npm - @gmod/bam - Versions diffs - 7.1.18 → 7.1.20 - Mend

@gmod/bam 7.1.18 → 7.1.20

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 (47) hide show

package/README.md CHANGED Viewed

@@ -11,8 +11,7 @@ $ npm install --save @gmod/bam
 ## Usage
 ```typescript
-const { BamFile } = require('@gmod/bam')
-// or import {BamFile} from '@gmod/bam'
+import { BamFile } from '@gmod/bam'
 const t = new BamFile({
   bamPath: 'test.bam',
@@ -29,7 +28,9 @@ The `bamPath` argument only works on nodejs. In the browser, you should pass
 `bamFilehandle` with a generic-filehandle2 e.g. `RemoteFile`
 ```typescript
-const { RemoteFile } = require('generic-filehandle2')
+import { RemoteFile } from 'generic-filehandle2'
+import { BamFile } from '@gmod/bam'
 const bam = new BamFile({
   bamFilehandle: new RemoteFile('yourfile.bam'), // or a full http url
   baiFilehandle: new RemoteFile('yourfile.bam.bai'), // or a full http url
@@ -46,7 +47,7 @@ Since 1.0.41 we support usage of the htsget protocol
 Here is a small code snippet for this
 ```typescript
-const { HtsgetFile } = require('@gmod/bam')
+import { HtsgetFile } from '@gmod/bam'
 const ti = new HtsgetFile({
   baseUrl: 'http://htsnexus.rnd.dnanex.us/v1/reads',

package/dist/bai.js CHANGED Viewed

@@ -27,6 +27,7 @@ function reg2bins(beg, end) {
     ];
 }
 class BAI extends indexFile_ts_1.default {
+    setupP;
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);
         return indexData.indices(refId)?.stats?.lineCount || 0;

package/dist/bai.js.map CHANGED Viewed

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

@@ -70,6 +70,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
         }[];
     }[] | undefined>;
     getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
+    _hasEnoughRefSeqData(uncba: Uint8Array, start: number): boolean;
     _parseRefSeqs(uncba: Uint8Array, start: number): {
         chrToIndex: Record<string, number>;
         indexToChr: {

package/dist/bamFile.js CHANGED Viewed

@@ -17,13 +17,21 @@ const util_ts_1 = require("./util.js");
 exports.BAM_MAGIC = 21840194;
 const blockLen = 1 << 16;
 class BamFile {
+    renameRefSeq;
+    bam;
+    header;
+    chrToIndex;
+    indexToChr;
+    index;
+    htsget = false;
+    headerP;
+    // Cache for parsed features by chunk
+    // When a new chunk overlaps a cached chunk, we evict the cached one
+    chunkFeatureCache = new quick_lru_1.default({
+        maxSize: 100,
+    });
+    RecordClass;
     constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
-        this.htsget = false;
-        // Cache for parsed features by chunk
-        // When a new chunk overlaps a cached chunk, we evict the cached one
-        this.chunkFeatureCache = new quick_lru_1.default({
-            maxSize: 100,
-        });
         this.renameRefSeq = renameRefSeqs;
         this.RecordClass = (recordClass ?? record_ts_1.default);
         if (bamFilehandle) {
@@ -81,26 +89,37 @@ class BamFile {
         const indexData = await this.index.parse(opts);
         // firstDataLine is not defined in cases where there is no data in the file
         // (just bam header and nothing else)
-        const buffer = indexData.firstDataLine === undefined
+        let readLen = indexData.firstDataLine === undefined
+            ? undefined
+            : indexData.firstDataLine.blockPosition + blockLen;
+        const buffer = readLen === undefined
             ? await this.bam.readFile()
-            : // the logic indexData.firstDataLine is a virtualOffset telling us
-                // where the data is. It is in the middle of a virtualOffset
-                // (provided by the bgzip block offset at blockPosition + the
-                // virtualOffset dataPosition, so we add one extra blockLen to make
-                // sure we consume the full header)
-                await this.bam.read(indexData.firstDataLine.blockPosition + blockLen, 0);
-        const uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
+            : await this.bam.read(readLen, 0);
+        let uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
         const dataView = new DataView(uncba.buffer);
         if (dataView.getInt32(0, true) !== exports.BAM_MAGIC) {
             throw new Error('Not a BAM file');
         }
         const headLen = dataView.getInt32(4, true);
