@gmod/cram 7.0.3 → 8.0.1

package/dist/cramFile/record.js.map

@@ -1 +1 @@
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package/dist/cramFile/slice/decodeRecord.d.ts

@@ -1,11 +1,12 @@
 import { Cursors, DataTypeMapping } from '../codecs/_base.ts';
 import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes.ts';
 import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/compressionScheme.ts';
-import { ReadFeature } from '../record.ts';
+import { DecodeOptions, ReadFeature } from '../record.ts';
 import CramSlice, { SliceHeader } from './index.ts';
 import { CramFileBlock } from '../file.ts';
 export type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]] | undefined;
-export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSeriesDecoder, compressionScheme: CramContainerCompressionScheme, sliceHeader: SliceHeader, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors, majorVersion: number, recordNumber: number): {
+export type BulkByteRawDecoder = (dataSeriesName: 'QS' | 'BA', length: number) => Uint8Array | undefined;
+export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSeriesDecoder, compressionScheme: CramContainerCompressionScheme, sliceHeader: SliceHeader, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors, majorVersion: number, recordNumber: number, decodeOptions?: Required<DecodeOptions>, decodeBulkBytesRaw?: BulkByteRawDecoder): {
     readLength: number;
     sequenceId: number | undefined;
     cramFlags: number;
@@ -24,7 +25,7 @@ export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSer
     readFeatures: ReadFeature[] | undefined;
     lengthOnRef: number | undefined;
     mappingQuality: number | undefined;
-    qualityScores: number[] | null | undefined;
+    qualityScores: Uint8Array<ArrayBufferLike> | null | undefined;
     readBases: string | null | undefined;
     tags: Record<string, any>;
 };

