@gmod/bam 7.1.10 → 7.1.12

package/dist/record.js

@@ -71,6 +71,17 @@ class BamRecord {
     get b0() {
         return this.bytes.start + 36;
     }
+    get tagsStart() {
+        if (this._cachedTagsStart === undefined) {
+            this._cachedTagsStart =
+                this.b0 +
+                    this.read_name_length +
+                    this.num_cigar_bytes +
+                    this.num_seq_bytes +
+                    this.seq_length;
+        }
+        return this._cachedTagsStart;
+    }
     // batch fromCharCode: fastest for typical name lengths (see benchmarks/string-building.bench.ts)
     get name() {
         const len = this.read_name_length - 1;
@@ -84,80 +95,195 @@ class BamRecord {
     }
     get NUMERIC_MD() {
         if (this._cachedNUMERIC_MD === undefined) {
-            let p = this.b0 +
-                this.read_name_length +
-                this.num_cigar_bytes +
-                this.num_seq_bytes +
-                this.seq_length;
-            const blockEnd = this.bytes.end;
-            const ba = this.byteArray;
-            while (p < blockEnd) {
-                const tag1 = ba[p];
-                const tag2 = ba[p + 1];
-                const type = ba[p + 2];
-                p += 3;
-                // 'M' = 0x4D, 'D' = 0x44, 'Z' = 0x5A
-                if (tag1 === 0x4d && tag2 === 0x44 && type === 0x5a) {
-                    const start = p;
-                    while (p < blockEnd && ba[p] !== 0) {
-                        p++;
+            const result = this.getTagRaw('MD');
+            this._cachedNUMERIC_MD = result instanceof Uint8Array ? result : null;
+        }
+        return this._cachedNUMERIC_MD === null ? undefined : this._cachedNUMERIC_MD;
+    }
+    get tags() {
+        if (this._cachedTags === undefined) {
+            this._cachedTags = this._computeTags();
+        }
+        return this._cachedTags;
+    }
+    getTag(tagName) {
+        if (this._cachedTags !== undefined) {
+            return this._cachedTags[tagName];
+        }
+        return this._findTag(tagName, false);
+    }
+    getTagRaw(tagName) {
+        return this._findTag(tagName, true);
+    }
+    _findTag(tagName, raw) {
+        const tag1 = tagName.charCodeAt(0);
+        const tag2 = tagName.charCodeAt(1);
+        let p = this.tagsStart;
+        const blockEnd = this.bytes.end;
+        const ba = this.byteArray;
+        while (p < blockEnd) {
+            const currentTag1 = ba[p];
+            const currentTag2 = ba[p + 1];
+            const type = ba[p + 2];
+            p += 3;
+            const isMatch = currentTag1 === tag1 && currentTag2 === tag2;
+            switch (type) {
+                case 0x41: // 'A'
+                    if (isMatch) {
+                        return String.fromCharCode(ba[p]);
+                    }
+                    p += 1;
+                    break;
+                case 0x69: // 'i'
+                    if (isMatch) {
+                        return this._dataView.getInt32(p, true);
+                    }
+                    p += 4;
+                    break;
+                case 0x49: // 'I'
+                    if (isMatch) {
+                        return this._dataView.getUint32(p, true);
+                    }
+                    p += 4;
+                    break;
+                case 0x63: // 'c'
+                    if (isMatch) {
+                        return this._dataView.getInt8(p);
+                    }
+                    p += 1;
+                    break;
+                case 0x43: // 'C'
+                    if (isMatch) {
+                        return this._dataView.getUint8(p);
+                    }
+                    p += 1;
+                    break;
+                case 0x73: // 's'
+                    if (isMatch) {
+                        return this._dataView.getInt16(p, true);
                     }
-                    this._cachedNUMERIC_MD = ba.subarray(start, p);
+                    p += 2;
+                    break;
+                case 0x53: // 'S'
+                    if (isMatch) {
+                        return this._dataView.getUint16(p, true);
+                    }
+                    p += 2;
+                    break;
+                case 0x66: // 'f'
+                    if (isMatch) {
+                        return this._dataView.getFloat32(p, true);
+                    }
+                    p += 4;
+                    break;
+                case 0x5a: // 'Z'
+                case 0x48: {
+                    // 'H'
+                    if (isMatch) {
+                        const start = p;
+                        while (p < blockEnd && ba[p] !== 0) {
+                            p++;
+                        }
+                        if (raw) {
+                            return ba.subarray(start, p);
+                        }
+                        const value = [];
+                        for (let i = start; i < p; i++) {
+                            value.push(String.fromCharCode(ba[i]));
