npm - @gmod/bam - Versions diffs - 7.1.9 → 7.1.11 - Mend

@gmod/bam 7.1.9 → 7.1.11

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (42) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -1,19 +1,17 @@
-## [7.1.9](https://github.com/GMOD/bam-js/compare/v7.1.8...v7.1.9) (2025-12-13)
+## [7.1.11](https://github.com/GMOD/bam-js/compare/v7.1.10...v7.1.11) (2025-12-16)
-## [7.1.8](https://github.com/GMOD/bam-js/compare/v7.1.7...v7.1.8) (2025-12-13)
+## [7.1.10](https://github.com/GMOD/bam-js/compare/v7.1.9...v7.1.10) (2025-12-15)
+## [7.1.9](https://github.com/GMOD/bam-js/compare/v7.1.8...v7.1.9) (2025-12-13)
+## [7.1.8](https://github.com/GMOD/bam-js/compare/v7.1.7...v7.1.8) (2025-12-13)
 ## [7.1.7](https://github.com/GMOD/bam-js/compare/v7.1.6...v7.1.7) (2025-12-13)
 ## [7.1.6](https://github.com/GMOD/bam-js/compare/v7.1.5...v7.1.6) (2025-12-13)
 ## [7.1.5](https://github.com/GMOD/bam-js/compare/v7.1.4...v7.1.5) (2025-12-13)
 ## [7.1.4](https://github.com/GMOD/bam-js/compare/v7.1.3...v7.1.4) (2025-12-13)

package/README.md CHANGED Viewed

@@ -93,24 +93,6 @@ Note: you must run getHeader before running getRecordsForRange
 - `opts.maxInsertSize` - control the viewAsPairs option behavior to limit
   distance within a chromosome to fetch. default: 200kb
-### async \*streamRecordsForRange(refName, start, end, opts)
-This is a async generator function that takes the same signature as
-`getRecordsForRange` but results can be processed using
-```typescript
-for await (const chunk of file.streamRecordsForRange(
-  refName,
-  start,
-  end,
-  opts,
-)) {
-}
-```
-The `getRecordsForRange` simply wraps this process by concatenating chunks into
-an array
 ### async getHeader(opts: {....anything to pass to generic-filehandle2 opts})
 This obtains the header from `HtsgetFile` or `BamFile`. Retrieves BAM file and

package/dist/bai.js CHANGED Viewed

@@ -162,7 +162,7 @@ class BAI extends indexFile_ts_1.default {
         if (!seqIdx) {
             return [];
         }
-        const { linearIndex = [], stats } = seqIdx;
+        const { linearIndex, stats } = seqIdx;
         if (linearIndex.length === 0) {
             return [];
         }

package/dist/bai.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/bamFile.d.ts CHANGED Viewed

@@ -14,12 +14,19 @@ export interface BamRecordLike {
     fileOffset: number;
     next_pos: number;
     next_refid: number;
+    flags: number;
+    tags: Record<string, unknown>;
 }
 export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
     bytes: Bytes;
     fileOffset: number;
 }) => T;
 export declare const BAM_MAGIC = 21840194;
+interface ChunkEntry<T> {
+    minBlock: number;
+    maxBlock: number;
+    features: T[];
+}
 export default class BamFile<T extends BamRecordLike = BAMFeature> {
     renameRefSeq: (a: string) => string;
     bam: GenericFilehandle;
@@ -32,16 +39,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     index?: BAI | CSI;
     htsget: boolean;
     headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
-    cache: QuickLRU<string, {
-        bytesRead: number;
-        buffer: Uint8Array;
-        nextIn: number;
-    }>;
-    chunkFeatureCache: QuickLRU<string, {
-        minBlock: number;
-        maxBlock: number;
-        features: T[];
-    }>;
+    chunkFeatureCache: QuickLRU<string, ChunkEntry<T>>;
     private RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, }: {
         bamFilehandle?: GenericFilehandle;
@@ -80,12 +78,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         }[];
     };
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
-    streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
     private chunkCacheKey;
     private blocksOverlap;
     private evictOverlappingChunks;
-    _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
-    fetchPairs(chrId: number, feats: T[][], opts: BamOpts): Promise<T[]>;
+    private _fetchChunkFeaturesDirect;
+    fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
     _readChunk({ chunk, opts }: {
         chunk: Chunk;
         opts: BaseOpts;
@@ -107,3 +104,4 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         end: number;
     }[], opts?: BaseOpts): Promise<number>;
 }
+export {};

