@gmod/bam 1.1.18 → 2.0.1

package/dist/util.js

@@ -8,8 +8,12 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
 };
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.optimizeChunks = exports.makeOpts = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = exports.timeout = void 0;
+exports.parseNameBytes = exports.findFirstData = exports.parsePseudoBin = exports.optimizeChunks = exports.makeOpts = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = exports.timeout = void 0;
+const long_1 = __importDefault(require("long"));
 function timeout(ms) {
     return new Promise(resolve => setTimeout(resolve, ms));
 }
@@ -39,15 +43,15 @@ function checkAbortSignal(signal) {
     }
     if (signal.aborted) {
         // console.log('bam aborted!')
-        if (typeof DOMException !== 'undefined') {
-            throw new DOMException('aborted', 'AbortError');
-        }
-        else {
+        if (typeof DOMException === 'undefined') {
             const e = new Error('aborted');
             //@ts-ignore
             e.code = 'ERR_ABORTED';
             throw e;
         }
+        else {
+            throw new DOMException('aborted', 'AbortError');
+        }
     }
 }
 exports.checkAbortSignal = checkAbortSignal;
@@ -75,22 +79,17 @@ function makeOpts(obj = {}) {
 exports.makeOpts = makeOpts;
 function optimizeChunks(chunks, lowest) {
     const mergedChunks = [];
-    let lastChunk = null;
+    let lastChunk;
     if (chunks.length === 0) {
         return chunks;
     }
     chunks.sort((c0, c1) => {
         const dif = c0.minv.blockPosition - c1.minv.blockPosition;
-        if (dif !== 0) {
-            return dif;
-        }
-        else {
-            return c0.minv.dataPosition - c1.minv.dataPosition;
-        }
+        return dif === 0 ? c0.minv.dataPosition - c1.minv.dataPosition : dif;
     });
-    chunks.forEach(chunk => {
+    for (const chunk of chunks) {
         if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
-            if (lastChunk === null) {
+            if (lastChunk === undefined) {
                 mergedChunks.push(chunk);
                 lastChunk = chunk;
             }
@@ -106,8 +105,41 @@ function optimizeChunks(chunks, lowest) {
                 }
             }
         }
-    });
+    }
     return mergedChunks;
 }
 exports.optimizeChunks = optimizeChunks;
+function parsePseudoBin(bytes, offset) {
+    const lineCount = longToNumber(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset, offset + 8), true));
+    return { lineCount };
+}
+exports.parsePseudoBin = parsePseudoBin;
+function findFirstData(firstDataLine, virtualOffset) {
+    return firstDataLine
+        ? firstDataLine.compareTo(virtualOffset) > 0
+            ? virtualOffset
+            : firstDataLine
+        : virtualOffset;
+}
+exports.findFirstData = findFirstData;
+function parseNameBytes(namesBytes, renameRefSeq = s => s) {
+    let currRefId = 0;
+    let currNameStart = 0;
+    const refIdToName = [];
+    const refNameToId = {};
+    for (let i = 0; i < namesBytes.length; i += 1) {
+        if (!namesBytes[i]) {
+            if (currNameStart < i) {
+                let refName = namesBytes.toString('utf8', currNameStart, i);
+                refName = renameRefSeq(refName);
+                refIdToName[currRefId] = refName;
+                refNameToId[refName] = currRefId;
+            }
+            currNameStart = i + 1;
+            currRefId += 1;
+        }
+    }
+    return { refNameToId, refIdToName };
+}
+exports.parseNameBytes = parseNameBytes;
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;AAAA,gDAAuB;AAIvB,SAAgB,OAAO,CAAC,EAAU;IAChC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAFD,0BAEC;AAED,SAAgB,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC,CAAC;QACD,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;IACrC,CAAC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AARD,oCAQC;AAED;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,OAAM;IACR,CAAC;IAED,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;QACnB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE,CAAC;YACxC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;YAC9B,YAAY;YACZ,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;QACT,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;QACjD,CAAC;IACH,CAAC;AACH,CAAC;AAhBD,4CAgBC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;QACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;QACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;IAC1B,CAAC;CAAA;AAHD,0CAGC;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AALD,wCAKC;AAaD,SAAgB,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAE,GAAgB,CAAA;AAC7E,CAAC;AAFD,4BAEC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAA4B,CAAA;IAEhC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IAED,MAAM,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACrB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;QAC3B,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC;YAChD,IAAI,SAAS,KAAK,SAAS,EAAE,CAAC;gBAC5B,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE,CAAC;oBACrC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC7C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;oBAC7B,CAAC;gBACH,CAAC;qBAAM,CAAC;oBACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;gBACnB,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAhCD,wCAgCC;AAED,SAAgB,cAAc,CAAC,KAAa,EAAE,MAAc;IAC1D,MAAM,SAAS,GAAG,YAAY,CAC5B,cAAI,CAAC,WAAW,CACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,GAAG,CAAC,CAAC,EACrD,IAAI,CACL,CACF,CAAA;IACD,OAAO,EAAE,SAAS,EAAE,CAAA;AACtB,CAAC;AARD,wCAQC;AAED,SAAgB,aAAa,CAC3B,aAAwC,EACxC,aAA4B;IAE5B,OAAO,aAAa;QAClB,CAAC,CAAC,aAAa,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;YAC1C,CAAC,CAAC,aAAa;YACf,CAAC,CAAC,aAAa;QACjB,CAAC,CAAC,aAAa,CAAA;AACnB,CAAC;AATD,sCASC;AAED,SAAgB,cAAc,CAC5B,UAAkB,EAClB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,MAAM,WAAW,GAA8B,EAAE,CAAA;IACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;gBAC3D,OAAO,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;gBAC/B,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;gBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;YAClC,CAAC;YACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;YACrB,SAAS,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AArBD,wCAqBC"}

