@gmod/bam 4.0.0 → 5.0.0

package/dist/htsget.js

@@ -15,185 +15,155 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
-var __rest = (this && this.__rest) || function (s, e) {
-    var t = {};
-    for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
-        t[p] = s[p];
-    if (s != null && typeof Object.getOwnPropertySymbols === "function")
-        for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
-            if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
-                t[p[i]] = s[p[i]];
-        }
-    return t;
-};
-var __await = (this && this.__await) || function (v) { return this instanceof __await ? (this.v = v, this) : new __await(v); }
-var __asyncValues = (this && this.__asyncValues) || function (o) {
-    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
-    var m = o[Symbol.asyncIterator], i;
-    return m ? m.call(o) : (o = typeof __values === "function" ? __values(o) : o[Symbol.iterator](), i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i);
-    function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }
-    function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }
-};
-var __asyncDelegator = (this && this.__asyncDelegator) || function (o) {
-    var i, p;
-    return i = {}, verb("next"), verb("throw", function (e) { throw e; }), verb("return"), i[Symbol.iterator] = function () { return this; }, i;
-    function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: false } : f ? f(v) : v; } : f; }
-};
-var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _arguments, generator) {
-    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
-    var g = generator.apply(thisArg, _arguments || []), i, q = [];
-    return i = Object.create((typeof AsyncIterator === "function" ? AsyncIterator : Object).prototype), verb("next"), verb("throw"), verb("return", awaitReturn), i[Symbol.asyncIterator] = function () { return this; }, i;
-    function awaitReturn(f) { return function (v) { return Promise.resolve(v).then(f, reject); }; }
-    function verb(n, f) { if (g[n]) { i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; if (f) i[n] = f(i[n]); } }
-    function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }
-    function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }
-    function fulfill(value) { resume("next", value); }
-    function reject(value) { resume("throw", value); }
-    function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }
-};
+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;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-const buffer_1 = require("buffer");
+const util_1 = require("./util");
 const bamFile_1 = __importStar(require("./bamFile"));
 const sam_1 = require("./sam");
-function concat(arr, opts) {
-    return __awaiter(this, void 0, void 0, function* () {
-        const res = yield Promise.all(arr.map((chunk) => __awaiter(this, void 0, void 0, function* () {
-            const { url, headers } = chunk;
-            if (url.startsWith('data:')) {
-                return buffer_1.Buffer.from(url.split(',')[1], 'base64');
-            }
-            else {
-                //remove referer header, it is not even allowed to be specified
-                // @ts-expect-error
-                const { referer } = headers, rest = __rest(headers, ["referer"]);
-                const res = yield fetch(url, Object.assign(Object.assign({}, opts), { headers: Object.assign(Object.assign({}, opts === null || opts === void 0 ? void 0 : opts.headers), rest) }));
-                if (!res.ok) {
-                    throw new Error(`HTTP ${res.status} fetching ${url}: ${yield res.text()}`);
-                }
-                return buffer_1.Buffer.from(yield res.arrayBuffer());
+async function concat(arr, opts) {
+    const res = await Promise.all(arr.map(async (chunk) => {
+        const { url, headers } = chunk;
+        if (url.startsWith('data:')) {
+            // @ts-expect-error
+            return Uint8Array.fromBase64(url.split(',')[1], 'base64');
+        }
+        else {
+            //remove referer header, it is not even allowed to be specified
+            // @ts-expect-error
+            const { referer, ...rest } = headers;
+            const res = await fetch(url, {
+                ...opts,
+                headers: { ...opts?.headers, ...rest },
+            });
+            if (!res.ok) {
+                throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
             }
-        })));
-        return buffer_1.Buffer.concat(yield Promise.all(res.map(elt => (0, bgzf_filehandle_1.unzip)(elt))));
-    });
+            return new Uint8Array(await res.arrayBuffer());
+        }
+    }));
+    return (0, util_1.concatUint8Array)(await Promise.all(res.map(elt => (0, bgzf_filehandle_1.unzip)(elt))));
 }
 class HtsgetFile extends bamFile_1.default {
+    baseUrl;
+    trackId;
     constructor(args) {
         super({ htsget: true });
         this.baseUrl = args.baseUrl;
         this.trackId = args.trackId;
     }
-    streamRecordsForRange(chr, min, max, opts) {
-        return __asyncGenerator(this, arguments, function* streamRecordsForRange_1() {
-            var _a;
-            const base = `${this.baseUrl}/${this.trackId}`;
-            const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
-            const chrId = (_a = this.chrToIndex) === null || _a === void 0 ? void 0 : _a[chr];
-            if (chrId === undefined) {
-                yield yield __await([]);
+    async *streamRecordsForRange(chr, min, max, opts) {
+        const base = `${this.baseUrl}/${this.trackId}`;
+        const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
+        const chrId = this.chrToIndex?.[chr];
+        if (chrId === undefined) {
+            yield [];
+        }
+        else {
+            const result = await fetch(url, { ...opts });
+            if (!result.ok) {
+                throw new Error(`HTTP ${result.status} fetching ${url}: ${await result.text()}`);
             }
-            else {
-                const result = yield __await(fetch(url, Object.assign({}, opts)));
-                if (!result.ok) {
-                    throw new Error(`HTTP ${result.status} fetching ${url}: ${yield __await(result.text())}`);
-                }
-                const data = yield __await(result.json());
-                const uncba = yield __await(concat(data.htsget.urls.slice(1), opts));
-                yield __await(yield* __asyncDelegator(__asyncValues(this._fetchChunkFeatures([
