npm - @gmod/bam - Versions diffs - 7.1.10 → 7.1.12 - Mend

@gmod/bam 7.1.10 → 7.1.12

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/record.js CHANGED Viewed

@@ -66,6 +66,17 @@ export default 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;
@@ -79,80 +90,195 @@ export default 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 = {};
@@ -221,8 +347,11 @@ export default 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;
                     }
@@ -232,8 +361,11 @@ export default 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;
                     }
@@ -243,8 +375,11 @@ export default 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;
                     }
@@ -254,8 +389,11 @@ export default 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;
                     }
@@ -275,8 +413,11 @@ export default 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/esm/record.js.map CHANGED Viewed

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

@@ -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/esm/util.js CHANGED Viewed

@@ -122,4 +122,26 @@ export async function gen2array(gen) {
     }
     return out;
 }
+export function filterReadFlag(flags, flagInclude, flagExclude) {
+    if ((flags & flagInclude) !== flagInclude) {
+        return true;
+    }
+    if (flags & flagExclude) {
+        return true;
+    }
+    return false;
+}
+export function filterTagValue(readVal, filterVal) {
+    return filterVal === '*'
+        ? readVal === undefined
+        : `${readVal}` !== `${filterVal}`;
+}
+export 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/esm/util.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "7.1.10",
+  "version": "7.1.12",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",

package/src/bai.ts CHANGED Viewed

@@ -192,7 +192,7 @@ export default class BAI extends IndexFile {
     if (!seqIdx) {
       return []
     }
-    const { linearIndex = [], stats } = seqIdx
+    const { linearIndex, stats } = seqIdx
     if (linearIndex.length === 0) {
       return []
     }