package/dist/bamFile.js CHANGED Viewed

@@ -19,12 +19,11 @@ const blockLen = 1 << 16;
 class BamFile {
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
         this.htsget = false;
-        this.cache = new quick_lru_1.default({
-            maxSize: 1000,
-        });
         // Cache for parsed features by chunk
         // When a new chunk overlaps a cached chunk, we evict the cached one
-        this.chunkFeatureCache = new quick_lru_1.default({ maxSize: 100 });
+        this.chunkFeatureCache = new quick_lru_1.default({
+            maxSize: 100,
+        });
         this.renameRefSeq = renameRefSeqs;
         this.RecordClass = (recordClass ?? record_ts_1.default);
         if (bamFilehandle) {
@@ -131,26 +130,26 @@ class BamFile {
             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 });
+            indexToChr.push({
+                refName,
+                length: lRef,
+            });
             p = p + 8 + lName;
         }
         return { chrToIndex, indexToChr };
     }
     async getRecordsForRange(chr, min, max, opts) {
-        return (0, util_ts_1.gen2array)(this.streamRecordsForRange(chr, min, max, opts));
-    }
-    async *streamRecordsForRange(chr, min, max, opts) {
         await this.getHeader(opts);
         const chrId = this.chrToIndex?.[chr];
         if (chrId === undefined || !this.index) {
-            return;
+            return [];
         }
         const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
-        yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts);
+        return this._fetchChunkFeaturesDirect(chunks, chrId, min, max, opts);
     }
-    chunkCacheKey(chunk) {
+    chunkCacheKey(chunk, filterBy) {
         const { minv, maxv } = chunk;
-        return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
+        return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}${(0, util_ts_1.filterCacheKey)(filterBy)}`;
     }
     blocksOverlap(minBlock1, maxBlock1, minBlock2, maxBlock2) {
         return minBlock1 <= maxBlock2 && maxBlock1 >= minBlock2;
@@ -159,28 +158,23 @@ class BamFile {
     evictOverlappingChunks(minBlock, maxBlock) {
         for (const [key, entry] of this.chunkFeatureCache) {
             if (this.blocksOverlap(minBlock, maxBlock, entry.minBlock, entry.maxBlock)) {
-                // console.log(
-                //   `[BAM Cache] Evicting overlapping chunk: ${key} (${entry.features.length} features, blocks ${entry.minBlock}-${entry.maxBlock})`,
-                // )
                 this.chunkFeatureCache.delete(key);
             }
         }
     }
-    async *_fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
-        const { viewAsPairs } = opts;
-        const feats = [];
-        let done = false;
-        // let cacheHits = 0
-        // let cacheMisses = 0
-        for (const chunk of chunks) {
-            const cacheKey = this.chunkCacheKey(chunk);
+    async _fetchChunkFeaturesDirect(chunks, chrId, min, max, opts = {}) {
+        const { viewAsPairs, filterBy } = opts;
+        const { flagInclude = 0, flagExclude = 0, tagFilter } = filterBy || {};
+        const result = [];
+        for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
+            const chunk = chunks[ci];
+            const cacheKey = this.chunkCacheKey(chunk, filterBy);
             const minBlock = chunk.minv.blockPosition;
             const maxBlock = chunk.maxv.blockPosition;
             let records;
             const cached = this.chunkFeatureCache.get(cacheKey);
             if (cached) {
                 records = cached.features;
-                // cacheHits++
             }
             else {
                 this.evictOverlappingChunks(minBlock, maxBlock);
@@ -188,86 +182,87 @@ class BamFile {
                     chunk,
                     opts,
                 });
-                records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
+                const allRecords = await this.readBamFeatures(data, cpositions, dpositions, chunk);
+                if (filterBy) {
+                    records = [];
+                    for (let i = 0, l = allRecords.length; i < l; i++) {
+                        const record = allRecords[i];
+                        if ((0, util_ts_1.filterReadFlag)(record.flags, flagInclude, flagExclude)) {
+                            continue;
+                        }
+                        if (tagFilter &&
+                            (0, util_ts_1.filterTagValue)(record.tags[tagFilter.tag], tagFilter.value)) {
+                            continue;
+                        }
+                        records.push(record);
+                    }
+                }
+                else {
+                    records = allRecords;
+                }
                 this.chunkFeatureCache.set(cacheKey, {
                     minBlock,
                     maxBlock,
                     features: records,
                 });
-                // cacheMisses++
             }
-            const recs = [];
-            for (const feature of records) {
+            let done = false;
+            for (let i = 0, l = records.length; i < l; i++) {
+                const feature = records[i];
                 if (feature.ref_id === chrId) {
                     if (feature.start >= max) {
                         done = true;
                         break;
                     }
                     else if (feature.end >= min) {
-                        recs.push(feature);
+                        result.push(feature);
                     }
                 }
             }
-            feats.push(recs);
