npm - @gmod/bam - Versions diffs - 7.2.4 → 7.3.1 - Mend

@gmod/bam 7.2.4 → 7.3.1

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 (28) hide show

package/README.md CHANGED Viewed

@@ -1,5 +1,5 @@
 [![NPM version](https://img.shields.io/npm/v/@gmod/bam.svg?style=flat-square)](https://npmjs.org/package/@gmod/bam)
-[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/bam-js/push.yml?branch=main)](https://github.com/GMOD/bam-js/actions?query=branch%3Amain+workflow%3APush+)
+![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/bam-js/publish.yml?branch=main)
 ## Install
@@ -93,6 +93,8 @@ 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)
 ### async getHeader(opts?)
@@ -171,6 +173,31 @@ 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 CHANGED Viewed

@@ -71,14 +71,15 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         }[];
     }[] | undefined>;
     getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
+    private getSeqId;
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
     private evictOverlappingChunks;
     private _fetchChunkFeaturesDirect;
     fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
     _readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<T[]>;
     readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<T[]>;
-    hasRefSeq(seqName: string): Promise<boolean>;
-    lineCount(seqName: string): Promise<number>;
+    hasRefSeq(seqName: string, opts?: BaseOpts): Promise<boolean>;
+    lineCount(seqName: string, opts?: BaseOpts): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<never[] | import("./bai.ts").IndexCovEntry[]>;
     blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[] | never[]>;
     clearFeatureCache(): void;

package/dist/bamFile.js CHANGED Viewed

@@ -117,9 +117,14 @@ class BamFile {
         await this.getHeader(opts);
         return this.header;
     }
-    async getRecordsForRange(chr, min, max, opts) {
+    // Resolve a reference name to its numeric id, ensuring the header (which
+    // populates chrToIndex) has been parsed first.
+    async getSeqId(seqName, opts) {
         await this.getHeader(opts);
-        const chrId = this.chrToIndex?.[chr];
+        return this.chrToIndex?.[seqName];
+    }
+    async getRecordsForRange(chr, min, max, opts) {
+        const chrId = await this.getSeqId(chr, opts);
         if (chrId === undefined || !this.index) {
             return [];
         }
@@ -135,8 +140,14 @@ class BamFile {
         }
     }
     async _fetchChunkFeaturesDirect(chunks, chrId, min, max, opts = {}) {
-        const { viewAsPairs, filterBy } = opts;
+        const { viewAsPairs, filterBy, onProgress } = opts;
         const result = [];
+        let totalBytes = 0;
+        for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
+            totalBytes += chunks[ci].fetchedSize();
+        }
+        let downloadedBytes = 0;
+        onProgress?.(0, totalBytes);
         for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
             const chunk = chunks[ci];
             const cacheKey = chunkCacheKey(chunk, filterBy);
@@ -157,6 +168,8 @@ class BamFile {
                     features: records,
                 });
             }
+            downloadedBytes += chunk.fetchedSize();
+            onProgress?.(downloadedBytes, totalBytes);
             (0, util_ts_1.appendInRange)(records, chrId, min, max, result);
         }
         if (viewAsPairs) {
@@ -213,7 +226,14 @@ class BamFile {
         return mateFeatLists.flat();
     }
     async _readChunkFeatures(chunk, opts) {
-        const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, opts);
+        // Don't forward onProgress to the inner read: getRecordsForRange already
+        // reports progress at chunk granularity (downloadedBytes/totalBytes). If the
+        // filehandle's own streaming onProgress also fired this callback it would
+        // report a different `total` (this chunk's size, not the whole query),
+        // making the determinate bar jump around.
+        const buf = await this.bam.read(chunk.fetchedSize(), chunk.minv.blockPosition, {
+            signal: opts.signal,
+        });
         const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk);
         return this.readBamFeatures(data, cpositions, dpositions, chunk);
     }
@@ -254,24 +274,24 @@ class BamFile {
         }
         return sink;
     }
-    async hasRefSeq(seqName) {
-        const seqId = this.chrToIndex?.[seqName];
+    async hasRefSeq(seqName, opts) {
+        const seqId = await this.getSeqId(seqName, opts);
         return !this.index || seqId === undefined
             ? false
             : this.index.hasRefSeq(seqId);
     }
-    async lineCount(seqName) {
-        const seqId = this.chrToIndex?.[seqName];
+    async lineCount(seqName, opts) {
+        const seqId = await this.getSeqId(seqName, opts);
         return !this.index || seqId === undefined ? 0 : this.index.lineCount(seqId);
     }
     async indexCov(seqName, start, end) {
-        const seqId = this.chrToIndex?.[seqName];
+        const seqId = await this.getSeqId(seqName);
         return !this.index || seqId === undefined
             ? []
             : this.index.indexCov(seqId, start, end);
     }
     async blocksForRange(seqName, start, end, opts) {
-        const seqId = this.chrToIndex?.[seqName];
+        const seqId = await this.getSeqId(seqName, opts);
         return !this.index || seqId === undefined
             ? []
             : this.index.blocksForRange(seqId, start, end, opts);
@@ -284,16 +304,9 @@ class BamFile {
             return 0;
         }
         await this.getHeader(opts);
-        const chrToIndex = this.chrToIndex;
-        if (!chrToIndex) {
-            throw new Error('Header not yet parsed');
-        }
         const mapped = regions.flatMap(r => {
-            const refId = chrToIndex[r.refName];
-            if (refId === undefined) {
-                return [];
-            }
-            return [{ refId, start: r.start, end: r.end }];
+            const refId = this.chrToIndex?.[r.refName];
+            return refId === undefined ? [] : [{ refId, start: r.start, end: r.end }];
         });
         return this.index.estimatedBytesForRegions(mapped, opts);
     }

