npm - @gmod/bam - Versions diffs - 7.1.0 → 7.1.1 - Mend

@gmod/bam 7.1.0 → 7.1.1

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 (9) hide show

package/CHANGELOG.md CHANGED Viewed

@@ -1,3 +1,7 @@
+## [7.1.1](https://github.com/GMOD/bam-js/compare/v7.1.0...v7.1.1) (2025-12-12)
 # [7.1.0](https://github.com/GMOD/bam-js/compare/v7.0.6...v7.1.0) (2025-12-11)

package/dist/bamFile.d.ts CHANGED Viewed

@@ -23,6 +23,11 @@ export default class BamFile {
         buffer: Uint8Array;
         nextIn: number;
     }>;
+    chunkFeatureCache: QuickLRU<string, {
+        minBlock: number;
+        maxBlock: number;
+        features: BAMFeature[];
+    }>;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
@@ -60,6 +65,9 @@ export default class BamFile {
     };
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
     streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
+    private chunkCacheKey;
+    private blocksOverlap;
+    private evictOverlappingChunks;
     _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
     _readChunk({ chunk, opts }: {
@@ -77,4 +85,5 @@ export default class BamFile {
     lineCount(seqName: string): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai.ts").IndexCovEntry[]>;
     blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
+    clearFeatureCache(): void;
 }

package/dist/bamFile.js CHANGED Viewed

@@ -22,6 +22,9 @@ class BamFile {
         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.renameRefSeq = renameRefSeqs;
         if (bamFilehandle) {
             this.bam = bamFilehandle;
@@ -144,26 +147,62 @@ class BamFile {
         const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
         yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts);
     }
+    chunkCacheKey(chunk) {
+        const { minv, maxv } = chunk;
+        return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
+    }
+    blocksOverlap(minBlock1, maxBlock1, minBlock2, maxBlock2) {
+        return minBlock1 <= maxBlock2 && maxBlock1 >= minBlock2;
+    }
+    // Evict any cached chunks that overlap with the given block range
+    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 { data, cpositions, dpositions } = await this._readChunk({
-                chunk,
-                opts,
-            });
-            const records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
+            const cacheKey = this.chunkCacheKey(chunk);
+            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);
+                const { data, cpositions, dpositions } = await this._readChunk({
+                    chunk,
+                    opts,
+                });
+                records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
+                this.chunkFeatureCache.set(cacheKey, {
+                    minBlock,
+                    maxBlock,
+                    features: records,
+                });
+                // cacheMisses++
+            }
             const recs = [];
             for (const feature of records) {
                 if (feature.ref_id === chrId) {
                     if (feature.start >= max) {
-                        // past end of range, can stop iterating
                         done = true;
                         break;
                     }
                     else if (feature.end >= min) {
-                        // must be in range
                         recs.push(feature);
                     }
                 }
@@ -174,6 +213,13 @@ class BamFile {
                 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);
         }
@@ -308,6 +354,9 @@ class BamFile {
             ? []
             : this.index.blocksForRange(seqId, start, end, opts);
     }
+    clearFeatureCache() {
+        this.chunkFeatureCache.clear();
+    }
 }
 exports.default = BamFile;
 //# sourceMappingURL=bamFile.js.map

package/dist/bamFile.js.map CHANGED Viewed

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

@@ -23,6 +23,11 @@ export default class BamFile {
         buffer: Uint8Array;
         nextIn: number;
     }>;
+    chunkFeatureCache: QuickLRU<string, {
+        minBlock: number;
+        maxBlock: number;
+        features: BAMFeature[];
+    }>;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
@@ -60,6 +65,9 @@ export default class BamFile {
     };
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
     streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
+    private chunkCacheKey;
+    private blocksOverlap;
+    private evictOverlappingChunks;
     _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
     _readChunk({ chunk, opts }: {
@@ -77,4 +85,5 @@ export default class BamFile {
     lineCount(seqName: string): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai.ts").IndexCovEntry[]>;
     blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
+    clearFeatureCache(): void;
 }

