@gmod/bam 6.1.1 → 7.0.1

package/CHANGELOG.md

@@ -1,10 +1,14 @@
-## [6.1.1](https://github.com/GMOD/bam-js/compare/v6.1.0...v6.1.1) (2025-10-02)
+## [7.0.1](https://github.com/GMOD/bam-js/compare/v7.0.0...v7.0.1) (2025-11-24)
 
 
 
-# [6.1.0](https://github.com/GMOD/bam-js/compare/v6.0.4...v6.1.0) (2025-10-01)
+# [7.0.0](https://github.com/GMOD/bam-js/compare/v6.1.1...v7.0.0) (2025-11-24)
+
 
 
+## [6.1.1](https://github.com/GMOD/bam-js/compare/v6.1.0...v6.1.1) (2025-10-02)
+
+# [6.1.0](https://github.com/GMOD/bam-js/compare/v6.0.4...v6.1.0) (2025-10-01)
 
 ## [6.0.4](https://github.com/GMOD/bam-js/compare/v6.0.3...v6.0.4) (2025-05-26)
 

package/dist/bamFile.d.ts

@@ -15,7 +15,6 @@ export default class BamFile {
         refName: string;
         length: number;
     }[];
-    yieldThreadTime: number;
     index?: BAI | CSI;
     htsget: boolean;
     headerP?: ReturnType<BamFile['getHeaderPre']>;
@@ -23,7 +22,7 @@ export default class BamFile {
         buffer: Uint8Array;
         nextIn: number;
     }>;
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime, renameRefSeqs, }: {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
         bamUrl?: string;
@@ -34,7 +33,6 @@ export default class BamFile {
         csiFilehandle?: GenericFilehandle;
         csiUrl?: string;
         renameRefSeqs?: (a: string) => string;
-        yieldThreadTime?: number;
         htsget?: boolean;
     });
     getHeaderPre(origOpts?: BaseOpts): Promise<{
@@ -52,13 +50,13 @@ export default class BamFile {
         }[];
     }[] | undefined>;
     getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
-    _readRefSeqs(start: number, refSeqBytes: number, opts?: BaseOpts): Promise<{
+    _parseRefSeqs(uncba: Uint8Array, start: number): {
         chrToIndex: Record<string, number>;
         indexToChr: {
             refName: string;
             length: number;
         }[];
-    }>;
+    };
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
     streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
@@ -72,7 +70,8 @@ export default class BamFile {
         dpositions: number[];
         chunk: Chunk;
     }>;
-    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
+    readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk, chrId?: number, min?: number, max?: number): Promise<BAMFeature[]>;
+    _shouldIncludeFeature(dataView: DataView, blockStart: number, chrId: number, max: number): boolean;
     hasRefSeq(seqName: string): Promise<boolean | undefined>;
     lineCount(seqName: string): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai.ts").IndexCovEntry[]>;

