@gmod/cram 1.6.3 → 1.7.0

package/src/{indexedCramFile.js → indexedCramFile.ts}

@@ -1,8 +1,31 @@
-import { CramUnimplementedError, CramSizeLimitError } from './errors'
+import { CramSizeLimitError, CramUnimplementedError } from './errors'
 
 import CramFile from './cramFile'
+import CramRecord from './cramFile/record'
+import { SeqFetch } from './cramFile/file'
+import { Filehandle } from './cramFile/filehandle'
+import { Slice } from './craiIndex'
+
+export type CramFileSource = {
+  cramFilehandle?: Filehandle
+  cramUrl?: string
+  cramPath?: string
+}
+
+export type CramIndexLike = {
+  getEntriesForRange: (
+    seqId: number,
+    start: number,
+    end: number,
+  ) => Promise<Slice[]>
+  hasDataForReferenceSequence: (seqId: number) => Promise<boolean>
+}
 
 export default class IndexedCramFile {
+  public cram: CramFile
+  public index: CramIndexLike
+  private fetchSizeLimit: number
+
   /**
    *
    * @param {object} args
@@ -13,7 +36,20 @@ export default class IndexedCramFile {
    * @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
    * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
    */
-  constructor(args) {
+  constructor(
+    args: {
+      index: CramIndexLike
+      fetchSizeLimit?: number
+    } & (
+      | { cram: CramFile }
+      | ({
+          cram?: undefined
+          seqFetch: SeqFetch
+          checkSequenceMD5: boolean
+          cacheSize?: number
+        } & CramFileSource)
+    ),
+  ) {
     // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
     if (args.cram) {
       this.cram = args.cram
@@ -47,7 +83,16 @@ export default class IndexedCramFile {
    * @param {number} end end of the range of interest. 1-based closed coordinates.
    * @returns {Promise[Array[CramRecord]]}
    */
-  async getRecordsForRange(seq, start, end, opts = {}) {
+  async getRecordsForRange(
+    seq: number,
+    start: number,
+    end: number,
+    opts: {
+      viewAsPairs?: boolean
+      pairAcrossChr?: boolean
+      maxInsertSize?: number
+    } = {},
+  ) {
     opts.viewAsPairs = opts.viewAsPairs || false
     opts.pairAcrossChr = opts.pairAcrossChr || false
     opts.maxInsertSize = opts.maxInsertSize || 200000
@@ -70,20 +115,24 @@ export default class IndexedCramFile {
     // TODO: do we need to merge or de-duplicate the blocks?
 
     // fetch all the slices and parse the feature data
-    const filter = feature =>
+    const filter = (feature: CramRecord) =>
       feature.sequenceId === seq &&
       feature.alignmentStart <= end &&
+      feature.lengthOnRef !== undefined &&
       feature.alignmentStart + feature.lengthOnRef - 1 >= start
     const sliceResults = await Promise.all(
       slices.map(slice => this.getRecordsInSlice(slice, filter)),
     )
 