package/dist/virtualOffset.js.map

@@ -1 +1 @@
-{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AAAA,MAAqB,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE;YACnB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;SACd;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC9B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE;gBAC9B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;aACd;SACF;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AA/BD,gCA+BC;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;KACnE;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC;AAdD,8BAcC"}
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AAAA,MAAqB,aAAa;IAGhC,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AA/BD,gCA+BC;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACpE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC;AAdD,8BAcC"}

package/esm/bai.d.ts

@@ -1,26 +1,45 @@
-/// <reference types="node" />
+import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
-import IndexFile from './indexFile';
 import { BaseOpts } from './util';
+import IndexFile from './indexFile';
 export default class BAI extends IndexFile {
-    baiP?: Promise<Buffer>;
-    parsePseudoBin(bytes: Buffer, offset: number): {
-        lineCount: number;
-    };
-    lineCount(refId: number, opts?: BaseOpts): Promise<any>;
-    fetchBai(opts?: BaseOpts): Promise<Buffer>;
-    _parse(): Promise<{
-        [key: string]: any;
+    setupP?: ReturnType<BAI['_parse']>;
+    lineCount(refId: number, opts?: BaseOpts): Promise<number>;
+    _parse(opts?: BaseOpts): Promise<{
+        bai: boolean;
+        firstDataLine: VirtualOffset | undefined;
+        maxBlockSize: number;
+        indices: {
+            binIndex: {
+                [key: string]: Chunk[];
+            };
+            linearIndex: VirtualOffset[];
+            stats?: {
+                lineCount: number;
+            } | undefined;
+        }[];
+        refCount: number;
     }>;
     indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<{
         start: number;
         end: number;
         score: number;
     }[]>;
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     * @returns {Array[number]}
-     */
-    reg2bins(beg: number, end: number): number[][];
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
+    parse(opts?: BaseOpts): Promise<{
+        bai: boolean;
+        firstDataLine: VirtualOffset | undefined;
+        maxBlockSize: number;
+        indices: {
+            binIndex: {
+                [key: string]: Chunk[];
+            };
+            linearIndex: VirtualOffset[];
+            stats?: {
+                lineCount: number;
+            } | undefined;
+        }[];
+        refCount: number;
+    }>;
+    hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
 }

