npm - @gmod/bam - Versions diffs - 2.0.4 → 3.0.0 - Mend

@gmod/bam 2.0.4 → 3.0.0

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 (35) hide show

package/esm/bamFile.js CHANGED Viewed

@@ -132,7 +132,7 @@ export default class BamFile {
     }
     getHeader(opts) {
         if (!this.headerP) {
-            this.headerP = this.getHeaderPre(opts).catch(e => {
+            this.headerP = this.getHeaderPre(opts).catch((e) => {
                 this.headerP = undefined;
                 throw e;
             });
@@ -196,13 +196,13 @@ export default class BamFile {
             const records = await this.featureCache.get(chunk.toString(), { chunk, opts }, opts.signal);
             const recs = [];
             for (const feature of records) {
-                if (feature.seq_id() === chrId) {
-                    if (feature.get('start') >= max) {
+                if (feature.ref_id === chrId) {
+                    if (feature.start >= max) {
                         // past end of range, can stop iterating
                         done = true;
                         break;
                     }
-                    else if (feature.get('end') >= min) {
+                    else if (feature.end >= min) {
                         // must be in range
                         recs.push(feature);
                     }
@@ -226,8 +226,8 @@ export default class BamFile {
         feats.map(ret => {
             const readNames = {};
             for (const element of ret) {
-                const name = element.name();
-                const id = element.id();
+                const name = element.name;
+                const id = element.id;
                 if (!readNames[name]) {
                     readNames[name] = 0;
                 }
@@ -243,10 +243,10 @@ export default class BamFile {
         const matePromises = [];
         feats.map(ret => {
             for (const f of ret) {
-                const name = f.name();
-                const start = f.get('start');
-                const pnext = f._next_pos();
-                const rnext = f._next_refid();
+                const name = f.name;
+                const start = f.start;
+                const pnext = f.next_pos;
+                const rnext = f.next_refid;
                 if (this.index &&
                     unmatedPairs[name] &&
                     (pairAcrossChr ||
@@ -271,7 +271,7 @@ export default class BamFile {
             });
             const mateRecs = [];
             for (const feature of await this.readBamFeatures(data, cpositions, dpositions, chunk)) {
-                if (unmatedPairs[feature.get('name')] && !readIds[feature.id()]) {
+                if (unmatedPairs[feature.name] && !readIds[feature.id]) {
                     mateRecs.push(feature);
                 }
             }
@@ -297,6 +297,7 @@ export default class BamFile {
             const blockSize = ba.readInt32LE(blockStart);
             const blockEnd = blockStart + 4 + blockSize - 1;
             // increment position to the current decompressed status
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
             if (dpositions) {
                 while (blockStart + chunk.minv.dataPosition >= dpositions[pos++]) { }
                 pos--;
@@ -335,6 +336,7 @@ export default class BamFile {
                             chunk.minv.dataPosition +
                             1
                         : // must be slice, not subarray for buffer polyfill on web
+                            // eslint-disable-next-line @typescript-eslint/no-deprecated
                             crc32.signed(ba.slice(blockStart, blockEnd)),
                 });
                 sink.push(feature);

package/esm/bamFile.js.map CHANGED Viewed

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

@@ -57,7 +57,7 @@ export default class CSI extends IndexFile {
      * calculate the list of bins that may overlap with region [beg,end)
      * (zero-based half-open)
      */
-    reg2bins(beg: number, end: number): number[][];
+    reg2bins(beg: number, end: number): (readonly [number, number])[];
     parse(opts?: BaseOpts): Promise<{
         refNameToId?: Record<string, number> | undefined;
         refIdToName?: string[] | undefined;