-    let ret = Array.prototype.concat(...sliceResults)
+    let ret: CramRecord[] = Array.prototype.concat(...sliceResults)
     if (opts.viewAsPairs) {
-      const readNames = {}
-      const readIds = {}
+      const readNames: Record<string, number> = {}
+      const readIds: Record<string, number> = {}
       for (let i = 0; i < ret.length; i += 1) {
         const name = ret[i].readName
+        if (name === undefined) {
+          throw new Error()
+        }
         const id = ret[i].uniqueId
         if (!readNames[name]) {
           readNames[name] = 0
@@ -91,7 +140,7 @@ export default class IndexedCramFile {
         readNames[name] += 1
         readIds[id] = 1
       }
-      const unmatedPairs = {}
+      const unmatedPairs: Record<string, boolean> = {}
       Object.entries(readNames).forEach(([k, v]) => {
         if (v === 1) {
           unmatedPairs[k] = true
@@ -99,18 +148,22 @@ export default class IndexedCramFile {
       })
       const matePromises = []
       for (let i = 0; i < ret.length; i += 1) {
-        const name = ret[i].readName
+        const cramRecord = ret[i]
+        const name = cramRecord.readName
+        if (name === undefined) {
+          throw new Error()
+        }
         if (
           unmatedPairs[name] &&
-          ret[i].mate &&
-          (ret[i].mate.sequenceId === seqId || opts.pairAcrossChr) &&
-          Math.abs(ret[i].alignmentStart - ret[i].mate.alignmentStart) <
+          cramRecord.mate &&
+          (cramRecord.mate.sequenceId === seqId || opts.pairAcrossChr) &&
+          Math.abs(cramRecord.alignmentStart - cramRecord.mate.alignmentStart) <
             opts.maxInsertSize
         ) {
           const mateSlices = this.index.getEntriesForRange(
-            ret[i].mate.sequenceId,
-            ret[i].mate.alignmentStart,
-            ret[i].mate.alignmentStart + 1,
+            cramRecord.mate.sequenceId,
+            cramRecord.mate.alignmentStart,
+            cramRecord.mate.alignmentStart + 1,
           )
           matePromises.push(mateSlices)
         }
@@ -129,7 +182,7 @@ export default class IndexedCramFile {
         )
 
       const mateRecordPromises = []
-      const mateFeatPromises = []
+      const mateFeatPromises: Array<Promise<CramRecord[]>> = []
 
       const mateTotalSize = mateChunks
         .map(s => s.sliceBytes)
@@ -151,6 +204,9 @@ export default class IndexedCramFile {
           const mateRecs = []
           for (let i = 0; i < feats.length; i += 1) {
             const feature = feats[i]
+            if (feature.readName === undefined) {
+              throw new Error()
+            }
             if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
               mateRecs.push(feature)
             }
@@ -171,8 +227,12 @@ export default class IndexedCramFile {
   }
 
   getRecordsInSlice(
-    { containerStart, sliceStart, sliceBytes },
-    filterFunction,
+    {
+      containerStart,
+      sliceStart,
+      sliceBytes,
+    }: { containerStart: number; sliceStart: number; sliceBytes: number },
+    filterFunction: (r: CramRecord) => boolean,
   ) {
     const container = this.cram.getContainerAtPosition(containerStart)
     const slice = container.getSlice(sliceStart, sliceBytes)
@@ -185,7 +245,7 @@ export default class IndexedCramFile {
    * @returns {Promise} true if the CRAM file contains data for the given
    * reference sequence numerical ID
    */
-  hasDataForReferenceSequence(seqId) {
+  hasDataForReferenceSequence(seqId: number) {
     return this.index.hasDataForReferenceSequence(seqId)
   }
 }

package/src/io/{index.js → index.ts}

@@ -1,16 +1,21 @@
 import url from 'url'
-import RemoteFile from './remoteFile'
-import LocalFile from './localFile'
+import { ensureNotNullish } from '../typescript'
+import { Filehandle } from '../cramFile/filehandle'
+import { LocalFile, RemoteFile } from 'generic-filehandle'
 
-function fromUrl(source) {
+function fromUrl(source: string) {
   const { protocol, pathname } = url.parse(source)
   if (protocol === 'file:') {
-    return new LocalFile(unescape(pathname))
+    return new LocalFile(unescape(ensureNotNullish(pathname)))
   }
   return new RemoteFile(source)
 }
 
