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/esm/bamFile.js CHANGED Viewed

@@ -7,18 +7,17 @@ import CSI from "./csi.js";
 import NullFilehandle from "./nullFilehandle.js";
 import BAMFeature from "./record.js";
 import { parseHeaderText } from "./sam.js";
-import { gen2array, makeOpts } from "./util.js";
+import { filterCacheKey, filterReadFlag, filterTagValue, makeOpts, } from "./util.js";
 export const BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
 export default class BamFile {
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
         this.htsget = false;
-        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.chunkFeatureCache = new QuickLRU({
+            maxSize: 100,
+        });
         this.renameRefSeq = renameRefSeqs;
         this.RecordClass = (recordClass ?? BAMFeature);
         if (bamFilehandle) {
@@ -125,26 +124,26 @@ export default 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 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}${filterCacheKey(filterBy)}`;
     }
     blocksOverlap(minBlock1, maxBlock1, minBlock2, maxBlock2) {
         return minBlock1 <= maxBlock2 && maxBlock1 >= minBlock2;
@@ -153,28 +152,23 @@ export default 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);
@@ -182,86 +176,87 @@ export default 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 (filterReadFlag(record.flags, flagInclude, flagExclude)) {
+                            continue;
+                        }
+                        if (tagFilter &&
+                            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) => {
@@ -270,8 +265,11 @@ export default 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);
                 }
             }
@@ -281,7 +279,7 @@ export default class BamFile {
     }
     async _readChunk({ chunk, opts }) {
         const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
-        const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk, this.cache);
+        const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buf, chunk);
         return { data, cpositions, dpositions, chunk };
     }
     async readBamFeatures(ba, cpositions, dpositions, chunk) {
@@ -355,14 +353,17 @@ export default 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);
     }
 }
 //# sourceMappingURL=bamFile.js.map

package/esm/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/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/esm/htsget.js CHANGED Viewed

@@ -37,62 +37,36 @@ export default class HtsgetFile extends BamFile {
         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`;

package/esm/htsget.js.map CHANGED Viewed

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

@@ -1,5 +1,8 @@
 export { default as BAI } from './bai.ts';
-export { type BamRecordClass, type BamRecordLike, default as BamFile, } from './bamFile.ts';
+export { default as BamFile } from './bamFile.ts';
 export { default as CSI } from './csi.ts';
-export { type Bytes, default as BamRecord } from './record.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/index.js CHANGED Viewed

@@ -1,5 +1,5 @@
 export { default as BAI } from "./bai.js";
-export { default as BamFile, } from "./bamFile.js";
+export { default as BamFile } from "./bamFile.js";
 export { default as CSI } from "./csi.js";
 export { default as BamRecord } from "./record.js";
 export { default as HtsgetFile } from "./htsget.js";

package/esm/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,~~EAGL~~,OAAO,IAAI,OAAO,~~GACnB~~,MAAM,cAAc,CAAA;~~AACrB~~,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,~~EAAc~~,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;~~AAC9D~~,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA"}

package/esm/record.d.ts CHANGED Viewed

@@ -5,13 +5,16 @@ export interface Bytes {
 }
 interface CIGAR_AND_LENGTH {
     length_on_ref: number;
-    NUMERIC_CIGAR: Uint32Array;
+    NUMERIC_CIGAR: Uint32Array | number[];
 }
 export default class BamRecord {
     fileOffset: number;
     private bytes;
     private _dataView;
     private _cachedFlags?;
+    private _cachedRefId?;
+    private _cachedStart?;
+    private _cachedEnd?;
     private _cachedTags?;
     private _cachedCigarAndLength?;
     private _cachedNUMERIC_MD?;
@@ -48,7 +51,7 @@ export default class BamRecord {
     get cigarAndLength(): CIGAR_AND_LENGTH;
     private _computeCigarAndLength;
     get length_on_ref(): number;
-    get NUMERIC_CIGAR(): Uint32Array<ArrayBufferLike>;
+    get NUMERIC_CIGAR(): number[] | Uint32Array<ArrayBufferLike>;
     get CIGAR(): string;
     get num_cigar_ops(): number;
     get num_cigar_bytes(): number;