-                    // fake stuff to pretend to be a Chunk
-                    {
-                        buffer: uncba,
-                        _fetchedSize: undefined,
-                        bin: 0,
-                        compareTo() {
-                            return 0;
-                        },
-                        toUniqueString() {
-                            return `${chr}_${min}_${max}`;
-                        },
-                        fetchedSize() {
-                            return 0;
-                        },
-                        minv: {
-                            dataPosition: 0,
-                            blockPosition: 0,
-                            compareTo: () => 0,
-                        },
-                        maxv: {
-                            dataPosition: Number.MAX_SAFE_INTEGER,
-                            blockPosition: 0,
-                            compareTo: () => 0,
-                        },
-                        toString() {
-                            return `${chr}_${min}_${max}`;
-                        },
+            const data = await result.json();
+            const uncba = await concat(data.htsget.urls.slice(1), opts);
+            yield* this._fetchChunkFeatures([
+                // fake stuff to pretend to be a Chunk
+                {
+                    buffer: uncba,
+                    _fetchedSize: undefined,
+                    bin: 0,
+                    compareTo() {
+                        return 0;
                     },
-                ], chrId, min, max, opts))));
-            }
-        });
+                    toUniqueString() {
+                        return `${chr}_${min}_${max}`;
+                    },
+                    fetchedSize() {
+                        return 0;
+                    },
+                    minv: {
+                        dataPosition: 0,
+                        blockPosition: 0,
+                        compareTo: () => 0,
+                    },
+                    maxv: {
+                        dataPosition: Number.MAX_SAFE_INTEGER,
+                        blockPosition: 0,
+                        compareTo: () => 0,
+                    },
+                    toString() {
+                        return `${chr}_${min}_${max}`;
+                    },
+                },
+            ], chrId, min, max, opts);
+        }
     }
-    _readChunk(_a) {
-        return __awaiter(this, arguments, void 0, function* ({ chunk }) {
-            if (!chunk.buffer) {
-                throw new Error('expected chunk.buffer in htsget');
-            }
-            return { data: chunk.buffer, cpositions: [], dpositions: [], chunk };
-        });
+    // @ts-expect-error
+    async _readChunk({ chunk }) {
+        if (!chunk.buffer) {
+            throw new Error('expected chunk.buffer in htsget');
+        }
+        return {
+            data: chunk.buffer,
+            cpositions: [],
+            dpositions: [],
+            chunk,
+        };
     }
-    getHeader() {
-        return __awaiter(this, arguments, void 0, function* (opts = {}) {
-            const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
-            const result = yield fetch(url, opts);
-            if (!result.ok) {
-                throw new Error(`HTTP ${result.status} fetching ${url}: ${yield result.text()}`);
-            }
-            const data = yield result.json();
-            const uncba = yield concat(data.htsget.urls, opts);
-            if (uncba.readInt32LE(0) !== bamFile_1.BAM_MAGIC) {
-                throw new Error('Not a BAM file');
-            }
-            const headLen = uncba.readInt32LE(4);
-            const headerText = uncba.toString('utf8', 8, 8 + headLen);
-            const samHeader = (0, sam_1.parseHeaderText)(headerText);
-            // use the @SQ lines in the header to figure out the
-            // mapping between ref ref ID numbers and names
-            const idToName = [];
-            const nameToId = {};
-            const sqLines = samHeader.filter(l => l.tag === 'SQ');
-            for (const [refId, sqLine] of sqLines.entries()) {
-                let refName = '';
-                let length = 0;
-                for (const item of sqLine.data) {
-                    if (item.tag === 'SN') {
-                        refName = item.value;
-                    }
-                    else if (item.tag === 'LN') {
-                        length = +item.value;
-                    }
+    async getHeader(opts = {}) {
+        const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
+        const result = await fetch(url, opts);
+        if (!result.ok) {
+            throw new Error(`HTTP ${result.status} fetching ${url}: ${await result.text()}`);
+        }
+        const data = await result.json();
+        const uncba = await concat(data.htsget.urls, opts);
+        const dataView = new DataView(uncba.buffer);
+        if (dataView.getInt32(0, true) !== bamFile_1.BAM_MAGIC) {
+            throw new Error('Not a BAM file');
+        }
+        const headLen = dataView.getInt32(4, true);
+        const decoder = new TextDecoder('utf8');
+        const headerText = decoder.decode(uncba.subarray(8, 8 + headLen));
+        const samHeader = (0, sam_1.parseHeaderText)(headerText);
+        // use the @SQ lines in the header to figure out the
+        // mapping between ref ref ID numbers and names
+        const idToName = [];
+        const nameToId = {};
+        const sqLines = samHeader.filter(l => l.tag === 'SQ');
+        for (const [refId, sqLine] of sqLines.entries()) {
+            let refName = '';
+            let length = 0;
+            for (const item of sqLine.data) {
+                if (item.tag === 'SN') {
+                    refName = item.value;
+                }
+                else if (item.tag === 'LN') {
+                    length = +item.value;
                 }
-                nameToId[refName] = refId;
-                idToName[refId] = { refName, length };
             }
-            this.chrToIndex = nameToId;
-            this.indexToChr = idToName;
-            return samHeader;
-        });
+            nameToId[refName] = refId;
+            idToName[refId] = { refName, length };
+        }
+        this.chrToIndex = nameToId;
+        this.indexToChr = idToName;
+        return samHeader;
     }
 }
 exports.default = HtsgetFile;

