npm - @gmod/bam - Versions diffs - 7.4.0 → 7.5.0 - Mend

@gmod/bam 7.4.0 → 7.5.0

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 (24) hide show

package/esm/bamFile.js CHANGED Viewed

@@ -6,17 +6,13 @@ import CSI from "./csi.js";
 import NullFilehandle from "./nullFilehandle.js";
 import BAMFeature from "./record.js";
 import { parseHeaderText } from "./sam.js";
-import { appendInRange, applyFilters, parseRefSeqs } from "./util.js";
+import { appendInRange, parseRefSeqs } from "./util.js";
 export const BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
 function resolveFilehandle(filehandle, path, url) {
     return (filehandle ??
         (path ? new LocalFile(path) : url ? new RemoteFile(url) : undefined));
 }
-// Keyed on the chunk's byte span only, not on filterBy: the cached value is the
-// unfiltered parsed records (decompression + parse is the expensive part).
-// Filters are applied cheaply on retrieval so toggling a filter over the same
-// region is a cache hit rather than a re-decompress.
 function chunkCacheKey(chunk) {
     const { minv, maxv } = chunk;
     return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
@@ -25,7 +21,9 @@ function chunkCacheKey(chunk) {
 // caching one entry pins that whole buffer — 8MB apiece on the nanopore and
 // 2kb-read test files, and optimizeChunks merges spans up to 5MB *compressed*,
 // so tens of MB is possible. A count-based LRU therefore gives no bound on
-// memory at all, which is why this budgets by decompressed bytes instead.
+// memory at all, which is why this budgets by decompressed bytes instead. It is
+// the *only* bound: a query keeps every chunk it parsed, since a chunk dropped
+// here costs a re-download and re-decompress the next time the view moves.
 export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
 class ChunkFeatureCache {
     maxBytes;
@@ -85,8 +83,7 @@ export default class BamFile {
     index;
     htsget = false;
     headerP;
-    // Cache for parsed features by chunk
-    // When a new chunk overlaps a cached chunk, we evict the cached one
+    // Cache for parsed features by chunk, bounded by decompressed bytes
     chunkFeatureCache;
     RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = DEFAULT_MAX_CACHE_BYTES, }) {
@@ -182,16 +179,21 @@ export default class BamFile {
         const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
         return this._fetchChunkFeatures(chunks, chrId, min, max, opts);
     }
-    // Evict any cached chunks whose block range overlaps [minBlock, maxBlock]
-    evictOverlappingChunks(minBlock, maxBlock) {
-        for (const [key, entry] of this.chunkFeatureCache) {
-            if (minBlock <= entry.maxBlock && maxBlock >= entry.minBlock) {
-                this.chunkFeatureCache.delete(key);
-            }
+    // Parsed records for a chunk, reading and decompressing it only on a miss.
+    // Every path that wants a chunk's features goes through here — mate lookups
+    // included, since a viewAsPairs query revisits the same mate chunks each time
+    // the view moves.
+    async _cachedChunkFeatures(chunk, opts) {
+        const cacheKey = chunkCacheKey(chunk);
+        let entry = this.chunkFeatureCache.get(cacheKey);
+        if (!entry) {
+            entry = await this._readChunkFeatures(chunk, opts);
+            this.chunkFeatureCache.set(cacheKey, entry);
         }
+        return entry.features;
     }
     async _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
-        const { viewAsPairs, filterBy, onProgress } = opts;
+        const { viewAsPairs, onProgress } = opts;
         const result = [];
         let totalBytes = 0;
         for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
@@ -201,22 +203,10 @@ export default class BamFile {
         onProgress?.(0, totalBytes);
         for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
             const chunk = chunks[ci];
-            const cacheKey = chunkCacheKey(chunk);
-            const minBlock = chunk.minv.blockPosition;
-            const maxBlock = chunk.maxv.blockPosition;
-            let cached = this.chunkFeatureCache.get(cacheKey);
-            if (!cached) {
-                this.evictOverlappingChunks(minBlock, maxBlock);
-                const { features, bytes } = await this._readChunkFeatures(chunk, opts);
-                cached = { minBlock, maxBlock, bytes, features };
-                this.chunkFeatureCache.set(cacheKey, cached);
-            }
-            const records = filterBy
-                ? applyFilters(cached.features, filterBy)
-                : cached.features;
+            const features = await this._cachedChunkFeatures(chunk, opts);
             downloadedBytes += chunk.fetchedSize();
             onProgress?.(downloadedBytes, totalBytes);
-            appendInRange(records, chrId, min, max, result);
+            appendInRange(features, chrId, min, max, result);
         }
         if (viewAsPairs) {
             const pairs = await this.fetchPairs(chrId, result, opts);
@@ -261,7 +251,7 @@ export default class BamFile {
             }
         }
         const mateFeatLists = await Promise.all([...map.values()].map(async (c) => {
-            const { features } = await this._readChunkFeatures(c, opts);
+            const features = await this._cachedChunkFeatures(c, opts);
             const mateRecs = [];
             for (let i = 0, l = features.length; i < l; i++) {
                 const feature = features[i];