package/dist/cramFile/slice/decodeRecord.js

@@ -4,16 +4,20 @@ exports.default = decodeRecord;
 const errors_ts_1 = require("../../errors.js");
 const record_ts_1 = require("../record.js");
 const sectionParsers_ts_1 = require("../sectionParsers.js");
+// Reusable TextDecoder instance for string decoding (ASCII/Latin1)
+const textDecoder = new TextDecoder('latin1');
 /**
  * given a Buffer, read a string up to the first null character
  * @private
  */
 function readNullTerminatedString(buffer) {
-    let r = '';
-    for (let i = 0; i < buffer.length && buffer[i] !== 0; i++) {
-        r += String.fromCharCode(buffer[i]);
+    // Find the null terminator
+    let end = 0;
+    while (end < buffer.length && buffer[end] !== 0) {
+        end++;
     }
-    return r;
+    // Decode using TextDecoder (faster than char-by-char concatenation)
+    return textDecoder.decode(buffer.subarray(0, end));
 }
 /**
  * parse a BAM tag's array value from a binary buffer
@@ -109,56 +113,64 @@ function parseTagData(tagType, buffer) {
     }
     throw new errors_ts_1.CramMalformedError(`Unrecognized tag type ${tagType}`);
 }
-function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion) {
+// Pre-defined schema lookup tables (version-independent entries)
+const data1SchemaBase = {
+    B: ['character', 'BA'],
+    X: ['number', 'BS'],
+    D: ['number', 'DL'],
+    I: ['string', 'IN'],
+    i: ['character', 'BA'],
+    b: ['string', 'BB'],
+    q: ['numArray', 'QQ'],
+    Q: ['number', 'QS'],
+    H: ['number', 'HC'],
+    P: ['number', 'PD'],
+    N: ['number', 'RS'],
+};
+// Version-specific S entry
+const data1SchemaV1 = {
+    ...data1SchemaBase,
+    S: ['string', 'IN'],
+};
+const data1SchemaV2Plus = {
+    ...data1SchemaBase,
+    S: ['string', 'SC'],
+};
+// Second data item schema for read features that have two values
+const data2Schema = {
+    B: ['number', 'QS'],
+};
+function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, _compressionScheme, majorVersion) {
     let currentReadPos = 0;
     let currentRefPos = alignmentStart - 1;
     const readFeatures = new Array(readFeatureCount);
+    // Select the appropriate schema based on version (once per call, not per iteration)
+    const data1Schema = majorVersion > 1 ? data1SchemaV2Plus : data1SchemaV1;
     function decodeRFData([type, dataSeriesName]) {
         const data = decodeDataSeries(dataSeriesName);
         if (type === 'character') {
             return String.fromCharCode(data);
         }
         else if (type === 'string') {
-            let r = '';
-            for (let i = 0; i < data.byteLength; i++) {
-                r += String.fromCharCode(data[i]);
-            }
-            return r;
+            return textDecoder.decode(data);
         }
         else if (type === 'numArray') {
             return Array.from(data);
         }
-        // else if (type === 'number') {
-        //   return data[0]
-        // }
         return data;
     }
     for (let i = 0; i < readFeatureCount; i++) {
         const code = String.fromCharCode(decodeDataSeries('FC'));
         const readPosDelta = decodeDataSeries('FP');
-        // map of operator name -> data series name
-        const data1Schema = {
-            B: ['character', 'BA'],
-            S: ['string', majorVersion > 1 ? 'SC' : 'IN'], // IN if cram v1, SC otherwise
-            X: ['number', 'BS'],
-            D: ['number', 'DL'],
-            I: ['string', 'IN'],
-            i: ['character', 'BA'],
-            b: ['string', 'BB'],
-            q: ['numArray', 'QQ'],
-            Q: ['number', 'QS'],
-            H: ['number', 'HC'],
-            P: ['number', 'PD'],
-            N: ['number', 'RS'],
-        }[code];
-        if (!data1Schema) {
+        const schema = data1Schema[code];
+        if (!schema) {
             throw new errors_ts_1.CramMalformedError(`invalid read feature code "${code}"`);
         }
-        let data = decodeRFData(data1Schema);
-        // if this is a tag with two data items, make the data an array and add the second item
-        const data2Schema = { B: ['number', 'QS'] }[code];
-        if (data2Schema) {
-            data = [data, decodeRFData(data2Schema)];
+        let data = decodeRFData(schema);
+        // if this is a read feature with two data items, make the data an array
+        const schema2 = data2Schema[code];
+        if (schema2) {
+            data = [data, decodeRFData(schema2)];
         }
         currentReadPos += readPosDelta;
