@gmod/cram 3.0.7 → 4.0.0

package/esm/cramFile/file.d.ts

@@ -1,11 +1,10 @@
-import { Buffer } from 'buffer';
 import QuickLRU from 'quick-lru';
-import { BlockHeader, CompressionMethod } from './sectionParsers';
 import CramContainer from './container';
 import CramRecord from './record';
-import { Filehandle } from './filehandle';
+import { BlockHeader, CompressionMethod } from './sectionParsers';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export interface CramFileSource {
-    filehandle?: Filehandle;
+    filehandle?: GenericFilehandle;
     url?: string;
     path?: string;
 }
@@ -19,7 +18,7 @@ export type CramFileBlock = BlockHeader & {
     _endPosition: number;
     contentPosition: number;
     _size: number;
-    content: Buffer;
+    content: Uint8Array;
     crc32?: number;
 };
 export default class CramFile {
@@ -33,11 +32,8 @@ export default class CramFile {
     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>;
+    stat(): Promise<import("generic-filehandle2").Stats>;
+    read(length: number, position: number): Promise<Uint8Array<ArrayBuffer>>;
     getDefinition(): Promise<{
         magic: string;
         majorVersion: number;
@@ -71,14 +67,14 @@ export default class CramFile {
     }) | undefined>;
     _parseSection<T>(section: {
         maxLength: number;
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             offset: number;
             value: T;
         };
-    }, position: number, size?: number, preReadBuffer?: Buffer): Promise<(T & {
+    }, position: number, size?: number, preReadBuffer?: Uint8Array): Promise<(T & {
         _endPosition: number;
         _size: number;
     }) | undefined>;
-    _uncompress(compressionMethod: CompressionMethod, inputBuffer: Buffer, outputBuffer: Buffer): Promise<void>;
+    _uncompress(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<any>;
     readBlock(position: number): Promise<CramFileBlock | undefined>;
 }