-            yield recs;
             if (done) {
                 break;
             }
         }
-        // const total = cacheHits + cacheMisses
-        // if (total > 0) {
-        //   const hitRate = (cacheHits / total) * 100
-        //   console.log(
-        //     `[BAM Cache] chunks: ${total}, hits: ${cacheHits}, misses: ${cacheMisses}, rate: ${hitRate.toFixed(1)}%, cacheSize: ${this.chunkFeatureCache.size}`,
-        //   )
-        // }
         if (viewAsPairs) {
-            yield this.fetchPairs(chrId, feats, opts);
+            const pairs = await this.fetchPairs(chrId, result, opts);
+            for (let i = 0, l = pairs.length; i < l; i++) {
+                result.push(pairs[i]);
+            }
         }
+        return result;
     }
-    async fetchPairs(chrId, feats, opts) {
+    async fetchPairs(chrId, records, opts) {
         const { pairAcrossChr, maxInsertSize = 200000 } = opts;
-        const unmatedPairs = {};
+        const readNameCounts = {};
         const readIds = {};
-        for (const ret of feats) {
-            const readNames = {};
-            for (const element of ret) {
-                const name = element.name;
-                const id = element.fileOffset;
-                if (!readNames[name]) {
-                    readNames[name] = 0;
-                }
-                readNames[name]++;
-                readIds[id] = 1;
-            }
-            for (const [k, v] of Object.entries(readNames)) {
-                if (v === 1) {
-                    unmatedPairs[k] = true;
-                }
-            }
+        for (let i = 0, l = records.length; i < l; i++) {
+            const r = records[i];
+            const name = r.name;
+            readNameCounts[name] = (readNameCounts[name] || 0) + 1;
+            readIds[r.fileOffset] = 1;
         }
         const matePromises = [];
-        for (const ret of feats) {
-            for (const f of ret) {
-                const name = f.name;
-                const start = f.start;
-                const pnext = f.next_pos;
-                const rnext = f.next_refid;
-                if (this.index &&
-                    unmatedPairs[name] &&
-                    (pairAcrossChr ||
-                        (rnext === chrId && Math.abs(start - pnext) < maxInsertSize))) {
-                    matePromises.push(this.index.blocksForRange(rnext, pnext, pnext + 1, opts));
-                }
+        for (let i = 0, l = records.length; i < l; i++) {
+            const f = records[i];
+            const name = f.name;
+            if (this.index &&
+                readNameCounts[name] === 1 &&
+                (pairAcrossChr ||
+                    (f.next_refid === chrId &&
+                        Math.abs(f.start - f.next_pos) < maxInsertSize))) {
+                matePromises.push(this.index.blocksForRange(f.next_refid, f.next_pos, f.next_pos + 1, opts));
             }
         }
-        // filter out duplicate chunks (the blocks are lists of chunks, blocks are
-        // concatenated, then filter dup chunks)
         const map = new Map();
         const res = await Promise.all(matePromises);
-        for (const m of res.flat()) {
-            if (!map.has(m.toString())) {
-                map.set(m.toString(), m);
+        for (let i = 0, l = res.length; i < l; i++) {
+            const chunks = res[i];
+            for (let j = 0, jl = chunks.length; j < jl; j++) {
+                const m = chunks[j];
+                const key = m.toString();
+                if (!map.has(key)) {
+                    map.set(key, m);
+                }
             }
         }
         const mateFeatPromises = await Promise.all([...map.values()].map(async (c) => {
@@ -276,8 +271,11 @@ class BamFile {
                 opts,
             });
             const mateRecs = [];
-            for (const feature of await this.readBamFeatures(data, cpositions, dpositions, chunk)) {
-                if (unmatedPairs[feature.name] && !readIds[feature.fileOffset]) {
+            const features = await this.readBamFeatures(data, cpositions, dpositions, chunk);
+            for (let i = 0, l = features.length; i < l; i++) {
+                const feature = features[i];
+                if (readNameCounts[feature.name] === 1 &&
+                    !readIds[feature.fileOffset]) {
                     mateRecs.push(feature);
                 }
             }
@@ -287,7 +285,7 @@ class BamFile {
     }
     async _readChunk({ chunk, opts }) {
         const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
-        const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk, this.cache);
+        const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk);
         return { data, cpositions, dpositions, chunk };
     }
     async readBamFeatures(ba, cpositions, dpositions, chunk) {
@@ -361,14 +359,17 @@ class BamFile {
         if (!this.chrToIndex) {
             throw new Error('Header not yet parsed');
         }
-        const regionsWithIds = regions.map(r => {
+        return this.index.estimatedBytesForRegions(regions.map(r => {
             const refId = this.chrToIndex[r.refName];
             if (refId === undefined) {
                 throw new Error(`Unknown reference name: ${r.refName}`);
             }
-            return { refId, start: r.start, end: r.end };
-        });
-        return this.index.estimatedBytesForRegions(regionsWithIds, opts);
+            return {
+                refId,
+                start: r.start,
+                end: r.end,
+            };
+        }), opts);
     }
 }
 exports.default = BamFile;