package/esm/bamFile.js CHANGED Viewed

@@ -16,6 +16,9 @@ export default class BamFile {
         this.cache = new QuickLRU({
             maxSize: 1000,
         });
+        // Cache for parsed features by chunk
+        // When a new chunk overlaps a cached chunk, we evict the cached one
+        this.chunkFeatureCache = new QuickLRU({ maxSize: 100 });
         this.renameRefSeq = renameRefSeqs;
         if (bamFilehandle) {
             this.bam = bamFilehandle;
@@ -138,26 +141,62 @@ export default class BamFile {
         const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
         yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts);
     }
+    chunkCacheKey(chunk) {
+        const { minv, maxv } = chunk;
+        return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
+    }
+    blocksOverlap(minBlock1, maxBlock1, minBlock2, maxBlock2) {
+        return minBlock1 <= maxBlock2 && maxBlock1 >= minBlock2;
+    }
+    // Evict any cached chunks that overlap with the given block range
+    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 { data, cpositions, dpositions } = await this._readChunk({
-                chunk,
-                opts,
-            });
-            const records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
+            const cacheKey = this.chunkCacheKey(chunk);
+            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);
+                const { data, cpositions, dpositions } = await this._readChunk({
+                    chunk,
+                    opts,
+                });
+                records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
+                this.chunkFeatureCache.set(cacheKey, {
+                    minBlock,
+                    maxBlock,
+                    features: records,
+                });
+                // cacheMisses++
+            }
             const recs = [];
             for (const feature of records) {
                 if (feature.ref_id === chrId) {
                     if (feature.start >= max) {
-                        // past end of range, can stop iterating
                         done = true;
                         break;
                     }
                     else if (feature.end >= min) {
-                        // must be in range
                         recs.push(feature);
                     }
                 }
@@ -168,6 +207,13 @@ export default class BamFile {
                 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);
         }
@@ -302,5 +348,8 @@ export default class BamFile {
             ? []
             : this.index.blocksForRange(seqId, start, end, opts);
     }
+    clearFeatureCache() {
+        this.chunkFeatureCache.clear();
+    }
 }
 //# sourceMappingURL=bamFile.js.map

package/esm/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.1.0",
+  "version": "7.1.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -50,9 +50,9 @@
     "genomics"
   ],
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^6.0.3",
+    "@gmod/bgzf-filehandle": "^6.0.5",
     "crc": "^4.3.2",
-    "generic-filehandle2": "^2.0.1",
+    "generic-filehandle2": "^2.0.16",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {

package/src/bamFile.ts CHANGED Viewed

@@ -34,6 +34,13 @@ export default class BamFile {
     maxSize: 1000,
   })
+  // Cache for parsed features by chunk
+  // When a new chunk overlaps a cached chunk, we evict the cached one
+  public chunkFeatureCache = new QuickLRU<
+    string,
+    { minBlock: number; maxBlock: number; features: BAMFeature[] }
+  >({ maxSize: 100 })
   constructor({
     bamFilehandle,
     bamPath,
@@ -209,6 +216,34 @@ export default class BamFile {
     yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts)
   }
+  private chunkCacheKey(chunk: Chunk) {
+    const { minv, maxv } = chunk
+    return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`
+  }
+  private blocksOverlap(
+    minBlock1: number,
+    maxBlock1: number,
+    minBlock2: number,
+    maxBlock2: number,
+  ) {
+    return minBlock1 <= maxBlock2 && maxBlock1 >= minBlock2
+  }
+  // Evict any cached chunks that overlap with the given block range
+  private evictOverlappingChunks(minBlock: number, maxBlock: number) {
+    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: Chunk[],
     chrId: number,
@@ -219,28 +254,46 @@ export default class BamFile {
     const { viewAsPairs } = opts
     const feats = [] as BAMFeature[][]
     let done = false
+    // let cacheHits = 0
+    // let cacheMisses = 0
     for (const chunk of chunks) {
-      const { data, cpositions, dpositions } = await this._readChunk({
-        chunk,
-        opts,
-      })
-      const records = await this.readBamFeatures(
-        data,
-        cpositions,
-        dpositions,
-        chunk,
-      )
+      const cacheKey = this.chunkCacheKey(chunk)
+      const minBlock = chunk.minv.blockPosition
+      const maxBlock = chunk.maxv.blockPosition
+      let records: BAMFeature[]
+      const cached = this.chunkFeatureCache.get(cacheKey)
+      if (cached) {
+        records = cached.features
+        // cacheHits++
+      } else {
+        this.evictOverlappingChunks(minBlock, maxBlock)
+        const { data, cpositions, dpositions } = await this._readChunk({
+          chunk,
+          opts,
+        })
+        records = await this.readBamFeatures(
+          data,
+          cpositions,
+          dpositions,
+          chunk,
+        )
+        this.chunkFeatureCache.set(cacheKey, {
+          minBlock,
+          maxBlock,
+          features: records,
+        })
+        // cacheMisses++
+      }
       const recs = [] as BAMFeature[]
       for (const feature of records) {
         if (feature.ref_id === chrId) {
           if (feature.start >= max) {
-            // past end of range, can stop iterating
             done = true
             break
           } else if (feature.end >= min) {
-            // must be in range
             recs.push(feature)
           }
         }
@@ -252,6 +305,14 @@ export default class BamFile {
       }
     }
+    // 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)
     }
@@ -438,4 +499,8 @@ export default class BamFile {
       ? []
       : this.index.blocksForRange(seqId, start, end, opts)
   }
+  clearFeatureCache() {
+    this.chunkFeatureCache.clear()
+  }
 }