npm - @gmod/bam - Versions diffs - 1.1.10 → 1.1.13 - Mend

@gmod/bam 1.1.10 → 1.1.13

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 (30) hide show

package/dist/record.js CHANGED Viewed

@@ -5,24 +5,21 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 /* eslint-disable @typescript-eslint/no-empty-function */
 var constants_1 = __importDefault(require("./constants"));
-var SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('').map(function (s) { return s.charCodeAt(0); });
+var SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
 var CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
 /**
  * Class of each BAM record returned by this API.
  */
 var BamRecord = /** @class */ (function () {
     function BamRecord(args) {
-        this._tagOffset = undefined;
+        this.data = {};
         this._tagList = [];
         this._allTagsParsed = false;
+        var bytes = args.bytes, fileOffset = args.fileOffset;
+        var byteArray = bytes.byteArray, start = bytes.start;
         this.data = {};
-        this.bytes = {
-            start: args.bytes.start,
-            end: args.bytes.end,
-            byteArray: args.bytes.byteArray,
-        };
-        this._id = args.fileOffset;
-        var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
+        this.bytes = bytes;
+        this._id = fileOffset;
         this._refID = byteArray.readInt32LE(start + 4);
         this.data.start = byteArray.readInt32LE(start + 8);
         this.flags = (byteArray.readInt32LE(start + 16) & 0xffff0000) >> 16;
@@ -73,7 +70,7 @@ var BamRecord = /** @class */ (function () {
             }
         });
         var seen = {};
-        tags = tags.filter(function (t) {
+        return tags.filter(function (t) {
             if ((t in _this.data && _this.data[t] === undefined) ||
                 t === 'CG' ||
                 t === 'cg') {
@@ -84,7 +81,6 @@ var BamRecord = /** @class */ (function () {
             seen[lt] = true;
             return !s;
         });
-        return tags;
     };
     BamRecord.prototype.parent = function () {
         return undefined;
@@ -114,18 +110,14 @@ var BamRecord = /** @class */ (function () {
         if (this.isSegmentUnmapped()) {
             return undefined;
         }
-        var byteArray = this.bytes.byteArray;
-        var p = this.bytes.start +
+        var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
+        var p = start +
             36 +
             this.get('_l_read_name') +
             this.get('_n_cigar_op') * 4 +
             this.get('_seq_bytes');
         var lseq = this.get('seq_length');
-        var qseq = Buffer.allocUnsafe(lseq);
-        for (var j = 0; j < lseq; ++j) {
-            qseq[j] = byteArray[p + j];
-        }
-        return qseq;
+        return byteArray.subarray(p, p + lseq);
     };
     BamRecord.prototype.strand = function () {
         return this.isReverseComplemented() ? -1 : 1;
@@ -141,7 +133,8 @@ var BamRecord = /** @class */ (function () {
     };
     BamRecord.prototype._read_name = function () {
         var nl = this.get('_l_read_name');
-        return this.bytes.byteArray.toString('ascii', this.bytes.start + 36, this.bytes.start + 36 + nl - 1);
+        var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
+        return byteArray.toString('ascii', start + 36, start + 36 + nl - 1);
     };
     /**
      * Get the value of a tag, parsing the tags as far as necessary.
@@ -154,9 +147,9 @@ var BamRecord = /** @class */ (function () {
         if (this._allTagsParsed) {
             return undefined;
         }
-        var byteArray = this.bytes.byteArray;
+        var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
         var p = this._tagOffset ||
-            this.bytes.start +
+            start +
                 36 +
                 this.get('_l_read_name') +
                 this.get('_n_cigar_op') * 4 +
@@ -452,25 +445,24 @@ var BamRecord = /** @class */ (function () {
         return this.seq();
     };
     BamRecord.prototype.seq = function () {
-        var byteArray = this.bytes.byteArray;
-        var p = this.bytes.start +
-            36 +
-            this.get('_l_read_name') +
-            this.get('_n_cigar_op') * 4;
+        var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
+        var p = start + 36 + this.get('_l_read_name') + this.get('_n_cigar_op') * 4;
         var seqBytes = this.get('_seq_bytes');
         var len = this.get('seq_length');
-        var buf = '';
-        var i = 0;
-        for (var j = 0; j < seqBytes; ++j) {
-            var sb = byteArray[p + j];
-            buf += String.fromCharCode(SEQRET_DECODER[(sb & 0xf0) >> 4]);
-            i++;
-            if (i < len) {
-                buf += String.fromCharCode(SEQRET_DECODER[sb & 0x0f]);
-                i++;
-            }
+        var buf = [];
+        for (var j = 0; j < seqBytes - 1; ++j) {
+            var sb_1 = byteArray[p + j];
+            buf.push(SEQRET_DECODER[(sb_1 & 0xf0) >> 4]);
+            buf.push(SEQRET_DECODER[sb_1 & 0x0f]);
+        }
+        // there are two bases per byte, so this handles the case where it is odd
+        // length
+        var sb = byteArray[p + seqBytes - 1];
+        buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
+        if (len % 2 === 0) {
+            buf.push(SEQRET_DECODER[sb & 0x0f]);
         }
-        return buf;
+        return buf.join('');
     };
     // adapted from igv.js
     BamRecord.prototype.getPairOrientation = function () {