         const pos = currentReadPos;
@@ -178,7 +190,7 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
     }
     return readFeatures;
 }
-function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber) {
+function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber, decodeOptions, decodeBulkBytesRaw) {
     let flags = decodeDataSeries('BF');
     // note: the C data type of compressionFlags is byte in cram v1 and int32 in
     // cram v2+, but that does not matter for us here in javascript land.
@@ -249,19 +261,25 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     // TN = tag names
     const TN = compressionScheme.getTagNames(TLindex);
     const ntags = TN.length;
+    const shouldDecodeTags = decodeOptions?.decodeTags !== false;
     for (let i = 0; i < ntags; i++) {
         const tagId = TN[i];
-        const tagName = tagId.slice(0, 2);
-        const tagType = tagId.slice(2, 3);
+        // Always decode to advance cursor position
         const tagData = compressionScheme
             .getCodecForTag(tagId)
             .decode(slice, coreDataBlock, blocksByContentId, cursors);
-        tags[tagName] =
-            tagData === undefined
-                ? undefined
-                : typeof tagData === 'number'
-                    ? tagData
-                    : parseTagData(tagType, tagData);
+        // Only parse tags if requested (default: true)
+        if (shouldDecodeTags) {
+            // Use direct character access instead of slice() to avoid string allocation
+            const tagName = tagId[0] + tagId[1];
+            const tagType = tagId[2];
+            tags[tagName] =
+                tagData === undefined
+                    ? undefined
+                    : typeof tagData === 'number'
+                        ? tagData
+                        : parseTagData(tagType, tagData);
+        }
     }
     let readFeatures;
     let lengthOnRef;
@@ -297,9 +315,17 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         // mapping quality
         mappingQuality = decodeDataSeries('MQ');
         if (record_ts_1.CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
-            qualityScores = new Array(readLength);
-            for (let i = 0; i < qualityScores.length; i++) {
-                qualityScores[i] = decodeDataSeries('QS');
+            // Try raw bytes first (most efficient - just a subarray view)
+            const rawQS = decodeBulkBytesRaw?.('QS', readLength);
+            if (rawQS) {
+                qualityScores = rawQS;
+            }
+            else {
+                // Fallback to single-byte decoding into new Uint8Array
+                qualityScores = new Uint8Array(readLength);
+                for (let i = 0; i < readLength; i++) {
+                    qualityScores[i] = decodeDataSeries('QS');
+                }
             }
         }
     }
@@ -308,15 +334,31 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         qualityScores = null;
     }
     else {
-        const bases = new Array(readLength);
-        for (let i = 0; i < bases.length; i++) {
-            bases[i] = decodeDataSeries('BA');
+        // Try raw bytes first for TextDecoder (most efficient)
+        const rawBA = decodeBulkBytesRaw?.('BA', readLength);
+        if (rawBA) {
+            readBases = textDecoder.decode(rawBA);
+        }
+        else {
+            // Fallback to single-byte decoding
+            let s = '';
+            for (let i = 0; i < readLength; i++) {
+                s += String.fromCharCode(decodeDataSeries('BA'));
+            }
+            readBases = s;
         }
-        readBases = String.fromCharCode(...bases);
         if (record_ts_1.CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
-            qualityScores = new Array(readLength);
-            for (let i = 0; i < bases.length; i++) {
-                qualityScores[i] = decodeDataSeries('QS');
+            // Try raw bytes first (most efficient - just a subarray view)
+            const rawQS = decodeBulkBytesRaw?.('QS', readLength);
+            if (rawQS) {
+                qualityScores = rawQS;
+            }
+            else {
+                // Fallback to single-byte decoding into new Uint8Array
+                qualityScores = new Uint8Array(readLength);
+                for (let i = 0; i < readLength; i++) {
+                    qualityScores[i] = decodeDataSeries('QS');
+                }
             }
         }
     }