package/esm/cramFile/file.js

@@ -1,18 +1,16 @@
-import { Buffer } from 'buffer';
-import crc32 from 'crc/crc32';
-import QuickLRU from 'quick-lru';
-import htscodecs from '../htscodecs';
 import bzip2 from 'bzip2';
+import crc32 from 'crc/calculators/crc32';
+import QuickLRU from 'quick-lru';
 import { XzReadableStream } from 'xz-decompress';
 import { CramMalformedError, CramUnimplementedError } from '../errors';
-// locals
-import { unzip } from '../unzip';
-import ransuncompress from '../rans';
-import { cramFileDefinition, getSectionParsers, } from './sectionParsers';
-import CramContainer from './container';
+import htscodecs from '../htscodecs';
 import { open } from '../io';
-import { parseItem, tinyMemoize } from './util';
+import ransuncompress from '../rans';
 import { parseHeaderText } from '../sam';
+import { unzip } from '../unzip';
+import CramContainer from './container';
+import { cramFileDefinition, getSectionParsers, } from './sectionParsers';
+import { concatUint8Array, parseItem, tinyMemoize } from './util';
 function bufferToStream(buf) {
     return new ReadableStream({
         start(controller) {
@@ -37,13 +35,12 @@ function getEndianness() {
 }
 export default class CramFile {
     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,
-            cacheSize: (_a = args.cacheSize) !== null && _a !== void 0 ? _a : 20000,
+            cacheSize: args.cacheSize ?? 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
@@ -55,19 +52,18 @@ export default class CramFile {
             throw new Error('Detected big-endian machine, may be unable to run');
         }
     }
-    // can just read this object like a filehandle
-    read(buffer, offset, length, position) {
-        return this.file.read(buffer, offset, length, position);
-    }
     // can just stat this object like a filehandle
     stat() {
         return this.file.stat();
     }
+    // can just stat this object like a filehandle
+    read(length, position) {
+        return this.file.read(length, position);
+    }
     // memoized
     async getDefinition() {
         const { maxLength, parser } = cramFileDefinition();
-        const headbytes = Buffer.allocUnsafe(maxLength);
-        await this.file.read(headbytes, 0, maxLength, 0);
+        const headbytes = await this.file.read(maxLength, 0);
         const definition = parser(headbytes).value;
         if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
             throw new CramUnimplementedError(`CRAM version ${definition.majorVersion} not supported`);
@@ -84,12 +80,16 @@ export default class CramFile {
         if (firstBlock === undefined) {
             return parseHeaderText('');
         }
-        const content = firstBlock.content;
-        const headerLength = content.readInt32LE(0);
-        const textStart = 4;
-        const text = content.toString('utf8', textStart, textStart + headerLength);
-        this.header = text;
-        return parseHeaderText(text);
+        else {
+            const content = firstBlock.content;
+            const dataView = new DataView(content.buffer);
+            const headerLength = dataView.getInt32(0, true);
+            const textStart = 4;
+            const decoder = new TextDecoder('utf8');
+            const text = decoder.decode(content.subarray(textStart, textStart + headerLength));
+            this.header = text;
+            return parseHeaderText(text);
+        }
     }
     async getHeaderText() {
         await this.getSamHeader();
@@ -136,9 +136,11 @@ export default class CramFile {
         return currentContainer;
     }
     async checkCrc32(position, length, recordedCrc32, description) {
-        const b = Buffer.allocUnsafe(length);
-        await this.file.read(b, 0, length, position);
-        const calculatedCrc32 = crc32.unsigned(b);
+        const b = await this.file.read(length, position);
+        // this shift >>> 0 is equivalent to crc32(b).unsigned but uses the
+        // internal calculator of crc32 to avoid accidentally importing buffer
+        // https://github.com/alexgorbatchev/crc/blob/31fc3853e417b5fb5ec83335428805842575f699/src/define_crc.ts#L5
+        const calculatedCrc32 = crc32(b) >>> 0;
         if (calculatedCrc32 !== recordedCrc32) {
             throw new CramMalformedError(`crc mismatch in ${description}: recorded CRC32 = ${recordedCrc32}, but calculated CRC32 = ${calculatedCrc32}`);
         }
@@ -191,8 +193,7 @@ export default class CramFile {
         if (position + cramBlockHeader.maxLength >= fileSize) {
             return undefined;