package/esm/bai.js

@@ -1,8 +1,7 @@
-import Long from 'long';
 import { fromBytes } from './virtualOffset';
 import Chunk from './chunk';
+import { optimizeChunks, parsePseudoBin, findFirstData } from './util';
 import IndexFile from './indexFile';
-import { longToNumber, optimizeChunks } from './util';
 const BAI_MAGIC = 21578050; // BAI\1
 function roundDown(n, multiple) {
     return n - (n % multiple);
@@ -10,88 +9,90 @@ function roundDown(n, multiple) {
 function roundUp(n, multiple) {
     return n - (n % multiple) + multiple;
 }
+function reg2bins(beg, end) {
+    end -= 1;
+    return [
+        [0, 0],
+        [1 + (beg >> 26), 1 + (end >> 26)],
+        [9 + (beg >> 23), 9 + (end >> 23)],
+        [73 + (beg >> 20), 73 + (end >> 20)],
+        [585 + (beg >> 17), 585 + (end >> 17)],
+        [4681 + (beg >> 14), 4681 + (end >> 14)],
+    ];
+}
 export default class BAI extends IndexFile {
-    parsePseudoBin(bytes, offset) {
-        const lineCount = longToNumber(Long.fromBytesLE(Array.prototype.slice.call(bytes, offset + 16, offset + 24), true));
-        return { lineCount };
-    }
-    async lineCount(refId, opts = {}) {
-        const prom = await this.parse(opts);
-        const index = prom.indices[refId];
-        if (!index) {
-            return -1;
-        }
-        const ret = index.stats || {};
-        return ret.lineCount === undefined ? -1 : ret.lineCount;
-    }
-    fetchBai(opts = {}) {
-        if (!this.baiP) {
-            this.baiP = this.filehandle.readFile(opts).catch(e => {
-                this.baiP = undefined;
-                throw e;
-            });
-        }
-        return this.baiP;
+    async lineCount(refId, opts) {
+        var _a, _b;
+        const indexData = await this.parse(opts);
+        return ((_b = (_a = indexData.indices[refId]) === null || _a === void 0 ? void 0 : _a.stats) === null || _b === void 0 ? void 0 : _b.lineCount) || 0;
     }
     // fetch and parse the index
-    async _parse() {
-        const data = { bai: true, maxBlockSize: 1 << 16 };
-        const bytes = await this.fetchBai();
+    async _parse(opts) {
+        const bytes = (await this.filehandle.readFile(opts));
         // check BAI magic numbers
         if (bytes.readUInt32LE(0) !== BAI_MAGIC) {
             throw new Error('Not a BAI file');
         }
-        data.refCount = bytes.readInt32LE(4);
+        const refCount = bytes.readInt32LE(4);
         const depth = 5;
         const binLimit = ((1 << ((depth + 1) * 3)) - 1) / 7;
         // read the indexes for each reference sequence
-        data.indices = new Array(data.refCount);
-        let currOffset = 8;
-        for (let i = 0; i < data.refCount; i += 1) {
+        let curr = 8;
+        let firstDataLine;
+        const indices = new Array(refCount);
+        for (let i = 0; i < refCount; i++) {
             // the binning index
-            const binCount = bytes.readInt32LE(currOffset);
+            const binCount = bytes.readInt32LE(curr);
             let stats;
-            currOffset += 4;
+            curr += 4;
             const binIndex = {};
             for (let j = 0; j < binCount; j += 1) {
-                const bin = bytes.readUInt32LE(currOffset);
-                currOffset += 4;
+                const bin = bytes.readUInt32LE(curr);
+                curr += 4;
                 if (bin === binLimit + 1) {
-                    currOffset += 4;
-                    stats = this.parsePseudoBin(bytes, currOffset);
-                    currOffset += 32;
+                    curr += 4;
+                    stats = parsePseudoBin(bytes, curr + 16);
+                    curr += 32;
                 }
                 else if (bin > binLimit + 1) {
                     throw new Error('bai index contains too many bins, please use CSI');
                 }
                 else {
-                    const chunkCount = bytes.readInt32LE(currOffset);
-                    currOffset += 4;
+                    const chunkCount = bytes.readInt32LE(curr);
+                    curr += 4;
                     const chunks = new Array(chunkCount);
-                    for (let k = 0; k < chunkCount; k += 1) {
-                        const u = fromBytes(bytes, currOffset);
-                        const v = fromBytes(bytes, currOffset + 8);
-                        currOffset += 16;
-                        this._findFirstData(data, u);
+                    for (let k = 0; k < chunkCount; k++) {
+                        const u = fromBytes(bytes, curr);
+                        curr += 8;
+                        const v = fromBytes(bytes, curr);
+                        curr += 8;
+                        firstDataLine = findFirstData(firstDataLine, u);
                         chunks[k] = new Chunk(u, v, bin);
                     }
                     binIndex[bin] = chunks;
                 }
             }
-            const linearCount = bytes.readInt32LE(currOffset);
-            currOffset += 4;
-            // as we're going through the linear index, figure out
-            // the smallest virtual offset in the indexes, which
-            // tells us where the BAM header ends
+            const linearCount = bytes.readInt32LE(curr);