package/dist/bamFile.js.map CHANGED Viewed

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

@@ -72,6 +72,7 @@ class HtsgetFile extends bamFile_ts_1.default {
         this.trackId = args.trackId;
     }
     async getRecordsForRange(chr, min, max, opts) {
+        await this.getHeader(opts);
         const base = `${this.baseUrl}/${this.trackId}`;
         const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
         const chrId = this.chrToIndex?.[chr];

package/dist/htsget.js.map CHANGED Viewed

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

@@ -36,7 +36,7 @@ export default class BamRecord {
     get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
     get tags(): Record<string, unknown>;
     getTag(tagName: string): unknown;
-    getTagRaw(tagName: string): string | number | Uint8Array<ArrayBufferLike> | number[] | Uint32Array<ArrayBufferLike> | Int32Array<ArrayBufferLike> | Int16Array<ArrayBufferLike> | Uint16Array<ArrayBufferLike> | Int8Array<ArrayBufferLike> | Float32Array<ArrayBufferLike> | undefined;
+    getTagRaw(tagName: string): string | number | Uint8Array<ArrayBufferLike> | number[] | Int8Array<ArrayBufferLike> | Int16Array<ArrayBufferLike> | Uint16Array<ArrayBufferLike> | Int32Array<ArrayBufferLike> | Uint32Array<ArrayBufferLike> | Float32Array<ArrayBufferLike> | undefined;
     private _findTag;
     private _computeTags;
     isPaired(): boolean;

