@gmod/bam 5.0.4 → 5.0.6

package/dist/csi.js

@@ -1,46 +1,14 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || (function () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-const virtualOffset_1 = __importStar(require("./virtualOffset"));
+const quick_lru_1 = __importDefault(require("quick-lru"));
 const chunk_1 = __importDefault(require("./chunk"));
-const util_1 = require("./util");
 const indexFile_1 = __importDefault(require("./indexFile"));
+const util_1 = require("./util");
+const virtualOffset_1 = require("./virtualOffset");
 const CSI1_MAGIC = 21582659; // CSI\1
 const CSI2_MAGIC = 38359875; // CSI\2
 function lshift(num, bits) {
@@ -56,7 +24,7 @@ class CSI extends indexFile_1.default {
     setupP;
     async lineCount(refId, opts) {
         const indexData = await this.parse(opts);
-        return indexData.indices[refId]?.stats?.lineCount || 0;
+        return indexData.indices(refId)?.stats?.lineCount || 0;
     }
     async indexCov() {
         return [];
@@ -109,14 +77,43 @@ class CSI extends indexFile_1.default {
         this.minShift = dataView.getInt32(4, true);
         this.depth = dataView.getInt32(8, true);
         this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
+        const maxBinNumber = this.maxBinNumber;
         const auxLength = dataView.getInt32(12, true);
         const aux = auxLength >= 30 ? this.parseAuxData(bytes, 16) : undefined;
         const refCount = dataView.getInt32(16 + auxLength, true);
         // read the indexes for each reference sequence
         let curr = 16 + auxLength + 4;
         let firstDataLine;
-        const indices = new Array(refCount);
+        const offsets = [];
         for (let i = 0; i < refCount; i++) {
+            offsets.push(curr);
+            const binCount = dataView.getInt32(curr, true);
+            curr += 4;
+            for (let j = 0; j < binCount; j++) {
+                const bin = dataView.getUint32(curr, true);
+                curr += 4;
+                if (bin > this.maxBinNumber) {
+                    curr += 28 + 16;
+                }
+                else {
+                    curr += 8;
+                    const chunkCount = dataView.getInt32(curr, true);
+                    curr += 4;
+                    for (let k = 0; k < chunkCount; k += 1) {
+                        curr += 8;
+                        curr += 8;
+                    }
+                }
+            }
+        }
+        const indicesCache = new quick_lru_1.default({
+            maxSize: 5,
+        });
+        function getIndices(refId) {
+            let curr = offsets[refId];
+            if (curr === undefined) {
+                return undefined;
+            }
             // the binning index
             const binCount = dataView.getInt32(curr, true);
             curr += 4;
@@ -125,7 +122,7 @@ class CSI extends indexFile_1.default {
             for (let j = 0; j < binCount; j++) {
                 const bin = dataView.getUint32(curr, true);
                 curr += 4;
-                if (bin > this.maxBinNumber) {
+                if (bin > maxBinNumber) {
                     stats = (0, util_1.parsePseudoBin)(bytes, curr + 28);
                     curr += 28 + 16;
                 }
@@ -146,12 +143,24 @@ class CSI extends indexFile_1.default {
                     binIndex[bin] = chunks;
                 }
             }
-            indices[i] = { binIndex, stats };
+            return {
+                binIndex,
+                stats,
+            };
         }
         return {
             csiVersion,
             firstDataLine,
-            indices,
+            indices: (refId) => {
+                if (!indicesCache.has(refId)) {
+                    const result = getIndices(refId);
+                    if (result) {
+                        indicesCache.set(refId, result);
+                    }
+                    return result;
+                }
+                return indicesCache.get(refId);
+            },
             refCount,
             csi: true,
             maxBlockSize: 1 << 16,
@@ -163,8 +172,7 @@ class CSI extends indexFile_1.default {
             min = 0;
         }
         const indexData = await this.parse(opts);
-        const ba = indexData.indices[refId];
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        const ba = indexData.indices(refId);
         if (!ba) {
             return [];
         }
@@ -176,7 +184,6 @@ class CSI extends indexFile_1.default {
         // 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) {
@@ -185,7 +192,7 @@ class CSI extends indexFile_1.default {
                 }
             }
         }
-        return (0, util_1.optimizeChunks)(chunks, new virtualOffset_1.default(0, 0));
+        return (0, util_1.optimizeChunks)(chunks, new virtualOffset_1.VirtualOffset(0, 0));
     }
     /**
      * calculate the list of bins that may overlap with region [beg,end)
@@ -225,7 +232,7 @@ class CSI extends indexFile_1.default {
     }
     async hasRefSeq(seqId, opts = {}) {
         const header = await this.parse(opts);
-        return !!header.indices[seqId]?.binIndex;
+        return !!header.indices(seqId)?.binIndex;
     }
 }
 exports.default = CSI;

