buffer, offset: number) => {
+            offset: number;
+            value: {
+                crc32: number;
+            };
+        };
         maxLength: number;
     };
+    cramDataSeriesEncodingMap: {
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                mapSize: number;
+                ents: {
+                    key: string;
+                    value: Value;
+                }[];
+                mapCount: number;
+            };
+            offset: number;
+        };
+    };
+    cramTagEncodingMap: {
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                mapSize: number;
+                ents: {
+                    key: string;
+                    value: Value;
+                }[];
+                mapCount: number;
+            };
+            offset: number;
+        };
+    };
     cramCompressionHeader: {
-        parser: Parser<CramCompressionHeader>;
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                dataSeriesEncoding: DataSeriesEncodingMap;
+                preservation: CramPreservationMap;
+                tagEncoding: Record<string, CramEncoding>;
+            };
+            offset: number;
+        };
     };
-    cramMappedSliceHeader: {
-        parser: Parser<MappedSliceHeader>;
-        maxLength: (numContentIds: number) => number;
+    cramEncoding: {
+        parser: (buffer: Buffer, offset: number) => {
+            value: Value;
+            offset: number;
+        };
     };
     cramUnmappedSliceHeader: {
-        parser: Parser<UnmappedSliceHeader>;
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                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;
+            };
+            offset: number;
+        };
+        maxLength: (numContentIds: number) => number;
+    };
+    cramMappedSliceHeader: {
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                md5: [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number] | undefined;
+                numBlocks: number;
+                numRecords: number;
+                numContentIds: number;
+                refSeqSpan: number;
+                refSeqId: number;
+                refSeqStart: number;
+                recordCounter: number;
+                refBaseBlockId: number;
+                contentIds: number[];
+            };
+            offset: number;
+        };
         maxLength: (numContentIds: number) => number;
     };
+    cramContainerHeader1: {
+        maxLength: number;
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                length: number;
+                refSeqId: number;
+                refSeqStart: number;
+                alignmentSpan: number;
+                numBlocks: number;
+                numLandmarks: number;
+                numBases: number | undefined;
+                recordCounter: number;
+                numRecords: number;
+            };
+            offset: number;
+        };
+    };
+    cramContainerHeader2: {
+        parser: (buffer: Buffer, offset: number) => {
+            value: {
+                numLandmarks: number;
+                landmarks: number[];
+                crc32?: number | undefined;
+            };
+            offset: number;
+        };
+        maxLength: (numLandmarks: number) => number;
+    };
 };
-export { cramFileDefinition, getSectionParsers };
+export {};