package/esm/csi.js CHANGED Viewed

@@ -126,7 +126,8 @@ export default class CSI extends IndexFile {
             min = 0;
         }
         const indexData = await this.parse(opts);
-        const ba = indexData === null || indexData === void 0 ? void 0 : indexData.indices[refId];
+        const ba = indexData.indices[refId];
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (!ba) {
             return [];
         }
@@ -138,6 +139,7 @@ export default class CSI extends IndexFile {
         // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
         for (const [start, end] of overlappingBins) {
             for (let bin = start; bin <= end; bin++) {
+                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                 if (ba.binIndex[bin]) {
                     const binChunks = ba.binIndex[bin];
                     for (const c of binChunks) {
@@ -177,7 +179,7 @@ export default class CSI extends IndexFile {
     }
     async parse(opts = {}) {
         if (!this.setupP) {
-            this.setupP = this._parse(opts).catch(e => {
+            this.setupP = this._parse(opts).catch((e) => {
                 this.setupP = undefined;
                 throw e;
             });

package/esm/csi.js.map CHANGED Viewed

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

@@ -1,42 +1,30 @@
-/**
- * Class of each BAM record returned by this API.
- */
+import type { Buffer } from 'buffer';
+interface Bytes {
+    start: number;
+    end: number;
+    byteArray: Buffer;
+}
 export default class BamRecord {
-    private data;
+    fileOffset: number;
     private bytes;
-    private _id;
-    private _tagOffset;
-    private _tagList;
-    private _allTagsParsed;
-    flags: any;
-    _refID: number;
-    constructor(args: any);
-    get(field: string): any;
-    end(): any;
-    seq_id(): number;
-    _get(field: string): any;
-    _tags(): string[];
-    parent(): void;
-    children(): any;
-    id(): number;
-    /**
-     * Mapping quality score.
-     */
-    mq(): number | undefined;
-    score(): any;
-    qual(): string | undefined;
-    qualRaw(): Buffer | undefined;
-    strand(): 1 | -1;
-    multi_segment_next_segment_strand(): 1 | -1 | undefined;
-    name(): any;
-    _read_name(): string;
-    /**
-     * Get the value of a tag, parsing the tags as far as necessary.
-     * Only called if we have not already parsed that field.
-     */
-    _parseTag(tagName?: string): string | number | undefined;
-    _parseAllTags(): void;
-    _parseCigar(cigar: string): (string | number)[][];
+    constructor(args: {
+        bytes: Bytes;
+        fileOffset: number;
+    });
+    get byteArray(): Buffer;
+    get flags(): number;
+    get ref_id(): number;
+    get start(): number;
+    get end(): number;
+    get id(): number;
+    get mq(): number | undefined;
+    get score(): number | undefined;
+    get qual(): string | undefined;
+    get qualRaw(): Buffer | undefined;
+    get strand(): 1 | -1;
+    get b0(): number;
+    get name(): string;
+    get tags(): Record<string, unknown>;
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both
      * segments are mapped
@@ -64,22 +52,23 @@ export default class BamRecord {
     isDuplicate(): boolean;
     /** @returns {boolean} true if this is a supplementary alignment */
     isSupplementary(): boolean;
-    cigar(): any;
-    length_on_ref(): any;
-    _n_cigar_op(): number;
-    _l_read_name(): number;
-    /**
-     * number of bytes in the sequence field
-     */
-    _seq_bytes(): number;
-    getReadBases(): string;
-    seq(): string;
-    getPairOrientation(): string;
-    _bin_mq_nl(): number;
-    _flag_nc(): number;
-    seq_length(): number;
-    _next_refid(): number;
-    _next_pos(): number;
-    template_length(): number;
+    get cigarAndLength(): {
+        length_on_ref: number;
+        CIGAR: string;
+    };
+    get length_on_ref(): number;
+    get CIGAR(): string;
+    get num_cigar_ops(): number;
+    get read_name_length(): number;
+    get num_seq_bytes(): number;
+    get seq(): string;
+    get pair_orientation(): string;
+    get bin_mq_nl(): number;
+    get flag_nc(): number;
+    get seq_length(): number;
+    get next_refid(): number;
+    get next_pos(): number;
+    get template_length(): number;
     toJSON(): Record<string, any>;
 }
+export {};