package/dist/csi.js.map

@@ -1 +1 @@
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+{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,0DAAgC;AAEhC,oDAA2B;AAC3B,4DAAmC;AACnC,iCAMe;AACf,mDAA0D;AAE1D,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,MAAqB,GAAI,SAAQ,mBAAS;IAChC,YAAY,GAAG,CAAC,CAAA;IAChB,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEb,MAAM,CAA4B;IAEzC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GACV,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EACnC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,IAAA,qBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAA8B;QACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,IAAI,UAAU,CAAA;QACd,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAEzC,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;YAC1C,oDAAoD;QACtD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,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,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;oBACX,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,YAAY,GAAG,IAAI,mBAAQ,CAAwC;YACvE,OAAO,EAAE,CAAC;SACX,CAAC,CAAA;QAEF,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA,CAAC,iDAAiD;YAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,KAAK,GAAG,IAAA,qBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACxC,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,IAAA,oBAAa,EAAC,aAAa,EAAE,IAAA,yBAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACpE,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oB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package/dist/htsget.d.ts

@@ -1,6 +1,6 @@
-import { BaseOpts, BamOpts } from './util';
 import BamFile from './bamFile';
 import Chunk from './chunk';
+import { BamOpts, BaseOpts } from './util';
 export default class HtsgetFile extends BamFile {
     private baseUrl;
     private trackId;

package/dist/htsget.js

@@ -34,9 +34,9 @@ var __importStar = (this && this.__importStar) || (function () {
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-const util_1 = require("./util");
 const bamFile_1 = __importStar(require("./bamFile"));
 const sam_1 = require("./sam");
+const util_1 = require("./util");
 async function concat(arr, opts) {
     const res = await Promise.all(arr.map(async (chunk) => {
         const { url, headers } = chunk;
@@ -51,7 +51,7 @@ async function concat(arr, opts) {
             return new Uint8Array(ret);
         }
         else {
-            //remove referer header, it is not even allowed to be specified
+            // remove referer header, it is not even allowed to be specified
             // @ts-expect-error
             const { referer, ...rest } = headers;
             const res = await fetch(url, {

package/dist/htsget.js.map

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

@@ -1,12 +1,12 @@
-import { GenericFilehandle } from 'generic-filehandle2';
 import Chunk from './chunk';
 import { BaseOpts } from './util';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
     /**
      * @param {filehandle} filehandle
-     * @param {function} [renameRefSeqs]
+     * @param {function} renameRefSeqs
      */
     constructor({ filehandle, renameRefSeq, }: {
         filehandle: GenericFilehandle;

package/dist/indexFile.js

@@ -5,7 +5,7 @@ class IndexFile {
     renameRefSeq;
     /**
      * @param {filehandle} filehandle
-     * @param {function} [renameRefSeqs]
+     * @param {function} renameRefSeqs
      */
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;

package/dist/indexFile.js.map

@@ -1 +1 @@
-{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAIA,MAA8B,SAAS;IAC9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAE1C;;;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;CAcF;AA/BD,4BA+BC"}
+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAKA,MAA8B,SAAS;IAC9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAE1C;;;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;CAcF;AA/BD,4BA+BC"}

package/dist/long.d.ts

@@ -0,0 +1,3 @@
+export declare const TWO_PWR_16_DBL: number;
+export declare const TWO_PWR_32_DBL: number;
+export declare function longFromBytesToUnsigned(source: Uint8Array, i?: number): number;

package/dist/long.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL = void 0;
+exports.longFromBytesToUnsigned = longFromBytesToUnsigned;
+exports.TWO_PWR_16_DBL = 1 << 16;
+exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL * exports.TWO_PWR_16_DBL;
+function longFromBytesToUnsigned(source, i = 0) {
+    const low = source[i] |
+        (source[i + 1] << 8) |
+        (source[i + 2] << 16) |
+        (source[i + 3] << 24);
+    const high = source[i + 4] |
+        (source[i + 5] << 8) |
+        (source[i + 6] << 16) |
+        (source[i + 7] << 24);
+    return (high >>> 0) * exports.TWO_PWR_32_DBL + (low >>> 0);
+}
+//# sourceMappingURL=long.js.map

package/dist/long.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":";;;AAGA,0DAYC;AAfY,QAAA,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AACxB,QAAA,cAAc,GAAG,sBAAc,GAAG,sBAAc,CAAA;AAE7D,SAAgB,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,sBAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}

package/dist/nullFilehandle.d.ts

@@ -0,0 +1,6 @@
+export default class NullFilehandle {
+    read(): Promise<any>;
+    stat(): Promise<any>;
+    readFile(): Promise<any>;
+    close(): Promise<any>;
+}

package/dist/nullFilehandle.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+class NullFilehandle {
+    read() {
+        throw new Error('never called');
+    }
+    stat() {
+        throw new Error('never called');
+    }
+    readFile() {
+        throw new Error('never called');
+    }
+    close() {
+        throw new Error('never called');
+    }
+}
+exports.default = NullFilehandle;
+//# sourceMappingURL=nullFilehandle.js.map