package/dist/record.js.map CHANGED Viewed

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

@@ -9,7 +9,7 @@ export default class BAI extends IndexFile {
     };
     lineCount(refId: number, opts?: BaseOpts): Promise<any>;
     fetchBai(opts?: BaseOpts): Promise<Buffer>;
-    _parse(opts?: BaseOpts): Promise<{
+    _parse(): Promise<{
         [key: string]: any;
     }>;
     indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<{

package/esm/bai.js CHANGED Viewed

@@ -2,7 +2,7 @@ import Long from 'long';
 import { fromBytes } from './virtualOffset';
 import Chunk from './chunk';
 import IndexFile from './indexFile';
-import { longToNumber, abortBreakPoint, optimizeChunks } from './util';
+import { longToNumber, optimizeChunks } from './util';
 const BAI_MAGIC = 21578050; // BAI\1
 function roundDown(n, multiple) {
     return n - (n % multiple);
@@ -34,7 +34,7 @@ export default class BAI extends IndexFile {
         return this.baiP;
     }
     // fetch and parse the index
-    async _parse(opts = {}) {
+    async _parse() {
         const data = { bai: true, maxBlockSize: 1 << 16 };
         const bytes = await this.fetchBai();
         // check BAI magic numbers
@@ -48,7 +48,6 @@ export default class BAI extends IndexFile {
         data.indices = new Array(data.refCount);
         let currOffset = 8;
         for (let i = 0; i < data.refCount; i += 1) {
-            await abortBreakPoint(opts.signal);
             // the binning index
             const binCount = bytes.readInt32LE(currOffset);
             let stats;
@@ -159,7 +158,8 @@ export default class BAI extends IndexFile {
         if (!ba) {
             return [];
         }
-        const overlappingBins = this.reg2bins(min, max); // List of bin #s that overlap min, max
+        // List of bin #s that overlap min, max
+        const overlappingBins = this.reg2bins(min, max);
         const chunks = [];
         // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
         for (const [start, end] of overlappingBins) {
@@ -172,7 +172,8 @@ export default class BAI extends IndexFile {
                 }
             }
         }
-        // Use the linear index to find minimum file position of chunks that could contain alignments in the region
+        // Use the linear index to find minimum file position of chunks that could
+        // contain alignments in the region
         const nintv = ba.linearIndex.length;
         let lowest = null;
         const minLin = Math.min(min >> 14, nintv - 1);

package/esm/bai.js.map CHANGED Viewed

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

@@ -74,4 +74,5 @@ export default class BamFile {
         end: number;
         score: number;
     }[]>;
+    blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
 }