package/dist/record.js CHANGED Viewed

@@ -23,6 +23,88 @@ const textDecoder = new TextDecoder();
 // 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;
+// Decode a 'B' (array) tag value starting at `p` (the byte after type+subtype+
+// count). When the data is naturally aligned we return a typed-array view over
+// the underlying buffer (zero-copy); otherwise we copy element-by-element since
+// typed-array views require alignment. Shared by getTag and the full-tag parse.
+function decodeBArrayTag(ba, dataView, p, Btype, limit) {
+    const absOffset = ba.byteOffset + p;
+    switch (Btype) {
+        case 0x69: {
+            // 'i'
+            if (absOffset % 4 === 0) {
+                return new Int32Array(ba.buffer, absOffset, limit);
+            }
+            const arr = new Array(limit);
+            for (let i = 0; i < limit; i++) {
+                arr[i] = dataView.getInt32(p + i * 4, true);
+            }
+            return arr;
+        }
+        case 0x49: {
+            // 'I'
+            if (absOffset % 4 === 0) {
+                return new Uint32Array(ba.buffer, absOffset, limit);
+            }
+            const arr = new Array(limit);
+            for (let i = 0; i < limit; i++) {
+                arr[i] = dataView.getUint32(p + i * 4, true);
+            }
+            return arr;
+        }
+        case 0x73: {
+            // 's'
+            if (absOffset % 2 === 0) {
+                return new Int16Array(ba.buffer, absOffset, limit);
+            }
+            const arr = new Array(limit);
+            for (let i = 0; i < limit; i++) {
+                arr[i] = dataView.getInt16(p + i * 2, true);
+            }
+            return arr;
+        }
+        case 0x53: {
+            // 'S'
+            if (absOffset % 2 === 0) {
+                return new Uint16Array(ba.buffer, absOffset, limit);
+            }
+            const arr = new Array(limit);
+            for (let i = 0; i < limit; i++) {
+                arr[i] = dataView.getUint16(p + i * 2, true);
+            }
+            return arr;
+        }
+        case 0x63: // 'c'
+            return new Int8Array(ba.buffer, absOffset, limit);
+        case 0x43: // 'C'
+            return new Uint8Array(ba.buffer, absOffset, limit);
+        case 0x66: {
+            // 'f'
+            if (absOffset % 4 === 0) {
+                return new Float32Array(ba.buffer, absOffset, limit);
+            }
+            const arr = new Array(limit);
+            for (let i = 0; i < limit; i++) {
+                arr[i] = dataView.getFloat32(p + i * 4, true);
+            }
+            return arr;
+        }
+        default:
+            return undefined;
+    }
+}
+// Byte span of a 'B' tag's element payload, for advancing the cursor past it.
+function bArrayByteLength(Btype, limit) {
+    if (Btype === 0x69 || Btype === 0x49 || Btype === 0x66) {
+        return limit << 2;
+    }
+    else if (Btype === 0x73 || Btype === 0x53) {
+        return limit << 1;
+    }
+    else {
+        return limit;
+    }
+}
 class BamRecord {
     fileOffset;
     _byteArray;
@@ -46,7 +128,10 @@ class BamRecord {
         return this._byteArray;
     }
     get flags() {
-        return (this._dataView.getInt32(this._start + 16, true) & 0xffff0000) >> 16;
+        // FLAG is the high 16 bits of flag_nc (byte offset 18). Read it directly as
+        // a uint16 — masking flag_nc and arithmetic-shifting would sign-extend any
+        // value >= 0x8000.
+        return this._dataView.getUint16(this._start + 18, true);
     }
     get ref_id() {
         return this._dataView.getInt32(this._start + 4, true);
@@ -67,12 +152,15 @@ class BamRecord {
     get score() {
         return this.mq;
     }
+    // QUAL is present whenever the record has bases — independent of the unmapped
+    // flag (unmapped reads routinely carry SEQ/QUAL). A zero-length SEQ means
+    // there is no quality to return.
     get qual() {
-        if (this.isSegmentUnmapped()) {
+        const seqLen = this.seq_length;
+        if (seqLen === 0) {
             return null;
         }
         else {
-            const seqLen = this.seq_length;
             const p = this.seqStart + ((seqLen + 1) >> 1);
             return this._byteArray.subarray(p, p + seqLen);
         }
@@ -210,83 +298,17 @@ class BamRecord {
                     const Btype = ba[p++];
                     const limit = this._dataView.getInt32(p, true);
                     p += 4;
-                    const absOffset = ba.byteOffset + p;
                     if (isMatch) {
-                        if (Btype === 0x69) {
-                            // 'i'
-                            if (absOffset % 4 === 0) {
-                                return new Int32Array(ba.buffer, absOffset, limit);
-                            }