package/dist/nullFilehandle.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"nullFilehandle.js","sourceRoot":"","sources":["../src/nullFilehandle.ts"],"names":[],"mappings":";;AAAA,MAAqB,cAAc;IAC1B,IAAI;QACT,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IACM,IAAI;QACT,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,QAAQ;QACb,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,KAAK;QACV,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;CACF;AAfD,iCAeC"}

package/dist/record.js

@@ -332,14 +332,13 @@ class BamRecord {
         return (this.seq_length + 1) >> 1;
     }
     get seq() {
-        const { byteArray } = this.bytes;
         const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
         const seqBytes = this.num_seq_bytes;
         const len = this.seq_length;
         const buf = [];
         let i = 0;
         for (let j = 0; j < seqBytes; ++j) {
-            const sb = byteArray[p + j];
+            const sb = this.byteArray[p + j];
             buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
             i++;
             if (i < len) {
@@ -408,7 +407,7 @@ class BamRecord {
             if (k.startsWith('_') || k === 'bytes') {
                 continue;
             }
-            //@ts-ignore
+            // @ts-ignore
             data[k] = this[k];
         }
         return data;

package/dist/record.js.map

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

@@ -1,5 +1,5 @@
 import Chunk from './chunk';
-import VirtualOffset from './virtualOffset';
+import { Offset, VirtualOffset } from './virtualOffset';
 export declare function timeout(ms: number): Promise<unknown>;
 /**
  * Properly check if the given AbortSignal is aborted.
@@ -32,7 +32,7 @@ export interface BaseOpts {
     signal?: AbortSignal;
 }
 export declare function makeOpts(obj?: AbortSignal | BaseOpts): BaseOpts;
-export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
+export declare function optimizeChunks(chunks: Chunk[], lowest?: Offset): Chunk[];
 export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
     lineCount: number;
 };
@@ -43,3 +43,4 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
 };
 export declare function sum(array: Uint8Array[]): number;
 export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
+export declare function gen2array<T>(gen: AsyncIterable<T[]>): Promise<T[]>;

package/dist/util.js

@@ -11,7 +11,8 @@ exports.findFirstData = findFirstData;
 exports.parseNameBytes = parseNameBytes;
 exports.sum = sum;
 exports.concatUint8Array = concatUint8Array;
-const longfn_1 = require("longfn");
+exports.gen2array = gen2array;
+const long_1 = require("./long");
 function timeout(ms) {
     return new Promise(resolve => setTimeout(resolve, ms));
 }
@@ -35,7 +36,7 @@ function checkAbortSignal(signal) {
         // console.log('bam aborted!')
         if (typeof DOMException === 'undefined') {
             const e = new Error('aborted');
-            //@ts-ignore
+            // @ts-ignore
             e.code = 'ERR_ABORTED';
             throw e;
         }
@@ -94,7 +95,7 @@ function optimizeChunks(chunks, lowest) {
 }
 function parsePseudoBin(bytes, offset) {
     return {
-        lineCount: (0, longfn_1.toNumber)((0, longfn_1.fromBytesLE)(bytes.subarray(offset, offset + 8), true)),
+        lineCount: (0, long_1.longFromBytesToUnsigned)(bytes, offset),
     };
 }
 function findFirstData(firstDataLine, virtualOffset) {
@@ -142,4 +143,11 @@ function concatUint8Array(args) {
     }
     return mergedArray;
 }
+async function gen2array(gen) {
+    let out = [];
+    for await (const x of gen) {
+        out = out.concat(x);
+    }
+    return out;
+}
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

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

@@ -1,9 +1,14 @@
-export default class VirtualOffset {
+export interface Offset {
+    blockPosition: number;
+    dataPosition: number;
+    toString(): string;
+    compareTo(arg: Offset): number;
+}
+export declare class VirtualOffset {
     blockPosition: number;
     dataPosition: number;
     constructor(blockPosition: number, dataPosition: number);
     toString(): string;
     compareTo(b: VirtualOffset): number;
-    static min(...args: VirtualOffset[]): VirtualOffset;
 }
 export declare function fromBytes(bytes: Uint8Array, offset?: number, bigendian?: boolean): VirtualOffset;

package/dist/virtualOffset.js

@@ -1,5 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.VirtualOffset = void 0;
 exports.fromBytes = fromBytes;
 class VirtualOffset {
     blockPosition;
@@ -14,21 +15,8 @@ class VirtualOffset {
     compareTo(b) {
         return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
     }
-    static min(...args) {
-        let min;
-        let i = 0;
-        for (; !min; i += 1) {
-            min = args[i];
-        }
-        for (; i < args.length; i += 1) {
-            if (min.compareTo(args[i]) > 0) {
-                min = args[i];
-            }
-        }
-        return min;
-    }
 }
-exports.default = VirtualOffset;
+exports.VirtualOffset = VirtualOffset;
 function fromBytes(bytes, offset = 0, bigendian = false) {
     if (bigendian) {
         throw new Error('big-endian virtual file offsets not implemented');

package/dist/virtualOffset.js.map

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