package/esm/bamFile.js.map CHANGED Viewed

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

@@ -4,5 +4,4 @@ export { default as CSI } from './csi.ts';
 export { default as BamRecord } from './record.ts';
 export { default as HtsgetFile } from './htsget.ts';
 export type { Bytes } from './record.ts';
-export type { FilterBy, TagFilter } from './util.ts';
 export type { BamRecordClass, BamRecordLike } from './bamFile.ts';

package/esm/record.js CHANGED Viewed

@@ -42,6 +42,42 @@ const ASCII_CIGAR_CODES = [
     77, 73, 68, 78, 83, 72, 80, 61, 88, 63, 63, 63, 63, 63, 63, 63,
 ];
 const textDecoder = new TextDecoder();
+// Interned two-char tag names keyed on the packed byte pair. Worth more than
+// the saved String.fromCharCode: the tags object is null-prototype and so in
+// dictionary mode, and handing it a string V8 has already hashed halves the
+// per-tag insert cost.
+const TAG_NAMES = new Map();
+function tagName(b0, b1) {
+    const key = (b0 << 8) | b1;
+    let name = TAG_NAMES.get(key);
+    if (name === undefined) {
+        name = String.fromCharCode(b0, b1);
+        TAG_NAMES.set(key, name);
+    }
+    return name;
+}
+// TextDecoder carries ~0.35us of fixed setup per call, which dominates for the
+// short values Z/H tags usually hold (MD, RG, PG, ...): char codes are 4x
+// faster at 8 bytes, 2x at 16, and the two cross over at 32.
+const SHORT_STRING_THRESHOLD = 32;
+// Z/H tag values are spec'd as printable ASCII, but a non-conforming writer
+// would make the char-code path mis-decode UTF-8, so bail to TextDecoder on any
+// high byte.
+function decodeTagString(ba, start, end) {
+    const len = end - start;
+    if (len < SHORT_STRING_THRESHOLD) {
+        const codes = new Array(len);
+        for (let i = 0; i < len; i++) {
+            const byte = ba[start + i];
+            if (byte > 0x7f) {
+                return textDecoder.decode(ba.subarray(start, end));
+            }
+            codes[i] = byte;
+        }
+        return String.fromCharCode(...codes);
+    }
+    return textDecoder.decode(ba.subarray(start, end));
+}
 // Bitmask for ops that consume ref: M=0, D=2, N=3, P=6, ==7, X=8
 // Binary: 0b111001101 = 0x1CD
 const CIGAR_CONSUMES_REF_MASK = 0x1cd;
@@ -201,9 +237,7 @@ function decodeTagValue(ba, dataView, type, p, end, raw) {
             return dataView.getFloat32(p, true);
         case 0x5a: // 'Z'
         case 0x48: // 'H'
-            return raw
-                ? ba.subarray(p, end - 1)
-                : textDecoder.decode(ba.subarray(p, end - 1));
+            return raw ? ba.subarray(p, end - 1) : decodeTagString(ba, p, end - 1);
         default: {
             // 'B'
             const Btype = ba[p];
@@ -292,6 +326,13 @@ export default class BamRecord {
         return this.seqStart + ((seqLen + 1) >> 1) + seqLen;
     }
     // batch fromCharCode: fastest for typical name lengths (see benchmarks/string-building.bench.ts)
+    //
+    // Deliberately NOT memoized, unlike end/tags/length_on_ref. Consumers read a
+    // read name about once — jbrowse-components' buildBaseFeatureData copies it
+    // straight into its own FeatureData — so a cache would pay a field slot on
+    // every record (+180KB per 22k-record chunk) to save zero decodes, and would
+    // pin every name string for as long as the chunk stays cached (+520KB) where
+    // today it dies with the consumer's copy.
     get name() {
         const len = this.read_name_length - 1;
         const start = this.b0;
@@ -353,7 +394,7 @@ export default class BamRecord {
         const tags = Object.create(null);
         let p = this.tagsStart;
         while (p < blockEnd) {
-            const tag = String.fromCharCode(ba[p], ba[p + 1]);
+            const tag = tagName(ba[p], ba[p + 1]);
             const type = ba[p + 2];
             const valueStart = p + 3;
             const end = tagValueEnd(ba, this._dataView, type, valueStart, blockEnd);