+            curr += 4;
+            // as we're going through the linear index, figure out the smallest
+            // virtual offset in the indexes, which tells us where the BAM header
+            // ends
             const linearIndex = new Array(linearCount);
-            for (let k = 0; k < linearCount; k += 1) {
-                linearIndex[k] = fromBytes(bytes, currOffset);
-                currOffset += 8;
-                this._findFirstData(data, linearIndex[k]);
+            for (let j = 0; j < linearCount; j++) {
+                const offset = fromBytes(bytes, curr);
+                curr += 8;
+                firstDataLine = findFirstData(firstDataLine, offset);
+                linearIndex[j] = offset;
             }
-            data.indices[i] = { binIndex, linearIndex, stats };
+            indices[i] = { binIndex, linearIndex, stats };
         }
-        return data;
+        return {
+            bai: true,
+            firstDataLine,
+            maxBlockSize: 1 << 16,
+            indices,
+            refCount,
+        };
     }
     async indexCov(seqId, start, end, opts = {}) {
         const v = 16384;
@@ -102,18 +103,14 @@ export default class BAI extends IndexFile {
             return [];
         }
         const { linearIndex = [], stats } = seqIdx;
-        if (!linearIndex.length) {
+        if (linearIndex.length === 0) {
             return [];
         }
-        const e = end !== undefined ? roundUp(end, v) : (linearIndex.length - 1) * v;
-        const s = start !== undefined ? roundDown(start, v) : 0;
-        let depths;
-        if (range) {
-            depths = new Array((e - s) / v);
-        }
-        else {
-            depths = new Array(linearIndex.length - 1);
-        }
+        const e = end === undefined ? (linearIndex.length - 1) * v : roundUp(end, v);
+        const s = start === undefined ? 0 : roundDown(start, v);
+        const depths = range
+            ? new Array((e - s) / v)
+            : new Array(linearIndex.length - 1);
         const totalSize = linearIndex[linearIndex.length - 1].blockPosition;
         if (e > (linearIndex.length - 1) * v) {
             throw new Error('query outside of range of linear index');
@@ -127,24 +124,10 @@ export default class BAI extends IndexFile {
             };
             currentPos = linearIndex[i + 1].blockPosition;
         }
-        return depths.map(d => {
-            return { ...d, score: (d.score * stats.lineCount) / totalSize };
-        });
-    }
-    /**
-     * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
-     * @returns {Array[number]}
-     */
-    reg2bins(beg, end) {
-        end -= 1;
-        return [
-            [0, 0],
-            [1 + (beg >> 26), 1 + (end >> 26)],
-            [9 + (beg >> 23), 9 + (end >> 23)],
-            [73 + (beg >> 20), 73 + (end >> 20)],
-            [585 + (beg >> 17), 585 + (end >> 17)],
-            [4681 + (beg >> 14), 4681 + (end >> 14)],
-        ];
+        return depths.map(d => ({
+            ...d,
+            score: (d.score * ((stats === null || stats === void 0 ? void 0 : stats.lineCount) || 0)) / totalSize,
+        }));
     }
     async blocksForRange(refId, min, max, opts = {}) {
         if (min < 0) {
@@ -159,15 +142,15 @@ export default class BAI extends IndexFile {
             return [];
         }
         // List of bin #s that overlap min, max
-        const overlappingBins = this.reg2bins(min, max);
+        const overlappingBins = reg2bins(min, max);
         const chunks = [];
         // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
         for (const [start, end] of overlappingBins) {
             for (let bin = start; bin <= end; bin++) {
                 if (ba.binIndex[bin]) {
                     const binChunks = ba.binIndex[bin];
-                    for (let c = 0; c < binChunks.length; ++c) {
-                        chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin));
+                    for (const binChunk of binChunks) {
+                        chunks.push(binChunk);
                     }
                 }
             }
@@ -175,18 +158,30 @@ export default class BAI extends IndexFile {
         // 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;
+        let lowest;
         const minLin = Math.min(min >> 14, nintv - 1);
         const maxLin = Math.min(max >> 14, nintv - 1);
         for (let i = minLin; i <= maxLin; ++i) {
             const vp = ba.linearIndex[i];
-            if (vp) {
-                if (!lowest || vp.compareTo(lowest) < 0) {
-                    lowest = vp;
-                }
+            if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
+                lowest = vp;
             }
         }
         return optimizeChunks(chunks, lowest);
     }
+    async parse(opts = {}) {
+        if (!this.setupP) {
+            this.setupP = this._parse(opts).catch(e => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
+    }
+    async hasRefSeq(seqId, opts = {}) {
+        var _a;
+        const header = await this.parse(opts);
+        return !!((_a = header.indices[seqId]) === null || _a === void 0 ? void 0 : _a.binIndex);
+    }
 }
 //# sourceMappingURL=bai.js.map