package/dist/htsget.js.map

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

@@ -1,4 +1,4 @@
-import { GenericFilehandle } from 'generic-filehandle';
+import { GenericFilehandle } from 'generic-filehandle2';
 import Chunk from './chunk';
 import { BaseOpts } from './util';
 export default abstract class IndexFile {

package/dist/indexFile.js

@@ -1,6 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 class IndexFile {
+    filehandle;
+    renameRefSeq;
     /**
      * @param {filehandle} filehandle
      * @param {function} [renameRefSeqs]

package/dist/indexFile.js.map

@@ -1 +1 @@
-{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAIA,MAA8B,SAAS;IAIrC;;;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":";;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"}

package/dist/nullIndex.js

@@ -1,13 +1,4 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -20,10 +11,8 @@ class NullIndex extends indexFile_1.default {
     _parse() {
         throw new Error('never called');
     }
-    indexCov() {
-        return __awaiter(this, void 0, void 0, function* () {
-            throw new Error('never called');
-        });
+    async indexCov() {
+        throw new Error('never called');
     }
     blocksForRange() {
         throw new Error('never called');

package/dist/nullIndex.js.map

@@ -1 +1 @@
-{"version":3,"file":"nullIndex.js","sourceRoot":"","sources":["../src/nullIndex.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,4DAAmC;AAEnC,MAAqB,SAAU,SAAQ,mBAAS;IACvC,SAAS;QACd,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IACS,MAAM;QACd,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEY,QAAQ;;YACnB,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;QACjC,CAAC;KAAA;IAEM,cAAc;QACnB,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;CACF;AAfD,4BAeC"}
+{"version":3,"file":"nullIndex.js","sourceRoot":"","sources":["../src/nullIndex.ts"],"names":[],"mappings":";;;;;AAAA,4DAAmC;AAEnC,MAAqB,SAAU,SAAQ,mBAAS;IACvC,SAAS;QACd,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IACS,MAAM;QACd,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,QAAQ;QACnB,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,cAAc;QACnB,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;CACF;AAfD,4BAeC"}

package/dist/record.d.ts

@@ -1,17 +1,17 @@
-import type { Buffer } from 'buffer';
 interface Bytes {
     start: number;
     end: number;
-    byteArray: Buffer;
+    byteArray: Uint8Array;
 }
 export default class BamRecord {
+    #private;
     fileOffset: number;
     private bytes;
     constructor(args: {
         bytes: Bytes;
         fileOffset: number;
     });
-    get byteArray(): Buffer;
+    get byteArray(): Uint8Array<ArrayBufferLike>;
     get flags(): number;
     get ref_id(): number;
     get start(): number;
@@ -19,7 +19,7 @@ export default class BamRecord {
     get id(): number;
     get mq(): number | undefined;
     get score(): number | undefined;
-    get qual(): Buffer | undefined;
+    get qual(): Uint8Array<ArrayBufferLike> | undefined;
     get strand(): 1 | -1;
     get b0(): number;
     get name(): string;
@@ -61,7 +61,7 @@ export default class BamRecord {
     get read_name_length(): number;
     get num_seq_bytes(): number;
     get seq(): string;
-    get pair_orientation(): string;
+    get pair_orientation(): string | undefined;
     get bin_mq_nl(): number;
     get flag_nc(): number;
     get seq_length(): number;