package/esm/record.js.map CHANGED Viewed

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

@@ -1,20 +1,10 @@
 import Chunk from './chunk.ts';
 import type { Offset, VirtualOffset } from './virtualOffset.ts';
-export interface TagFilter {
-    tag: string;
-    value?: string;
-}
-export interface FilterBy {
-    flagInclude?: number;
-    flagExclude?: number;
-    tagFilter?: TagFilter;
-}
 export interface BamOpts {
     viewAsPairs?: boolean;
     pairAcrossChr?: boolean;
     maxInsertSize?: number;
     signal?: AbortSignal;
-    filterBy?: FilterBy;
     /**
      * Called as the BGZF blocks covering the query are fetched, with cumulative
      * downloaded bytes and the total to fetch. Reported at block granularity (one
@@ -52,14 +42,6 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
     refIdToName: string[];
 };
 export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
-export declare function filterReadFlag(flags: number, flagInclude: number, flagExclude: number): boolean;
-export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;
-interface Filterable {
-    flags: number;
-    tags: Record<string, unknown>;
-    getTag?(tag: string): unknown;
-}
-export declare function applyFilters<T extends Filterable>(records: T[], filterBy: FilterBy): T[];
 interface Positioned {
     ref_id: number;
     start: number;

package/esm/util.js CHANGED Viewed

@@ -167,33 +167,6 @@ export function concatUint8Array(args) {
     }
     return mergedArray;
 }
-export function filterReadFlag(flags, flagInclude, flagExclude) {
-    return (flags & flagInclude) !== flagInclude || (flags & flagExclude) !== 0;
-}
-export function filterTagValue(readVal, filterVal) {
-    return filterVal === '*'
-        ? readVal === undefined
-        : `${readVal}` !== `${filterVal}`;
-}
-// Read a single tag, preferring the targeted accessor. Reaching for `tags`
-// instead would decode every unrelated tag on the record (NM/AS/ms/de/… — often
-// ~10 per read) just to test one, which measured 2.6x the cost of getTag.
-function readTag(record, tag) {
-    return record.getTag ? record.getTag(tag) : record.tags[tag];
-}
-// Apply flagInclude/flagExclude/tagFilter to a list of records.
-export function applyFilters(records, filterBy) {
-    const { flagInclude = 0, flagExclude = 0, tagFilter } = filterBy;
-    const out = [];
-    for (let i = 0, l = records.length; i < l; i++) {
-        const r = records[i];
-        if (!filterReadFlag(r.flags, flagInclude, flagExclude) &&
-            !(tagFilter && filterTagValue(readTag(r, tagFilter.tag), tagFilter.value))) {
-            out.push(r);
-        }
-    }
-    return out;
-}
 // Append records overlapping [min, max) on `chrId` into `out` (or a fresh
 // array if omitted). Records are assumed coordinate-sorted (by ref_id, then
 // start), so we stop scanning once we pass `max` within `chrId` or move past

package/esm/util.js.map CHANGED Viewed

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

@@ -1,6 +1,7 @@
 {
   "name": "@gmod/bam",
-  "version": "7.4.0",
+  "version": "7.5.0",
+  "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": {