+                        }
+                        return value.join('');
+                    }
+                    while (p <= blockEnd && ba[p++] !== 0) { }
+                    break;
                 }
-                switch (type) {
-                    case 0x41: // 'A'
-                        p += 1;
-                        break;
-                    case 0x69: // 'i'
-                    case 0x49: // 'I'
-                    case 0x66: // 'f'
-                        p += 4;
-                        break;
-                    case 0x63: // 'c'
-                    case 0x43: // 'C'
-                        p += 1;
-                        break;
-                    case 0x73: // 's'
-                    case 0x53: // 'S'
-                        p += 2;
-                        break;
-                    case 0x5a: // 'Z'
-                    case 0x48: // 'H'
-                        while (p <= blockEnd && ba[p++] !== 0) { }
-                        break;
-                    case 0x42: {
-                        // 'B'
-                        const Btype = ba[p++];
-                        const limit = this._dataView.getInt32(p, true);
-                        p += 4;
-                        if (Btype === 0x69 || Btype === 0x49 || Btype === 0x66) {
-                            p += limit << 2;
+                case 0x42: {
+                    // 'B'
+                    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 === 0x73 || Btype === 0x53) {
-                            p += limit << 1;
+                        else if (Btype === 0x43) {
+                            // 'C'
+                            return new Uint8Array(ba.buffer, absOffset, limit);
                         }
-                        else if (Btype === 0x63 || Btype === 0x43) {
-                            p += 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;
                         }
-                        break;
                     }
+                    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;
+                    }
+                    break;
                 }
             }
         }
-        return this._cachedNUMERIC_MD === null ? undefined : this._cachedNUMERIC_MD;
-    }
-    get tags() {
-        if (this._cachedTags === undefined) {
-            this._cachedTags = this._computeTags();
-        }
-        return this._cachedTags;
+        return undefined;
     }
     _computeTags() {
-        let p = this.b0 +
-            this.read_name_length +
-            this.num_cigar_bytes +
-            this.num_seq_bytes +
-            this.seq_length;
+        let p = this.tagsStart;
         const blockEnd = this.bytes.end;
         const ba = this.byteArray;
         const tags = {};
@@ -226,8 +352,11 @@ class BamRecord {
                             tags[tag] = new Int32Array(ba.buffer, absOffset, limit);
                         }
                         else {
-                            const bytes = ba.slice(p, p + (limit << 2));
-                            tags[tag] = new Int32Array(bytes.buffer, bytes.byteOffset, limit);
+                            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;
                     }
@@ -237,8 +366,11 @@ class BamRecord {
                             tags[tag] = new Uint32Array(ba.buffer, absOffset, limit);
                         }
                         else {
-                            const bytes = ba.slice(p, p + (limit << 2));
-                            tags[tag] = new Uint32Array(bytes.buffer, bytes.byteOffset, limit);
+                            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;
                     }
@@ -248,8 +380,11 @@ class BamRecord {
                             tags[tag] = new Int16Array(ba.buffer, absOffset, limit);
                         }
                         else {
-                            const bytes = ba.slice(p, p + (limit << 1));
-                            tags[tag] = new Int16Array(bytes.buffer, bytes.byteOffset, limit);
+                            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;
                     }
@@ -259,8 +394,11 @@ class BamRecord {
                             tags[tag] = new Uint16Array(ba.buffer, absOffset, limit);
                         }
                         else {
-                            const bytes = ba.slice(p, p + (limit << 1));
-                            tags[tag] = new Uint16Array(bytes.buffer, bytes.byteOffset, limit);
+                            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;
                     }
@@ -280,8 +418,11 @@ class BamRecord {
                             tags[tag] = new Float32Array(ba.buffer, absOffset, limit);
                         }
                         else {
-                            const bytes = ba.slice(p, p + (limit << 2));
-                            tags[tag] = new Float32Array(bytes.buffer, bytes.byteOffset, limit);
+                            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;
                     }