-                            const arr = new Array(limit);
-                            for (let i = 0; i < limit; i++) {
-                                arr[i] = this._dataView.getInt32(p + i * 4, true);
-                            }
-                            return arr;
-                        }
-                        else if (Btype === 0x49) {
-                            // 'I'
-                            if (absOffset % 4 === 0) {
-                                return new Uint32Array(ba.buffer, absOffset, limit);
-                            }
-                            const arr = new Array(limit);
-                            for (let i = 0; i < limit; i++) {
-                                arr[i] = this._dataView.getUint32(p + i * 4, true);
-                            }
-                            return arr;
-                        }
-                        else if (Btype === 0x73) {
-                            // 's'
-                            if (absOffset % 2 === 0) {
-                                return new Int16Array(ba.buffer, absOffset, limit);
-                            }
-                            const arr = new Array(limit);
-                            for (let i = 0; i < limit; i++) {
-                                arr[i] = this._dataView.getInt16(p + i * 2, true);
-                            }
-                            return arr;
-                        }
-                        else if (Btype === 0x53) {
-                            // 'S'
-                            if (absOffset % 2 === 0) {
-                                return new Uint16Array(ba.buffer, absOffset, limit);
-                            }
-                            const arr = new Array(limit);
-                            for (let i = 0; i < limit; i++) {
-                                arr[i] = this._dataView.getUint16(p + i * 2, true);
-                            }
-                            return arr;
-                        }
-                        else if (Btype === 0x63) {
-                            // 'c'
-                            return new Int8Array(ba.buffer, absOffset, limit);
-                        }
-                        else if (Btype === 0x43) {
-                            // 'C'
-                            return new Uint8Array(ba.buffer, absOffset, limit);
-                        }
-                        else if (Btype === 0x66) {
-                            // 'f'
-                            if (absOffset % 4 === 0) {
-                                return new Float32Array(ba.buffer, absOffset, limit);
-                            }
-                            const arr = new Array(limit);
-                            for (let i = 0; i < limit; i++) {
-                                arr[i] = this._dataView.getFloat32(p + i * 4, true);
-                            }
-                            return arr;
-                        }
-                    }
-                    if (Btype === 0x69 || Btype === 0x49 || Btype === 0x66) {
-                        p += limit << 2;
-                    }
-                    else if (Btype === 0x73 || Btype === 0x53) {
-                        p += limit << 1;
-                    }
-                    else if (Btype === 0x63 || Btype === 0x43) {
-                        p += limit;
+                        return decodeBArrayTag(ba, this._dataView, p, Btype, limit);
                     }
+                    p += bArrayByteLength(Btype, limit);
                     break;
                 }
+                default:
+                    if (type !== undefined) {
+                        console.error('Unknown BAM tag type', type);
+                    }
+                    break;
             }
         }
         return undefined;
@@ -349,87 +371,8 @@ class BamRecord {
                     const Btype = ba[p++];
                     const limit = this._dataView.getInt32(p, true);
                     p += 4;
-                    const absOffset = ba.byteOffset + p;
-                    if (Btype === 0x69) {
-                        // 'i'
-                        if (absOffset % 4 === 0) {
-                            tags[tag] = new Int32Array(ba.buffer, absOffset, limit);
-                        }
-                        else {
-                            const arr = new Array(limit);
-                            for (let i = 0; i < limit; i++) {
-                                arr[i] = this._dataView.getInt32(p + i * 4, true);
-                            }
-                            tags[tag] = arr;
-                        }
-                        p += limit << 2;
-                    }
-                    else if (Btype === 0x49) {
-                        // 'I'
-                        if (absOffset % 4 === 0) {