-        const decoder = new TextDecoder('utf8');
-        this.header = decoder.decode(uncba.subarray(8, 8 + headLen));
-        const { chrToIndex, indexToChr } = this._parseRefSeqs(uncba, headLen + 8);
-        this.chrToIndex = chrToIndex;
-        this.indexToChr = indexToChr;
-        return (0, sam_ts_1.parseHeaderText)(this.header);
+        this.header = new TextDecoder('utf8').decode(uncba.subarray(8, 8 + headLen));
+        // BAM files with many reference sequences may need more data than the
+        // initial read provides, so re-fetch with doubled size until it fits
+        const refSeqStart = headLen + 8;
+        const maxRetries = 5;
+        for (let attempt = 0; attempt < maxRetries; attempt++) {
+            if (this._hasEnoughRefSeqData(uncba, refSeqStart)) {
+                const { chrToIndex, indexToChr } = this._parseRefSeqs(uncba, refSeqStart);
+                this.chrToIndex = chrToIndex;
+                this.indexToChr = indexToChr;
+                return (0, sam_ts_1.parseHeaderText)(this.header);
+            }
+            if (readLen === undefined) {
+                throw new Error(`Insufficient data for reference sequences in ${uncba.length} bytes`);
+            }
+            readLen *= 2;
+            uncba = await (0, bgzf_filehandle_1.unzip)(await this.bam.read(readLen, 0));
+        }
+        throw new Error(`Insufficient data for reference sequences after ${maxRetries} retries`);
     }
     getHeader(opts) {
         if (!this.headerP) {
@@ -115,6 +134,22 @@ class BamFile {
         await this.getHeader(opts);
         return this.header;
     }
+    _hasEnoughRefSeqData(uncba, start) {
+        if (start + 4 > uncba.length) {
+            return false;
+        }
+        const dataView = new DataView(uncba.buffer);
+        const nRef = dataView.getInt32(start, true);
+        let p = start + 4;
+        for (let i = 0; i < nRef; i += 1) {
+            if (p + 8 > uncba.length) {
+                return false;
+            }
+            const lName = dataView.getInt32(p, true);
+            p = p + 8 + lName;
+        }
+        return true;
+    }
     _parseRefSeqs(uncba, start) {
         const dataView = new DataView(uncba.buffer);
         const nRef = dataView.getInt32(start, true);
@@ -123,9 +158,6 @@ class BamFile {
         const indexToChr = [];
         const decoder = new TextDecoder('utf8');
         for (let i = 0; i < nRef; i += 1) {
-            if (p + 8 > uncba.length) {
-                throw new Error(`Insufficient data for reference sequences: need more than ${uncba.length} bytes`);
-            }
             const lName = dataView.getInt32(p, true);
             const refName = this.renameRefSeq(decoder.decode(uncba.subarray(p + 4, p + 4 + lName - 1)));
             const lRef = dataView.getInt32(p + lName + 4, true);

package/dist/bamFile.js.map CHANGED Viewed

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

@@ -2,6 +2,11 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 // little class representing a chunk in the index
 class Chunk {
+    minv;
+    maxv;
+    bin;
+    _fetchedSize;
+    buffer;
     constructor(minv, maxv, bin, _fetchedSize) {
         this.minv = minv;
         this.maxv = maxv;

package/dist/chunk.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;~~IAGxB~~,YACS,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAQ;QACZ,SAAI,GAAJ,IAAI,CAAQ;QACZ,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AAlCD,wBAkCC"}
1	+ {"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAIf;IACA;IACA;IACA;IANF,MAAM,CAA0B;IAEvC,YACS,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAQ;QACZ,SAAI,GAAJ,IAAI,CAAQ;QACZ,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AAlCD,wBAkCC"}

package/dist/csi.js CHANGED Viewed

@@ -18,12 +18,10 @@ function rshift(num, bits) {
     return Math.floor(num / 2 ** bits);
 }
 class CSI extends indexFile_ts_1.default {
-    constructor() {
-        super(...arguments);
-        this.maxBinNumber = 0;
-        this.depth = 0;
-        this.minShift = 0;
-    }
+    maxBinNumber = 0;
+    depth = 0;
+    minShift = 0;
+    setupP;
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);
         return indexData.indices(refId)?.stats?.lineCount || 0;

package/dist/csi.js.map CHANGED Viewed

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