package/esm/bai.js.map

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+{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAsB,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,KAAK,MAAM,SAAS,CAAA;AAE3B,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,aAAa,EAAY,MAAM,QAAQ,CAAA;AAChF,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAED,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KACzC,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAGxC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,CAAA,MAAA,MAAA,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,0CAAE,KAAK,0CAAE,SAAS,KAAI,CAAC,CAAA;IACxD,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAAe;QAC1B,MAAM,KAAK,GAAG,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAA;QAE9D,0BAA0B;QAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE,CAAC;YACxC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACrC,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,aAAwC,CAAA;QAI5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAItB,QAAQ,CAAC,CAAA;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,oBAAoB;YACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;YACxC,IAAI,KAAK,CAAA;YAET,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA+B,EAAE,CAAA;YAE/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,IAAI,CAAC,CAAA;gBACpC,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,GAAG,cAAc,CAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACxC,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;oBAC1C,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;oBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;YAC3C,IAAI,IAAI,CAAC,CAAA;YACT,mEAAmE;YACnE,qEAAqE;YACrE,OAAO;YACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,MAAM,MAAM,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IAAI,CAAC,CAAA;gBACT,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,MAAM,CAAC,CAAA;gBACpD,WAAW,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;YACzB,CAAC;YAED,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;QAC/C,CAAC;QAED,OAAO;YACL,GAAG,EAAE,IAAI;YACT,aAAa;YACb,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,OAAO;YACP,QAAQ;SACT,CAAA;IACH,CAAC;IAED,KAAK,CAAC,QAAQ,CACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,OAAiB,EAAE;QAEnB,MAAM,CAAC,GAAG,KAAK,CAAA;QACf,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;QACjC,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACvC,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,WAAW,GAAG,EAAE,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;QAC1C,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;QAC5E,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QACvD,MAAM,MAAM,GAAG,KAAK;YAClB,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;YACxB,CAAC,CAAC,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,MAAM,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;QACnE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;QAC3D,CAAC;QACD,IAAI,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GA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package/esm/bamFile.d.ts