package/esm/bamFile.js CHANGED Viewed

@@ -77,10 +77,10 @@ export default class BamFile {
                 throw new Error('Error reading header');
             }
             if (bytesRead < ret) {
-                buffer = buffer.slice(0, bytesRead);
+                buffer = buffer.subarray(0, bytesRead);
             }
             else {
-                buffer = buffer.slice(0, ret);
+                buffer = buffer.subarray(0, ret);
             }
         }
         else {
@@ -114,10 +114,10 @@ export default class BamFile {
             throw new Error('Error reading refseqs from header');
         }
         if (bytesRead < refSeqBytes) {
-            buffer = buffer.slice(0, bytesRead);
+            buffer = buffer.subarray(0, bytesRead);
         }
         else {
-            buffer = buffer.slice(0, refSeqBytes);
+            buffer = buffer.subarray(0, refSeqBytes);
         }
         const uncba = await unzip(buffer);
         const nRef = uncba.readInt32LE(start);
@@ -171,7 +171,7 @@ export default class BamFile {
             }
         }
         const totalSize = chunks
-            .map((s) => s.fetchedSize())
+            .map(s => s.fetchedSize())
             .reduce((a, b) => a + b, 0);
         if (totalSize > this.fetchSizeLimit) {
             throw new Error(`data size of ${totalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
@@ -303,10 +303,10 @@ export default class BamFile {
         let { buffer } = res;
         checkAbortSignal(signal);
         if (bytesRead < bufsize) {
-            buffer = buffer.slice(0, bytesRead);
+            buffer = buffer.subarray(0, bytesRead);
         }
         else {
-            buffer = buffer.slice(0, bufsize);
+            buffer = buffer.subarray(0, bufsize);
         }
         const { buffer: data, cpositions, dpositions, } = await unzipChunkSlice(buffer, chunk);
         checkAbortSignal(signal);
@@ -354,7 +354,7 @@ export default class BamFile {
                             (blockStart - dpositions[pos]) +
                             chunk.minv.dataPosition +
                             1
-                        : crc32.signed(ba.slice(blockStart, blockEnd)),
+                        : crc32.signed(ba.subarray(blockStart, blockEnd)),
                 });
                 sink.push(feature);
                 if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
@@ -379,5 +379,10 @@ export default class BamFile {
         const seqId = this.chrToIndex && this.chrToIndex[seqName];
         return this.index.indexCov(seqId, start, end);
     }
+    async blocksForRange(seqName, start, end, opts) {
+        await this.index.parse();
+        const seqId = this.chrToIndex && this.chrToIndex[seqName];
+        return this.index.blocksForRange(seqId, start, end, opts);
+    }
 }
 //# sourceMappingURL=bamFile.js.map

package/esm/bamFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/csi.js CHANGED Viewed

@@ -58,7 +58,7 @@ export default class CSI extends IndexFile {
         data.metaChar = data.metaValue ? String.fromCharCode(data.metaValue) : '';
         data.skipLines = bytes.readInt32LE(offset + 20);
         const nameSectionLength = bytes.readInt32LE(offset + 24);
-        Object.assign(data, this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength)));
+        Object.assign(data, this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength)));
         return data;
     }
     _parseNameBytes(namesBytes) {
@@ -143,11 +143,6 @@ export default class CSI extends IndexFile {
         return data;
     }
     parsePseudoBin(bytes, offset) {
-        // const one = Long.fromBytesLE(bytes.slice(offset + 4, offset + 12), true)
-        // const two = Long.fromBytesLE(bytes.slice(offset + 12, offset + 20), true)
-        // const three = longToNumber(
-        //   Long.fromBytesLE(bytes.slice(offset + 20, offset + 28), true),
-        // )
         const lineCount = longToNumber(Long.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
         return { lineCount };
     }