         }
-        const buffer = Buffer.allocUnsafe(cramBlockHeader.maxLength);
-        await this.file.read(buffer, 0, cramBlockHeader.maxLength, position);
+        const buffer = await this.file.read(cramBlockHeader.maxLength, position);
         return parseItem(buffer, cramBlockHeader.parser, 0, position);
     }
     async _parseSection(section, position, size = section.maxLength, preReadBuffer) {
@@ -205,8 +206,7 @@ export default class CramFile {
             if (position + size >= fileSize) {
                 return undefined;
             }
-            buffer = Buffer.allocUnsafe(size);
-            await this.file.read(buffer, 0, size, position);
+            buffer = await this.file.read(size, position);
         }
         const data = parseItem(buffer, section.parser, 0, position);
         if (data._size !== size) {
@@ -214,46 +214,46 @@ export default class CramFile {
         }
         return data;
     }
-    async _uncompress(compressionMethod, inputBuffer, outputBuffer) {
+    async _uncompress(compressionMethod, inputBuffer, uncompressedSize) {
         if (compressionMethod === 'gzip') {
-            const result = unzip(inputBuffer);
-            result.copy(outputBuffer);
+            return unzip(inputBuffer);
         }
         else if (compressionMethod === 'bzip2') {
             const bits = bzip2.array(inputBuffer);
             let size = bzip2.header(bits);
-            let j = 0;
             let chunk;
+            const chunks = [];
             do {
                 chunk = bzip2.decompress(bits, size);
                 if (chunk !== -1) {
-                    Buffer.from(chunk).copy(outputBuffer, j);
-                    j += chunk.length;
+                    chunks.push(chunk);
                     size -= chunk.length;
                 }
             } while (chunk !== -1);
+            return concatUint8Array(chunks);
         }
         else if (compressionMethod === 'lzma') {
             const decompressedResponse = new Response(new XzReadableStream(bufferToStream(inputBuffer)));
-            const ret = Buffer.from(await decompressedResponse.arrayBuffer());
-            ret.copy(outputBuffer);
+            return new Uint8Array(await decompressedResponse.arrayBuffer());
         }
         else if (compressionMethod === 'rans') {
+            const outputBuffer = new Uint8Array(uncompressedSize);
             ransuncompress(inputBuffer, outputBuffer);
+            return outputBuffer;
             // htscodecs r4x8 is slower, but compatible.
             // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
         }
         else if (compressionMethod === 'rans4x16') {
-            htscodecs.r4x16_uncompress(inputBuffer, outputBuffer);
+            return htscodecs.r4x16_uncompress(inputBuffer);
         }
         else if (compressionMethod === 'arith') {
-            htscodecs.arith_uncompress(inputBuffer, outputBuffer);
+            return htscodecs.arith_uncompress(inputBuffer);
         }
         else if (compressionMethod === 'fqzcomp') {
-            htscodecs.fqzcomp_uncompress(inputBuffer, outputBuffer);
+            return htscodecs.fqzcomp_uncompress(inputBuffer);
         }
         else if (compressionMethod === 'tok3') {
-            htscodecs.tok3_uncompress(inputBuffer, outputBuffer);
+            return htscodecs.tok3_uncompress(inputBuffer);
         }
         else {
             throw new CramUnimplementedError(`${compressionMethod} decompression not yet implemented`);
@@ -267,21 +267,16 @@ export default class CramFile {
             return undefined;
         }
         const blockContentPosition = blockHeader._endPosition;
-        const uncompressedData = Buffer.allocUnsafe(blockHeader.uncompressedSize);
+        const d = await this.file.read(blockHeader.compressedSize, blockContentPosition);
+        const uncompressedData = blockHeader.compressionMethod !== 'raw'
+            ? await this._uncompress(blockHeader.compressionMethod, d, blockHeader.uncompressedSize)
+            : d;
         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);
-            await this._uncompress(blockHeader.compressionMethod, compressedData, uncompressedData);
-        }
-        else {
-            await this.read(uncompressedData, 0, blockHeader.uncompressedSize, blockContentPosition);
-        }
         if (majorVersion >= 3) {
             // parse the crc32
             const crc = await this._parseSection(sectionParsers.cramBlockCrc32, blockContentPosition + blockHeader.compressedSize);