package/dist/bamFile.js

@@ -17,7 +17,7 @@ const util_ts_1 = require("./util.js");
 exports.BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
 class BamFile {
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, }) {
         this.htsget = false;
         this.cache = new quick_lru_1.default({
             maxSize: 1000,
@@ -69,25 +69,18 @@ class BamFile {
         else {
             throw new Error('unable to infer index format');
         }
-        this.yieldThreadTime = yieldThreadTime;
     }
     async getHeaderPre(origOpts) {
         const opts = (0, util_ts_1.makeOpts)(origOpts);
         if (!this.index) {
-            return;
+            return undefined;
         }
         const indexData = await this.index.parse(opts);
-        const ret = indexData.firstDataLine
-            ? indexData.firstDataLine.blockPosition + 65535
-            : undefined;
-        let buffer;
-        if (ret) {
-            const s = ret + blockLen;
-            buffer = await this.bam.read(s, 0);
-        }
-        else {
-            buffer = await this.bam.readFile(opts);
-        }
+        // firstDataLine is not defined in cases where there is no data in the file
+        // (just bam header and nothing else)
+        const buffer = indexData.firstDataLine === undefined
+            ? await this.bam.readFile()
+            : await this.bam.read(indexData.firstDataLine.blockPosition + blockLen, 0);
         const uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
         const dataView = new DataView(uncba.buffer);
         if (dataView.getInt32(0, true) !== exports.BAM_MAGIC) {
@@ -96,7 +89,7 @@ class BamFile {
         const headLen = dataView.getInt32(4, true);
         const decoder = new TextDecoder('utf8');
         this.header = decoder.decode(uncba.subarray(8, 8 + headLen));
-        const { chrToIndex, indexToChr } = await this._readRefSeqs(headLen + 8, 65535, opts);
+        const { chrToIndex, indexToChr } = this._parseRefSeqs(uncba, headLen + 8);
         this.chrToIndex = chrToIndex;
         this.indexToChr = indexToChr;
         return (0, sam_ts_1.parseHeaderText)(this.header);
@@ -114,15 +107,7 @@ class BamFile {
         await this.getHeader(opts);
         return this.header;
     }
-    // the full length of the refseq block is not given in advance so this grabs
-    // a chunk and doubles it if all refseqs haven't been processed
-    async _readRefSeqs(start, refSeqBytes, opts) {
-        if (start > refSeqBytes) {
-            return this._readRefSeqs(start, refSeqBytes * 2, opts);
-        }
-        // const size = refSeqBytes + blockLen <-- use this?
-        const buffer = await this.bam.read(refSeqBytes, 0, opts);
-        const uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
+    _parseRefSeqs(uncba, start) {
         const dataView = new DataView(uncba.buffer);
         const nRef = dataView.getInt32(start, true);
         let p = start + 4;
@@ -130,16 +115,15 @@ class BamFile {
         const indexToChr = [];
         const decoder = new TextDecoder('utf8');
         for (let i = 0; i < nRef; i += 1) {
+            if (p + 8 > uncba.length) {
+                throw new Error(`Insufficient data for reference sequences: need more than ${uncba.length} bytes`);
+            }
             const lName = dataView.getInt32(p, true);
             const refName = this.renameRefSeq(decoder.decode(uncba.subarray(p + 4, p + 4 + lName - 1)));
             const lRef = dataView.getInt32(p + lName + 4, true);
             chrToIndex[refName] = i;
             indexToChr.push({ refName, length: lRef });
             p = p + 8 + lName;
-            if (p > uncba.length) {
-                console.warn(`BAM header is very big.  Re-fetching ${refSeqBytes} bytes.`);
-                return this._readRefSeqs(start, refSeqBytes * 2, opts);
-            }
         }
         return { chrToIndex, indexToChr };
     }
@@ -150,12 +134,10 @@ class BamFile {
         await this.getHeader(opts);
         const chrId = this.chrToIndex?.[chr];
         if (chrId === undefined || !this.index) {
-            yield [];
-        }
-        else {
-            const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
-            yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts);
+            return;
         }
+        const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
+        yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts);
     }
     async *_fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
         const { viewAsPairs } = opts;
@@ -166,7 +148,7 @@ class BamFile {
                 chunk,
                 opts,
             });
-            const records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
+            const records = await this.readBamFeatures(data, cpositions, dpositions, chunk, chrId, min, max);
             const recs = [];
             for (const feature of records) {
                 if (feature.ref_id === chrId) {
@@ -187,7 +169,6 @@ class BamFile {
                 break;
             }
         }
-        (0, util_ts_1.checkAbortSignal)(opts.signal);
         if (viewAsPairs) {
             yield this.fetchPairs(chrId, feats, opts);
         }
@@ -196,7 +177,7 @@ class BamFile {
         const { pairAcrossChr, maxInsertSize = 200000 } = opts;
         const unmatedPairs = {};
         const readIds = {};
-        feats.map(ret => {
+        for (const ret of feats) {
             const readNames = {};
             for (const element of ret) {
                 const name = element.name;
@@ -212,9 +193,9 @@ class BamFile {
                     unmatedPairs[k] = true;
                 }
             }
-        });
+        }
         const matePromises = [];
-        feats.map(ret => {
+        for (const ret of feats) {
             for (const f of ret) {
                 const name = f.name;