package/esm/csi.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AACvB,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,cAAc,EAAY,MAAM,QAAQ,CAAA;AAEhF,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACD,KAAK,CAAC,SAAS,CAAC,KAAa;QAC3B,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;QACpC,IAAI,CAAC,SAAS,EAAE;YACd,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE;YACR,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE;YACT,OAAO,KAAK,CAAC,SAAS,CAAA;SACvB;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAa,EAAE,MAAc,EAAE,SAAiB;QAC3D,IAAI,SAAS,GAAG,EAAE,EAAE;YAClB,OAAO,EAAE,CAAA;SACV;QAED,MAAM,IAAI,GAA2B,EAAE,CAAA;QACvC,IAAI,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC5C,IAAI,CAAC,cAAc;YACjB,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACxE,IAAI,CAAC,MAAM,GACT,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAGnC,CAAC,IAAI,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACzB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,qCAAqC,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;SACzE;QACD,IAAI,CAAC,aAAa,GAAG;YACnB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QACzE,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,CAAC,MAAM,CACX,IAAI,EACJ,IAAI,CAAC,eAAe,CAClB,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CACF,CAAA;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,eAAe,CAAC,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,MAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAA8B;QACzC,MAAM,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;QACzE,MAAM,MAAM,GAAG,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAA;QAC/D,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,CAAA;QAEjC,0BAA0B;QAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;YACxC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;SACpB;aAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;YAC/C,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;SACpB;aAAM;YACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACjC,oDAAoD;SACrD;QAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QACvC,IAAI,SAAS,EAAE;YACb,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,EAAE,SAAS,CAAC,CAAC,CAAA;SAC7D;QACD,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;QAEjD,+CAA+C;QAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QACvC,IAAI,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QACnC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;YACzC,MAAM,eAAe,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YAClC,oBAAoB;YACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YAC9C,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;YAC/C,IAAI,KAAK,CAAA,CAAC,iDAAiD;YAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;gBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;gBAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;oBAC3B,yDAAyD;oBACzD,qCAAqC;oBACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oBAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;iBAClC;qBAAM;oBACL,MAAM,OAAO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package/esm/indexFile.d.ts CHANGED Viewed

@@ -5,6 +5,7 @@ import { BaseOpts } from './util';
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
+    setupP?: Promise<any>;
     /**
      * @param {filehandle} filehandle
      * @param {function} [renameRefSeqs]
@@ -20,7 +21,7 @@ export default abstract class IndexFile {
         end: number;
         score: number;
     }[]>;
-    abstract blocksForRange(chrId: number, start: number, end: number, opts: BaseOpts): Promise<Chunk[]>;
+    abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
     _findFirstData(data: any, virtualOffset: VirtualOffset): void;
     parse(opts?: BaseOpts): Promise<any>;
     hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;

package/esm/indexFile.js CHANGED Viewed

@@ -18,7 +18,13 @@ export default class IndexFile {
         }
     }
     async parse(opts = {}) {
-        return this._parse(opts);
+        if (!this.setupP) {
+            this.setupP = this._parse(opts).catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
     }
     async hasRefSeq(seqId, opts = {}) {
         return !!((await this.parse(opts)).indices[seqId] || {}).binIndex;

package/esm/indexFile.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAKA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC;;;OAGG;IACH,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;IAgBD,cAAc,CAAC,IAAS,EAAE,aAA4B;QACpD,MAAM,UAAU,GAAG,IAAI,CAAC,aAAa,CAAA;QACrC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,aAAa;gBAChB,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,UAAU,CAAA;SACvE;aAAM;YACL,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;SACnC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAiB,EAAE;QAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;QAChD,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAA;IACnE,CAAC;CACF"}

package/esm/record.d.ts CHANGED Viewed

@@ -30,12 +30,12 @@ export default class BamRecord {
     strand(): 1 | -1;
     multi_segment_next_segment_strand(): 1 | -1 | undefined;
     name(): any;
-    _read_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): any;
+    _parseTag(tagName?: string): string | number | undefined;
     _parseAllTags(): void;
     _parseCigar(cigar: string): (string | number)[][];
     /**
@@ -76,12 +76,12 @@ export default class BamRecord {
     getReadBases(): string;
     seq(): string;
     getPairOrientation(): string | null;
-    _bin_mq_nl(): any;
-    _flag_nc(): any;
-    seq_length(): any;
-    _next_refid(): any;
-    _next_pos(): any;
-    template_length(): any;
+    _bin_mq_nl(): number;
+    _flag_nc(): number;
+    seq_length(): number;
+    _next_refid(): number;
+    _next_pos(): number;
+    template_length(): number;
     toJSON(): {
         [key: string]: any;
     };