package/esm/cramFile/file.js.map

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package/esm/cramFile/record.js

@@ -339,8 +339,8 @@ export default class CramRecord {
      */
     addReferenceSequence(refRegion, compressionScheme) {
         if (this.readFeatures) {
-            // use the reference bases to decode the bases
-            // substituted in each base substitution
+            // use the reference bases to decode the bases substituted in each base
+            // substitution
             this.readFeatures.forEach(readFeature => {
                 if (readFeature.code === 'X') {
                     decodeBaseSubstitution(this, refRegion, compressionScheme, readFeature);

package/esm/cramFile/record.js.map

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

@@ -2,7 +2,7 @@ import { TupleOf } from '../typescript';
 import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes';
 import { CramEncoding } from './encoding';
 export declare function cramFileDefinition(): {
-    parser: (buffer: Buffer, _startOffset?: number) => {
+    parser: (b: Uint8Array, _startOffset?: number) => {
         value: {
             magic: string;
             majorVersion: number;
@@ -14,7 +14,7 @@ export declare function cramFileDefinition(): {
     maxLength: number;
 };
 export declare function cramBlockHeader(): {
-    parser: (buffer: Buffer, _startOffset?: number) => {
+    parser: (buffer: Uint8Array, _startOffset?: number) => {
         offset: number;
         value: {
             uncompressedSize: number;
@@ -27,7 +27,7 @@ export declare function cramBlockHeader(): {
     maxLength: number;
 };
 export declare function cramBlockCrc32(): {
-    parser: (buffer: Buffer, offset: number) => {
+    parser: (buffer: Uint8Array, offset: number) => {
         offset: number;
         value: {
             crc32: number;
@@ -37,7 +37,7 @@ export declare function cramBlockCrc32(): {
 };
 export type CramTagDictionary = string[][];
 export declare function cramTagDictionary(): {
-    parser: (buffer: Buffer, offset: number) => {
+    parser: (buffer: Uint8Array, offset: number) => {
         value: {
             size: number;
             ents: string[][];
@@ -56,7 +56,7 @@ export interface CramPreservationMap {
     TD: CramTagDictionary;
 }
 export declare function cramPreservationMap(): {
-    parser: (buffer: Buffer, offset: number) => {
+    parser: (buffer: Uint8Array, offset: number) => {
         value: {
             mapSize: number;
             mapCount: number;
@@ -117,7 +117,7 @@ export interface CramCompressionHeader {
 }
 export declare function getSectionParsers(majorVersion: number): {
     cramFileDefinition: {
-        parser: (buffer: Buffer, _startOffset?: number) => {
+        parser: (b: Uint8Array, _startOffset?: number) => {
             value: {
                 magic: string;
                 majorVersion: number;
@@ -129,7 +129,7 @@ export declare function getSectionParsers(majorVersion: number): {
         maxLength: number;
     };
     cramBlockHeader: {
-        parser: (buffer: Buffer, _startOffset?: number) => {
+        parser: (buffer: Uint8Array, _startOffset?: number) => {
             offset: number;
             value: {
                 uncompressedSize: number;
@@ -142,7 +142,7 @@ export declare function getSectionParsers(majorVersion: number): {
         maxLength: number;
     };
     cramBlockCrc32: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             offset: number;
             value: {
                 crc32: number;
@@ -151,7 +151,7 @@ export declare function getSectionParsers(majorVersion: number): {
         maxLength: number;
     };
     cramDataSeriesEncodingMap: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 mapSize: number;
                 ents: {
@@ -164,7 +164,7 @@ export declare function getSectionParsers(majorVersion: number): {
         };
     };
     cramTagEncodingMap: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 mapSize: number;
                 ents: {
@@ -177,7 +177,7 @@ export declare function getSectionParsers(majorVersion: number): {
         };
     };
     cramCompressionHeader: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 dataSeriesEncoding: DataSeriesEncodingMap;
                 preservation: CramPreservationMap;
@@ -187,13 +187,13 @@ export declare function getSectionParsers(majorVersion: number): {
         };
     };
     cramEncoding: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: Value;
             offset: number;
         };
     };
     cramUnmappedSliceHeader: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 recordCounter: number;
                 md5: [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number] | undefined;
@@ -207,7 +207,7 @@ export declare function getSectionParsers(majorVersion: number): {
         maxLength: (numContentIds: number) => number;
     };
     cramMappedSliceHeader: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 md5: [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number] | undefined;
                 numBlocks: number;
@@ -226,7 +226,7 @@ export declare function getSectionParsers(majorVersion: number): {
     };
     cramContainerHeader1: {
         maxLength: number;
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 length: number;
                 refSeqId: number;
@@ -242,7 +242,7 @@ export declare function getSectionParsers(majorVersion: number): {
         };
     };
     cramContainerHeader2: {
-        parser: (buffer: Buffer, offset: number) => {
+        parser: (buffer: Uint8Array, offset: number) => {
             value: {
                 numLandmarks: number;
                 landmarks: number[];

package/esm/cramFile/sectionParsers.js

@@ -1,19 +1,18 @@
 import { parseItf8, parseLtf8 } from './util';
 export function cramFileDefinition() {
     return {
-        parser: (buffer, _startOffset = 0) => {
-            const b = buffer;
+        parser: (b, _startOffset = 0) => {
             const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+            const decoder = new TextDecoder('utf8');
             let offset = 0;
-            const magic = buffer.subarray(offset, offset + 4).toString();
+            const magic = decoder.decode(b.subarray(offset, offset + 4));
             offset += 4;
             const majorVersion = dataView.getUint8(offset);
             offset += 1;
             const minorVersion = dataView.getUint8(offset);
             offset += 1;
-            const fileId = b
-                .subarray(offset, offset + 20)
-                .toString()
+            const fileId = decoder
+                .decode(b.subarray(offset, offset + 20))
                 .replaceAll('\0', '');
             offset += 20;
             return {
@@ -100,7 +99,8 @@ export function cramBlockCrc32() {
     };
 }
 function makeTagSet(buffer, stringStart, stringEnd) {
-    const str = buffer.toString('utf8', stringStart, stringEnd);
+    const decoder = new TextDecoder('utf8');
+    const str = decoder.decode(buffer.subarray(stringStart, stringEnd));
     const tags = [];
     for (let i = 0; i < str.length; i += 3) {
         tags.push(str.slice(i, i + 3));