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

@@ -1,6 +1,6 @@
 import CramContainer from '../container/index.ts';
 import { CramFileBlock } from '../file.ts';
-import CramRecord from '../record.ts';
+import CramRecord, { DecodeOptions } from '../record.ts';
 import { MappedSliceHeader, UnmappedSliceHeader } from '../sectionParsers.ts';
 export type SliceHeader = CramFileBlock & {
     parsedContent: MappedSliceHeader | UnmappedSliceHeader;
@@ -45,6 +45,6 @@ export default class CramSlice {
         span: number;
     } | undefined>;
     getAllRecords(): Promise<CramRecord[]>;
-    _fetchRecords(): Promise<CramRecord[]>;
-    getRecords(filterFunction: (r: CramRecord) => boolean): Promise<CramRecord[]>;
+    _fetchRecords(decodeOptions: Required<DecodeOptions>): Promise<CramRecord[]>;
+    getRecords(filterFunction: (r: CramRecord) => boolean, decodeOptions?: DecodeOptions): Promise<CramRecord[]>;
 }

package/dist/cramFile/slice/index.js

@@ -1,4 +1,37 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -7,7 +40,8 @@ const errors_ts_1 = require("../../errors.js");
 const getBits_ts_1 = require("../codecs/getBits.js");
 const constants_ts_1 = __importDefault(require("../constants.js"));
 const decodeRecord_ts_1 = __importDefault(require("./decodeRecord.js"));
-const record_ts_1 = __importDefault(require("../record.js"));
+const external_ts_1 = __importDefault(require("../codecs/external.js"));
+const record_ts_1 = __importStar(require("../record.js"));
 const sectionParsers_ts_1 = require("../sectionParsers.js");
 const util_ts_1 = require("../util.js");
 /**
@@ -149,7 +183,25 @@ class CramSlice {
     // memoize
     async getBlocks() {
         const header = await this.getHeader();
-        // read all the blocks into memory and store them
+        if (this.sliceSize) {
+            // if we know the slice size (from the index), do one big read for all
+            // blocks and parse from the in-memory buffer
+            const containerHeader = await this.container.getHeader();
+            const sliceFilePosition = containerHeader._endPosition + this.containerPosition;
+            const blocksFilePosition = header._endPosition;
+            const headerSize = blocksFilePosition - sliceFilePosition;
+            const remainingBytes = this.sliceSize - headerSize;
+            const allBlocksBuffer = await this.file.read(remainingBytes, blocksFilePosition);
+            const blocks = new Array(header.parsedContent.numBlocks);
+            let bufferOffset = 0;
+            for (let i = 0; i < blocks.length; i++) {
+                const block = await this.file.readBlockFromBuffer(allBlocksBuffer, bufferOffset, blocksFilePosition + bufferOffset);
+                blocks[i] = block;
+                bufferOffset = block._endPosition - blocksFilePosition;
+            }
+            return blocks;
+        }
+        // fallback: read blocks one at a time (non-indexed access)
         let blockPosition = header._endPosition;
         const blocks = new Array(header.parsedContent.numBlocks);
         for (let i = 0; i < blocks.length; i++) {
@@ -232,7 +284,7 @@ class CramSlice {
     getAllRecords() {
         return this.getRecords(() => true);
     }
-    async _fetchRecords() {
+    async _fetchRecords(decodeOptions) {
         const { majorVersion } = await this.file.getDefinition();
         const compressionScheme = await this.container.getCompressionScheme();
         if (compressionScheme === undefined) {
@@ -293,10 +345,27 @@ class CramSlice {
             }
             return codec.decode(this, coreDataBlock, blocksByContentId, cursors);
         };
+        // Create bulk byte decoder for QS and BA data series if they use External codec
+        const qsCodec = compressionScheme.getCodecForDataSeries('QS');
+        const baCodec = compressionScheme.getCodecForDataSeries('BA');
+        const qsIsExternal = qsCodec instanceof external_ts_1.default;
+        const baIsExternal = baCodec instanceof external_ts_1.default;
+        // Create raw byte decoder for QS/BA decoding
+        const decodeBulkBytesRaw = qsIsExternal || baIsExternal
+            ? (dataSeriesName, length) => {
+                if (dataSeriesName === 'QS' && qsIsExternal) {
+                    return qsCodec.getBytesSubarray(blocksByContentId, cursors, length);
+                }
+                if (dataSeriesName === 'BA' && baIsExternal) {
+                    return baCodec.getBytesSubarray(blocksByContentId, cursors, length);
+                }
+                return undefined;
+            }
+            : undefined;
         const records = new Array(sliceHeader.parsedContent.numRecords);
         for (let i = 0; i < records.length; i += 1) {
             try {
-                const init = (0, decodeRecord_ts_1.default)(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
+                const init = (0, decodeRecord_ts_1.default)(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i, decodeOptions, decodeBulkBytesRaw);
                 records[i] = new record_ts_1.default({
                     ...init,
                     uniqueId: sliceHeader.contentPosition +
@@ -337,13 +406,17 @@ class CramSlice {
         }
         return records;
     }
-    async getRecords(filterFunction) {
+    async getRecords(filterFunction, decodeOptions) {
+        // Merge with defaults
+        const opts = { ...record_ts_1.defaultDecodeOptions, ...decodeOptions };
         // fetch the features if necessary, using the file-level feature cache
-        const cacheKey = this.container.filePosition + this.containerPosition;
-        let recordsPromise = this.file.featureCache.get(cacheKey.toString());
+        // Include decode options in cache key so different decode configs are cached separately
+        const optionsKey = `${opts.decodeTags ? 1 : 0}`;
+        const cacheKey = `${this.container.filePosition}:${this.containerPosition}:${optionsKey}`;
+        let recordsPromise = this.file.featureCache.get(cacheKey);
         if (!recordsPromise) {
-            recordsPromise = this._fetchRecords();
-            this.file.featureCache.set(cacheKey.toString(), recordsPromise);
+            recordsPromise = this._fetchRecords(opts);
+            this.file.featureCache.set(cacheKey, recordsPromise);
         }
         const unfiltered = await recordsPromise;
         const records = unfiltered.filter(filterFunction);

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

@@ -1 +1 @@
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package/dist/indexedCramFile.d.ts

@@ -1,7 +1,7 @@
 import { Slice } from './craiIndex.ts';
 import { SeqFetch } from './cramFile/file.ts';
 import CramFile from './cramFile/index.ts';
-import CramRecord from './cramFile/record.ts';
+import CramRecord, { DecodeOptions } from './cramFile/record.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export interface CramFileSource {
     cramFilehandle?: GenericFilehandle;
@@ -51,12 +51,12 @@ export default class IndexedCramFile {
         viewAsPairs?: boolean;
         pairAcrossChr?: boolean;
         maxInsertSize?: number;
-    }): Promise<CramRecord[]>;
+    } & DecodeOptions): Promise<CramRecord[]>;
     getRecordsInSlice({ containerStart, sliceStart, sliceBytes, }: {
         containerStart: number;
         sliceStart: number;
         sliceBytes: number;
-    }, filterFunction: (r: CramRecord) => boolean): Promise<CramRecord[]>;
+    }, filterFunction: (r: CramRecord) => boolean, decodeOptions?: DecodeOptions): Promise<CramRecord[]>;
     /**
      *
      * @param {number} seqId