@@ -67,6 +67,8 @@ async function concat(arr, opts) {
     return (0, util_ts_1.concatUint8Array)(await Promise.all(res.map(elt => (0, bgzf_filehandle_1.unzip)(elt))));
 }
 class HtsgetFile extends bamFile_ts_1.default {
+    baseUrl;
+    trackId;
     constructor(args) {
         super({ htsget: true, recordClass: args.recordClass });
         this.baseUrl = args.baseUrl;

package/dist/htsget.js.map CHANGED Viewed

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

@@ -2,6 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const util_ts_1 = require("./util.js");
 class IndexFile {
+    filehandle;
+    renameRefSeq;
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;

package/dist/indexFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AACA,uCAAoD;AAUpD,MAA8B,SAAS;~~IAIrC~~,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAeD,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,IAAA,wBAAc,EAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AA1CD,4BA0CC"}
1	+ {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AACA,uCAAoD;AAUpD,MAA8B,SAAS;IAC9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAE1C,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAeD,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,IAAA,wBAAc,EAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AA1CD,4BA0CC"}

package/dist/nullFilehandle.d.ts CHANGED Viewed

@@ -1,6 +1,6 @@
 export default class NullFilehandle {
-    read(): Promise<any>;
-    stat(): Promise<any>;
-    readFile(): Promise<any>;
-    close(): Promise<any>;
+    read(): Promise<never>;
+    stat(): Promise<never>;
+    readFile(): Promise<never>;
+    close(): Promise<never>;
 }

package/dist/nullIndex.d.ts CHANGED Viewed

@@ -1,7 +1,7 @@
 import IndexFile from './indexFile.ts';
 export default class NullIndex extends IndexFile {
-    lineCount(): Promise<any>;
-    protected _parse(): Promise<any>;
-    indexCov(): Promise<any>;
-    blocksForRange(): Promise<any>;
+    lineCount(): Promise<never>;
+    protected _parse(): Promise<never>;
+    indexCov(): Promise<never>;
+    blocksForRange(): Promise<never>;
 }

package/dist/record.d.ts CHANGED Viewed

@@ -72,6 +72,6 @@ export default class BamRecord {
     get next_pos(): number;
     get template_length(): number;
     seqAt(idx: number): string | undefined;
-    toJSON(): Record<string, any>;
+    toJSON(): Record<string, unknown>;
 }
 export {};

package/dist/record.js CHANGED Viewed

@@ -23,6 +23,17 @@ const ASCII_CIGAR_CODES = [
 // Binary: 0b111001101 = 0x1CD
 const CIGAR_CONSUMES_REF_MASK = 0x1cd;
 class BamRecord {
+    fileOffset;
+    bytes;
+    _dataView;
+    _cachedFlags;
+    _cachedRefId;
+    _cachedStart;
+    _cachedEnd;
+    _cachedTags;
+    _cachedCigarAndLength;
+    _cachedNUMERIC_MD;
+    _cachedTagsStart;
     constructor(args) {
         this.bytes = args.bytes;
         this.fileOffset = args.fileOffset;
@@ -613,10 +624,14 @@ class BamRecord {
         return buf.join('');
     }
     // adapted from igv.js
-    // uses precomputed lookup table indexed by flag bits + isize sign
+    // uses precomputed lookup table indexed by flag bits + isize sign.
+    // the BAM spec defines tlen as positive for the leftmost segment and
+    // negative for the rightmost, so tlen > 0 reliably indicates which
+    // read comes first without needing position-based correction
+    // (see also: gmod/cram-js src/cramFile/record.ts getPairOrientation)
     get pair_orientation() {
         const f = this.flags;
-        // combined check: unmapped (0x4) clear, mate unmapped (0x8) clear
+        // unmapped (0x4) or mate unmapped (0x8) -> undefined
         if (f & 0xc || this.ref_id !== this.next_refid) {
             return undefined;
         }

package/dist/record.js.map CHANGED Viewed

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

@@ -3,6 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.VirtualOffset = void 0;
 exports.fromBytes = fromBytes;
 class VirtualOffset {
+    blockPosition;
+    dataPosition;
     constructor(blockPosition, dataPosition) {
         this.blockPosition = blockPosition; // < offset of the compressed data block
         this.dataPosition = dataPosition; // < offset into the uncompressed data

package/dist/virtualOffset.js.map CHANGED Viewed

	@@ -1 +1 @@
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