package/src/bamFile.ts CHANGED Viewed

@@ -7,7 +7,7 @@ import CSI from './csi.ts'
 import NullFilehandle from './nullFilehandle.ts'
 import BAMFeature from './record.ts'
 import { parseHeaderText } from './sam.ts'
-import { appendInRange, applyFilters, parseRefSeqs } from './util.ts'
+import { appendInRange, parseRefSeqs } from './util.ts'
 import type Chunk from './chunk.ts'
 import type { Bytes } from './record.ts'
@@ -48,17 +48,11 @@ function resolveFilehandle(
 }
 interface ChunkEntry<T> {
-  minBlock: number
-  maxBlock: number
   // decompressed size of the chunk these features are views into
   bytes: number
   features: T[]
 }
-// Keyed on the chunk's byte span only, not on filterBy: the cached value is the
-// unfiltered parsed records (decompression + parse is the expensive part).
-// Filters are applied cheaply on retrieval so toggling a filter over the same
-// region is a cache hit rather than a re-decompress.
 function chunkCacheKey(chunk: Chunk) {
   const { minv, maxv } = chunk
   return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`
@@ -68,7 +62,9 @@ function chunkCacheKey(chunk: Chunk) {
 // caching one entry pins that whole buffer — 8MB apiece on the nanopore and
 // 2kb-read test files, and optimizeChunks merges spans up to 5MB *compressed*,
 // so tens of MB is possible. A count-based LRU therefore gives no bound on
-// memory at all, which is why this budgets by decompressed bytes instead.
+// memory at all, which is why this budgets by decompressed bytes instead. It is
+// the *only* bound: a query keeps every chunk it parsed, since a chunk dropped
+// here costs a re-download and re-decompress the next time the view moves.
 export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024
 class ChunkFeatureCache<T> {
@@ -139,8 +135,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
   public htsget = false
   public headerP?: ReturnType<BamFile<T>['getHeaderPre']>
-  // Cache for parsed features by chunk
-  // When a new chunk overlaps a cached chunk, we evict the cached one
+  // Cache for parsed features by chunk, bounded by decompressed bytes
   public chunkFeatureCache: ChunkFeatureCache<T>
   private RecordClass: BamRecordClass<T>
@@ -295,13 +290,18 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     return this._fetchChunkFeatures(chunks, chrId, min, max, opts)
   }
-  // Evict any cached chunks whose block range overlaps [minBlock, maxBlock]
-  private evictOverlappingChunks(minBlock: number, maxBlock: number) {
-    for (const [key, entry] of this.chunkFeatureCache) {
-      if (minBlock <= entry.maxBlock && maxBlock >= entry.minBlock) {
-        this.chunkFeatureCache.delete(key)
-      }
+  // Parsed records for a chunk, reading and decompressing it only on a miss.
+  // Every path that wants a chunk's features goes through here — mate lookups
+  // included, since a viewAsPairs query revisits the same mate chunks each time
+  // the view moves.
+  private async _cachedChunkFeatures(chunk: Chunk, opts: BaseOpts) {
+    const cacheKey = chunkCacheKey(chunk)
+    let entry = this.chunkFeatureCache.get(cacheKey)
+    if (!entry) {
+      entry = await this._readChunkFeatures(chunk, opts)
+      this.chunkFeatureCache.set(cacheKey, entry)
     }
+    return entry.features
   }
   private async _fetchChunkFeatures(
@@ -311,7 +311,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     max: number,
     opts: BamOpts = {},
   ) {
-    const { viewAsPairs, filterBy, onProgress } = opts
+    const { viewAsPairs, onProgress } = opts
     const result: T[] = []
     let totalBytes = 0
@@ -323,24 +323,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
       const chunk = chunks[ci]!
-      const cacheKey = chunkCacheKey(chunk)
-      const minBlock = chunk.minv.blockPosition
-      const maxBlock = chunk.maxv.blockPosition
-      let cached = this.chunkFeatureCache.get(cacheKey)
-      if (!cached) {
-        this.evictOverlappingChunks(minBlock, maxBlock)
-        const { features, bytes } = await this._readChunkFeatures(chunk, opts)
-        cached = { minBlock, maxBlock, bytes, features }
-        this.chunkFeatureCache.set(cacheKey, cached)
-      }
-      const records = filterBy
-        ? applyFilters(cached.features, filterBy)
-        : cached.features
+      const features = await this._cachedChunkFeatures(chunk, opts)
       downloadedBytes += chunk.fetchedSize()
       onProgress?.(downloadedBytes, totalBytes)
-      appendInRange(records, chrId, min, max, result)
+      appendInRange(features, chrId, min, max, result)
     }
     if (viewAsPairs) {
@@ -402,7 +389,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     const mateFeatLists = await Promise.all(
       [...map.values()].map(async c => {
-        const { features } = await this._readChunkFeatures(c, opts)
+        const features = await this._cachedChunkFeatures(c, opts)
         const mateRecs = [] as T[]
         for (let i = 0, l = features.length; i < l; i++) {
           const feature = features[i]!

package/src/index.ts CHANGED Viewed

@@ -5,5 +5,4 @@ export { default as BamRecord } from './record.ts'
 export { default as HtsgetFile } from './htsget.ts'
 export type { Bytes } from './record.ts'
-export type { FilterBy, TagFilter } from './util.ts'
 export type { BamRecordClass, BamRecordLike } from './bamFile.ts'