@@ -1,28 +1,27 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import { GenericFilehandle } from 'generic-filehandle';
+import BAI from './bai';
+import CSI from './csi';
 import Chunk from './chunk';
 import BAMFeature from './record';
 import { BamOpts, BaseOpts } from './util';
 export declare const BAM_MAGIC = 21840194;
 export default class BamFile {
-    private renameRefSeq;
-    private bam;
-    private index;
-    private chunkSizeLimit;
-    private fetchSizeLimit;
-    private header;
-    protected chrToIndex: any;
-    protected indexToChr: any;
-    private yieldThreadTime;
+    renameRefSeq: (a: string) => string;
+    bam: GenericFilehandle;
+    header?: string;
+    chrToIndex?: Record<string, number>;
+    indexToChr?: {
+        refName: string;
+        length: number;
+    }[];
+    yieldThreadTime: number;
+    index?: BAI | CSI;
+    htsget: boolean;
+    headerP?: ReturnType<BamFile['getHeaderPre']>;
     private featureCache;
-    /**
-     * @param {object} args
-     * @param {string} [args.bamPath]
-     * @param {FileHandle} [args.bamFilehandle]
-     * @param {string} [args.baiPath]
-     * @param {FileHandle} [args.baiFilehandle]
-     */
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, fetchSizeLimit, chunkSizeLimit, yieldThreadTime, renameRefSeqs, }: {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime, renameRefSeqs, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
         bamUrl?: string;
@@ -32,19 +31,25 @@ export default class BamFile {
         csiPath?: string;
         csiFilehandle?: GenericFilehandle;
         csiUrl?: string;
-        fetchSizeLimit?: number;
-        chunkSizeLimit?: number;
         renameRefSeqs?: (a: string) => string;
         yieldThreadTime?: number;
+        htsget?: boolean;
     });
-    getHeader(origOpts?: AbortSignal | BaseOpts): Promise<{
+    getHeaderPre(origOpts?: BaseOpts): Promise<{
         tag: string;
         data: {
             tag: string;
             value: string;
         }[];
-    }[]>;
-    getHeaderText(opts?: BaseOpts): Promise<any>;
+    }[] | undefined>;
+    getHeader(opts?: BaseOpts): Promise<{
+        tag: string;
+        data: {
+            tag: string;
+            value: string;
+        }[];
+    }[] | undefined>;
+    getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     _readRefSeqs(start: number, refSeqBytes: number, opts?: BaseOpts): Promise<{
         chrToIndex: {
             [key: string]: number;
@@ -56,19 +61,20 @@ export default class BamFile {
     }>;
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
     streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
-    _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
+    _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
+    _readRegion(position: number, size: number, opts?: BaseOpts): Promise<Buffer>;
     _readChunk({ chunk, opts }: {
         chunk: Chunk;
         opts: BaseOpts;
     }): Promise<{
-        data: any;
-        cpositions: any;
-        dpositions: any;
+        data: Buffer;
+        cpositions: number[];
+        dpositions: number[];
         chunk: Chunk;
     }>;
     readBamFeatures(ba: Buffer, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
-    hasRefSeq(seqName: string): Promise<boolean>;
+    hasRefSeq(seqName: string): Promise<boolean | undefined>;
     lineCount(seqName: string): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<{
         start: number;