                 const start = f.start;
@@ -227,7 +208,7 @@ class BamFile {
                     matePromises.push(this.index.blocksForRange(rnext, pnext, pnext + 1, opts));
                 }
             }
-        });
+        }
         // filter out duplicate chunks (the blocks are lists of chunks, blocks are
         // concatenated, then filter dup chunks)
         const map = new Map();
@@ -257,69 +238,52 @@ class BamFile {
         const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk, this.cache);
         return { data, cpositions, dpositions, chunk };
     }
-    async readBamFeatures(ba, cpositions, dpositions, chunk) {
+    async readBamFeatures(ba, cpositions, dpositions, chunk, chrId, min, max) {
         let blockStart = 0;
         const sink = [];
         let pos = 0;
-        let last = Date.now();
         const dataView = new DataView(ba.buffer);
+        const hasDpositions = dpositions.length > 0;
+        const hasCpositions = cpositions.length > 0;
+        const hasFilter = chrId !== undefined && min !== undefined && max !== undefined;
         while (blockStart + 4 < ba.length) {
             const blockSize = dataView.getInt32(blockStart, true);
             const blockEnd = blockStart + 4 + blockSize - 1;
-            // increment position to the current decompressed status
-            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-            if (dpositions) {
+            if (hasDpositions) {
                 while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]) { }
                 pos--;
             }
-            // only try to read the feature if we have all the bytes for it
             if (blockEnd < ba.length) {
+                if (hasFilter &&
+                    blockStart + 12 < ba.length &&
+                    !this._shouldIncludeFeature(dataView, blockStart, chrId, max)) {
+                    blockStart = blockEnd + 1;
+                    continue;
+                }
                 const feature = new record_ts_1.default({
                     bytes: {
                         byteArray: ba,
                         start: blockStart,
                         end: blockEnd,
                     },
-                    // the below results in an automatically calculated file-offset based
-                    // ID if the info for that is available, otherwise crc32 of the
-                    // features
-                    //
-                    // cpositions[pos] refers to actual file offset of a bgzip block
-                    // boundaries
-                    //
-                    // we multiply by (1 <<8) in order to make sure each block has a
-                    // "unique" address space so that data in that block could never
-                    // overlap
-                    //
-                    // then the blockStart-dpositions is an uncompressed file offset from
-                    // that bgzip block boundary, and since the cpositions are multiplied
-                    // by (1 << 8) these uncompressed offsets get a unique space
-                    //
-                    // this has an extra chunk.minv.dataPosition added on because it
-                    // blockStart starts at 0 instead of chunk.minv.dataPosition
-                    //
-                    // the +1 is just to avoid any possible uniqueId 0 but this does not
-                    // realistically happen
-                    fileOffset: cpositions.length > 0
+                    fileOffset: hasCpositions
                         ? cpositions[pos] * (1 << 8) +
                             (blockStart - dpositions[pos]) +
                             chunk.minv.dataPosition +
                             1
-                        : // 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
-                            (0, crc32_1.default)(ba.subarray(blockStart, blockEnd)) >>> 0,
+                        : (0, crc32_1.default)(ba.subarray(blockStart, blockEnd)) >>> 0,
                 });
                 sink.push(feature);
-                if (this.yieldThreadTime && Date.now() - last > this.yieldThreadTime) {
-                    await (0, util_ts_1.timeout)(1);
-                    last = Date.now();
-                }
             }
             blockStart = blockEnd + 1;
         }
         return sink;
     }
+    _shouldIncludeFeature(dataView, blockStart, chrId, max) {
+        const ref_id = dataView.getInt32(blockStart + 4, true);
+        const start = dataView.getInt32(blockStart + 8, true);
+        return ref_id === chrId && start < max;
+    }
     async hasRefSeq(seqName) {
         const seqId = this.chrToIndex?.[seqName];
         return seqId === undefined ? false : this.index?.hasRefSeq(seqId);

package/dist/bamFile.js.map

@@ -1 +1 @@
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package/dist/package.json

@@ -0,0 +1 @@
+{"type": "commonjs"}

package/dist/record.d.ts

@@ -4,9 +4,9 @@ interface Bytes {
     byteArray: Uint8Array;
 }
 export default class BamRecord {
-    #private;
     fileOffset: number;
     private bytes;
+    private _dataView;
     constructor(args: {
         bytes: Bytes;
         fileOffset: number;
@@ -52,14 +52,16 @@ export default class BamRecord {
     /** @returns {boolean} true if this is a supplementary alignment */
     isSupplementary(): boolean;
     get cigarAndLength(): {
+        NUMERIC_CIGAR: Uint32Array<ArrayBufferLike>;
         length_on_ref: number;
-        CIGAR: string;
     };
     get length_on_ref(): number;
+    get NUMERIC_CIGAR(): Uint32Array<ArrayBufferLike>;
     get CIGAR(): string;
     get num_cigar_ops(): number;
     get read_name_length(): number;
     get num_seq_bytes(): number;
+    get NUMERIC_SEQ(): Uint8Array<ArrayBuffer>;
     get seq(): string;
     get pair_orientation(): string | undefined;
     get bin_mq_nl(): number;