package/dist/record.js.map

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

@@ -1,11 +1,21 @@
 import Chunk from './chunk.ts';
 import { Offset, VirtualOffset } from './virtualOffset.ts';
 export declare function canMergeBlocks(chunk1: Chunk, chunk2: Chunk): boolean;
+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;
 }
 export interface BaseOpts {
     signal?: AbortSignal;
@@ -22,3 +32,6 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
 };
 export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
 export declare function gen2array<T>(gen: AsyncIterable<T[]>): Promise<T[]>;
+export declare function filterReadFlag(flags: number, flagInclude: number, flagExclude: number): boolean;
+export declare function filterTagValue(readVal: unknown, filterVal?: string): boolean;
+export declare function filterCacheKey(filterBy?: FilterBy): string;

package/dist/util.js

@@ -8,6 +8,9 @@ exports.findFirstData = findFirstData;
 exports.parseNameBytes = parseNameBytes;
 exports.concatUint8Array = concatUint8Array;
 exports.gen2array = gen2array;
+exports.filterReadFlag = filterReadFlag;
+exports.filterTagValue = filterTagValue;
+exports.filterCacheKey = filterCacheKey;
 const long_ts_1 = require("./long.js");
 function canMergeBlocks(chunk1, chunk2) {
     return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
@@ -132,4 +135,26 @@ async function gen2array(gen) {
     }
     return out;
 }
+function filterReadFlag(flags, flagInclude, flagExclude) {
+    if ((flags & flagInclude) !== flagInclude) {
+        return true;
+    }
+    if (flags & flagExclude) {
+        return true;
+    }
+    return false;
+}
+function filterTagValue(readVal, filterVal) {
+    return filterVal === '*'
+        ? readVal === undefined
+        : `${readVal}` !== `${filterVal}`;
+}
+function filterCacheKey(filterBy) {
+    if (!filterBy) {
+        return '';
+    }
+    const { flagInclude = 0, flagExclude = 0, tagFilter } = filterBy;
+    const tagPart = tagFilter ? `:${tagFilter.tag}=${tagFilter.value ?? '*'}` : '';
+    return `:f${flagInclude}x${flagExclude}${tagPart}`;
+}
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
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package/esm/bai.js

@@ -157,7 +157,7 @@ export default class BAI extends IndexFile {
         if (!seqIdx) {
             return [];
         }
-        const { linearIndex = [], stats } = seqIdx;
+        const { linearIndex, stats } = seqIdx;
         if (linearIndex.length === 0) {
             return [];
         }

package/esm/bai.js.map

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

@@ -14,6 +14,8 @@ export interface BamRecordLike {
     fileOffset: number;
     next_pos: number;
     next_refid: number;
+    flags: number;
+    tags: Record<string, unknown>;
 }
 export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
     bytes: Bytes;
@@ -76,12 +78,11 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         }[];
     };
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
-    streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
     private chunkCacheKey;
     private blocksOverlap;
     private evictOverlappingChunks;
-    _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<T[], void, unknown>;
-    fetchPairs(chrId: number, feats: T[][], opts: BamOpts): Promise<T[]>;
+    private _fetchChunkFeaturesDirect;
+    fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
     _readChunk({ chunk, opts }: {
         chunk: Chunk;
         opts: BaseOpts;