package/dist/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/htsget.d.ts CHANGED Viewed

@@ -1,5 +1,4 @@
 import BamFile from './bamFile.ts';
-import Chunk from './chunk.ts';
 import BamRecord from './record.ts';
 import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
 import type { BamOpts, BaseOpts } from './util.ts';
@@ -11,16 +10,7 @@ export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends Bam
         baseUrl: string;
         recordClass?: BamRecordClass<T>;
     });
-    streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
-    _readChunk({ chunk }: {
-        chunk: Chunk;
-        opts: BaseOpts;
-    }): Promise<{
-        data: Uint8Array<ArrayBuffer>;
-        cpositions: never[];
-        dpositions: never[];
-        chunk: Chunk;
-    }>;
+    getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
     getHeader(opts?: BaseOpts): Promise<{
         tag: string;
         data: {

package/dist/htsget.js CHANGED Viewed

@@ -72,62 +72,36 @@ class HtsgetFile extends bamFile_ts_1.default {
         this.baseUrl = args.baseUrl;
         this.trackId = args.trackId;
     }
-    async *streamRecordsForRange(chr, min, max, opts) {
+    async getRecordsForRange(chr, min, max, opts) {
         const base = `${this.baseUrl}/${this.trackId}`;
         const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
         const chrId = this.chrToIndex?.[chr];
         if (chrId === undefined) {
-            yield [];
+            return [];
         }
-        else {
-            const result = await fetch(url, { ...opts });
-            if (!result.ok) {
-                throw new Error(`HTTP ${result.status} fetching ${url}: ${await result.text()}`);
-            }
-            const data = await result.json();
-            const uncba = await concat(data.htsget.urls.slice(1), opts);
-            yield* this._fetchChunkFeatures([
-                // fake stuff to pretend to be a Chunk
-                {
-                    buffer: uncba,
-                    _fetchedSize: undefined,
-                    bin: 0,
-                    compareTo() {
-                        return 0;
-                    },
-                    toUniqueString() {
-                        return `${chr}_${min}_${max}`;
-                    },
-                    fetchedSize() {
-                        return 0;
-                    },
-                    minv: {
-                        dataPosition: 0,
-                        blockPosition: 0,
-                        compareTo: () => 0,
-                    },
-                    maxv: {
-                        dataPosition: Number.MAX_SAFE_INTEGER,
-                        blockPosition: 0,
-                        compareTo: () => 0,
-                    },
-                    toString() {
-                        return `${chr}_${min}_${max}`;
-                    },
-                },
-            ], chrId, min, max, opts);
+        const result = await fetch(url, { ...opts });
+        if (!result.ok) {
+            throw new Error(`HTTP ${result.status} fetching ${url}: ${await result.text()}`);
         }
-    }
-    async _readChunk({ chunk }) {
-        if (!chunk.buffer) {
-            throw new Error('expected chunk.buffer in htsget');
+        const data = await result.json();
+        const uncba = await concat(data.htsget.urls.slice(1), opts);
+        const allRecords = await this.readBamFeatures(uncba, [], [], {
+            minv: { dataPosition: 0, blockPosition: 0 },
+            maxv: { dataPosition: 0, blockPosition: 0 },
+        });
+        const records = [];
+        for (let i = 0, l = allRecords.length; i < l; i++) {
+            const feature = allRecords[i];
+            if (feature.ref_id === chrId) {
+                if (feature.start >= max) {
+                    break;
+                }
+                else if (feature.end >= min) {
+                    records.push(feature);
+                }
+            }
         }
-        return {
-            data: chunk.buffer,
-            cpositions: [],
-            dpositions: [],
-            chunk,
-        };
+        return records;
     }
     async getHeader(opts = {}) {
         const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;

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