@gmod/bam 7.4.0 → 7.5.0

package/README.md

@@ -59,8 +59,7 @@ const records = await ti.getRecordsForRange('1', 2000000, 2000001)
 Let us know if it doesn't work for your use case.
 
 Caveat: htsget `getRecordsForRange` does not honor `viewAsPairs`,
-`pairAcrossChr`, `maxInsertSize`, or `filterBy`. The range is fetched from the
-server as-is.
+`pairAcrossChr`, or `maxInsertSize`. The range is fetched from the server as-is.
 
 ## Documentation
 
@@ -93,8 +92,16 @@ Note: requires calling `getHeader` first.
   chromosomes. default: false
 - `opts.maxInsertSize` - control the viewAsPairs option behavior to limit
   distance within a chromosome to fetch. default: 200kb
-- `opts.filterBy` - a `FilterBy` object to filter records by flag bits or a tag
-  value (see `FilterBy` below)
+
+Records come back unfiltered. Filter the returned array yourself — the flag
+helpers (`record.isSecondary()` and friends) and `record.getTag(name)` cover it,
+and `getTag` decodes just the one tag rather than every tag on the read:
+
+```typescript
+const records = (await bam.getRecordsForRange('chr1', 0, 100000)).filter(
+  r => r.isProperlyPaired() && !r.isSecondary() && r.getTag('RG') === 'rg1',
+)
+```
 
 ### async getHeader(opts?)
 
@@ -173,31 +180,6 @@ record.seqAt(idx) // get single base at position
 record.toJSON() // serialize record
 ```
 
-### FilterBy
-
-```typescript
-interface FilterBy {
-  flagInclude?: number // only include reads where all these flag bits are set
-  flagExclude?: number // exclude reads where any of these flag bits are set
-  tagFilter?: {
-    tag: string // aux tag name, e.g. 'RG'
-    value?: string // omit to filter by tag presence only
-  }
-}
-```
-
-Example — fetch only properly-paired primary alignments from read-group `rg1`:
-
-```typescript
-const records = await bam.getRecordsForRange('chr1', 0, 100000, {
-  filterBy: {
-    flagInclude: 0x2, // properly paired
-    flagExclude: 0x900, // not secondary or supplementary
-    tagFilter: { tag: 'RG', value: 'rg1' },
-  },
-})
-```
-
 ### Custom BamRecord class
 
 You can provide your own BamRecord class to add custom properties or methods:

package/dist/bamFile.d.ts

@@ -23,8 +23,6 @@ export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
 }) => T;
 export declare const BAM_MAGIC = 21840194;
 interface ChunkEntry<T> {
-    minBlock: number;
-    maxBlock: number;
     bytes: number;
     features: T[];
 }
@@ -89,7 +87,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     private getSeqId;
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
-    private evictOverlappingChunks;
+    private _cachedChunkFeatures;
     private _fetchChunkFeatures;
     fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
     _readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<{

package/dist/bamFile.js

@@ -19,10 +19,6 @@ function resolveFilehandle(filehandle, path, url) {
     return (filehandle ??
         (path ? new generic_filehandle2_1.LocalFile(path) : url ? new generic_filehandle2_1.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}`;
@@ -31,7 +27,9 @@ 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.
 exports.DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
 class ChunkFeatureCache {
     maxBytes;
@@ -91,8 +89,7 @@ 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 = exports.DEFAULT_MAX_CACHE_BYTES, }) {
@@ -188,16 +185,21 @@ 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++) {
@@ -207,22 +209,10 @@ 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
-                ? (0, util_ts_1.applyFilters)(cached.features, filterBy)
-                : cached.features;
+            const features = await this._cachedChunkFeatures(chunk, opts);
             downloadedBytes += chunk.fetchedSize();
             onProgress?.(downloadedBytes, totalBytes);
-            (0, util_ts_1.appendInRange)(records, chrId, min, max, result);
+            (0, util_ts_1.appendInRange)(features, chrId, min, max, result);
         }
         if (viewAsPairs) {
             const pairs = await this.fetchPairs(chrId, result, opts);
@@ -267,7 +257,7 @@ 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/dist/bamFile.js.map

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

@@ -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/dist/record.js

@@ -47,6 +47,42 @@ 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;
@@ -206,9 +242,7 @@ 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];
@@ -297,6 +331,13 @@ 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;
@@ -358,7 +399,7 @@ 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/dist/record.js.map

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

@@ -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/dist/util.js

@@ -10,9 +10,6 @@ exports.parseRefSeqs = parseRefSeqs;
 exports.findFirstData = findFirstData;
 exports.parseNameBytes = parseNameBytes;
 exports.concatUint8Array = concatUint8Array;
-exports.filterReadFlag = filterReadFlag;
-exports.filterTagValue = filterTagValue;
-exports.applyFilters = applyFilters;
 exports.appendInRange = appendInRange;
 const chunk_ts_1 = __importDefault(require("./chunk.js"));
 const long_ts_1 = require("./long.js");
@@ -183,33 +180,6 @@ function concatUint8Array(args) {
     }
     return mergedArray;
 }
-function filterReadFlag(flags, flagInclude, flagExclude) {
-    return (flags & flagInclude) !== flagInclude || (flags & flagExclude) !== 0;
-}
-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.
-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/dist/util.js.map

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

@@ -23,8 +23,6 @@ export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
 }) => T;
 export declare const BAM_MAGIC = 21840194;
 interface ChunkEntry<T> {
-    minBlock: number;
-    maxBlock: number;
     bytes: number;
     features: T[];
 }
@@ -89,7 +87,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
     getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     private getSeqId;
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
-    private evictOverlappingChunks;
+    private _cachedChunkFeatures;
     private _fetchChunkFeatures;
     fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
     _readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<{