-                            tags[tag] = new Uint32Array(ba.buffer, absOffset, limit);
-                        }
-                        else {
-                            const arr = new Array(limit);
-                            for (let i = 0; i < limit; i++) {
-                                arr[i] = this._dataView.getUint32(p + i * 4, true);
-                            }
-                            tags[tag] = arr;
-                        }
-                        p += limit << 2;
-                    }
-                    else if (Btype === 0x73) {
-                        // 's'
-                        if (absOffset % 2 === 0) {
-                            tags[tag] = new Int16Array(ba.buffer, absOffset, limit);
-                        }
-                        else {
-                            const arr = new Array(limit);
-                            for (let i = 0; i < limit; i++) {
-                                arr[i] = this._dataView.getInt16(p + i * 2, true);
-                            }
-                            tags[tag] = arr;
-                        }
-                        p += limit << 1;
-                    }
-                    else if (Btype === 0x53) {
-                        // 'S'
-                        if (absOffset % 2 === 0) {
-                            tags[tag] = new Uint16Array(ba.buffer, absOffset, limit);
-                        }
-                        else {
-                            const arr = new Array(limit);
-                            for (let i = 0; i < limit; i++) {
-                                arr[i] = this._dataView.getUint16(p + i * 2, true);
-                            }
-                            tags[tag] = arr;
-                        }
-                        p += limit << 1;
-                    }
-                    else if (Btype === 0x63) {
-                        // 'c'
-                        tags[tag] = new Int8Array(ba.buffer, absOffset, limit);
-                        p += limit;
-                    }
-                    else if (Btype === 0x43) {
-                        // 'C'
-                        tags[tag] = new Uint8Array(ba.buffer, absOffset, limit);
-                        p += limit;
-                    }
-                    else if (Btype === 0x66) {
-                        // 'f'
-                        if (absOffset % 4 === 0) {
-                            tags[tag] = new Float32Array(ba.buffer, absOffset, limit);
-                        }
-                        else {
-                            const arr = new Array(limit);
-                            for (let i = 0; i < limit; i++) {
-                                arr[i] = this._dataView.getFloat32(p + i * 4, true);
-                            }
-                            tags[tag] = arr;
-                        }
-                        p += limit << 2;
-                    }
+                    tags[tag] = decodeBArrayTag(ba, this._dataView, p, Btype, limit);
+                    p += bArrayByteLength(Btype, limit);
                     break;
                 }
                 default:
@@ -494,9 +437,15 @@ class BamRecord {
     // Strategy: use plain array with |0 for small aligned (≤50 ops) and all unaligned,
     // Uint32Array view only for large aligned CIGARs.
     // CG tag pattern: first op is soft-clip consuming entire sequence, second op is N encoding length-on-ref
-    _isCGTagPattern(p) {
-        const cigop = this._dataView.getInt32(p, true);
-        return (cigop & 0xf) === cigar_ts_1.CIGAR_SOFT_CLIP && cigop >> 4 === this.seq_length;
+    _isCGTagPattern(p, numCigarOps) {
+        // htslib stores the placeholder as exactly two ops: <seqlen>S<reflen>N.
+        if (numCigarOps === 2) {
+            const cigop = this._dataView.getInt32(p, true);
+            return (cigop & 0xf) === cigar_ts_1.CIGAR_SOFT_CLIP && cigop >> 4 === this.seq_length;
+        }
+        else {
+            return false;
+        }
     }
     _computeLengthOnRef() {
         const flag_nc = this._dataView.getInt32(this._start + 16, true);
@@ -505,7 +454,7 @@ class BamRecord {
         }
         const numCigarOps = flag_nc & 0xffff;
         const p = this.b0 + this.read_name_length;
-        if (this._isCGTagPattern(p)) {
+        if (this._isCGTagPattern(p, numCigarOps)) {
             const cigop2 = this._dataView.getInt32(p + 4, true);
             if ((cigop2 & 0xf) !== cigar_ts_1.CIGAR_REF_SKIP) {
                 console.warn('CG tag with no N tag');
@@ -537,7 +486,7 @@ class BamRecord {
         }
         const numCigarOps = flag_nc & 0xffff;
         const p = this.b0 + this.read_name_length;
-        if (this._isCGTagPattern(p)) {
+        if (this._isCGTagPattern(p, numCigarOps)) {
             return (this.tags.CG ??
                 new Uint32Array(0));
         }