-function open(maybeUrl, maybePath, maybeFilehandle) {
+function open(
+  maybeUrl?: string,
+  maybePath?: string,
+  maybeFilehandle?: Filehandle,
+): Filehandle {
   if (maybeFilehandle) {
     return maybeFilehandle
   }

package/src/{sam.js → sam.ts}

@@ -1,6 +1,11 @@
-export function parseHeaderText(text) {
+export type HeaderDataItem = {
+  tag: string
+  data: Array<{ tag: string; value: string }>
+}
+
+export function parseHeaderText(text: string): HeaderDataItem[] {
   const lines = text.split(/\r?\n/)
-  const data = []
+  const data: HeaderDataItem[] = []
   lines.forEach(line => {
     const [tag, ...fields] = line.split(/\t/)
     const parsedFields = fields.map(f => {

package/src/typescript.ts

@@ -0,0 +1,17 @@
+export function ensureNotNullish<T>(x: T | null | undefined): T {
+  if (x === null || x === undefined) {
+    throw new Error('Value must not be nullish.')
+  }
+  return x
+}
+
+export type TupleOf<T, N extends number> = N extends N
+  ? number extends N
+    ? T[]
+    : _TupleOf<T, N, []>
+  : never
+export type _TupleOf<
+  T,
+  N extends number,
+  R extends unknown[],
+> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>

package/src/typings/binary-parser.d.ts

@@ -0,0 +1,44 @@
+declare module '@gmod/binary-parser' {
+  export type Options = {
+    stripNull?: boolean
+    formatter?: (item: any) => any
+    length?: number | string | ((this: { $parent: unknown }) => void)
+  }
+
+  export class Parser<T = unknown> {
+    public static start<TStart>(): Parser<TStart>
+
+    public uint8(name?: string | null, options?: Options): Parser
+
+    public itf8(name?: string | null, options?: Options): Parser
+
+    public ltf8(name?: string | null, options?: Options): Parser
+
+    public uint32(name?: string | null, options?: Options): Parser
+
+    public int32(name?: string | null, options?: Options): Parser
+
+    public buffer(name?: string | null, options?: Options): Parser
+
+    public string(name?: string | null, options?: Options): Parser
+
+    public namely(name: string): Parser
+
+    public nest(
+      name?: string | null,
+      options?: { type: Parser | string } & Options,
+    ): Parser
+
+    public choice(
+      name?: string | null,
+      options?: { tag: string; choices: any } & Options,
+    ): Parser
+
+    public array(
+      name?: string | null,
+      options?: { type: string | Parser } & Options,
+    ): Parser
+
+    parse(bytes: Buffer): { result: T; offset: number }
+  }
+}

package/src/typings/bzip2.d.ts

@@ -0,0 +1,7 @@
+declare type BitReader = { __type: void }
+
+declare const bzip2: {
+  array: (buffer: Buffer) => BitReader
+  header: (reader: BitReader) => number
+  decompress: (reader: BitReader, size: number, length?: number) => -1 | string
+}

package/src/typings/htscodecs.d.ts

@@ -0,0 +1,6 @@
+declare module '@jkbonfield/htscodecs' {
+  function r4x16_uncompress(input: Buffer, output: Buffer): void
+  function arith_uncompress(input: Buffer, output: Buffer): void
+  function fqzcomp_uncompress(input: Buffer, output: Buffer): void
+  function tok3_uncompress(input: Buffer, output: Buffer): void
+}

package/dist/io/bufferCache.d.ts

@@ -1,12 +0,0 @@
-export default class BufferCache {
-    constructor({ fetch, size, chunkSize }: {
-        fetch: any;
-        size?: number | undefined;
-        chunkSize?: number | undefined;
-    });
-    fetch: any;
-    chunkSize: number;
-    lruCache: any;
-    get(outputBuffer: any, offset: any, length: any, position: any): Promise<void>;
-    _getChunk(chunkNumber: any): any;
-}

package/dist/io/bufferCache.js

@@ -1,112 +0,0 @@
-"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 __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-var quick_lru_1 = __importDefault(require("quick-lru"));
-var BufferCache = /** @class */ (function () {
-    function BufferCache(_a) {
-        var fetch = _a.fetch, _b = _a.size, size = _b === void 0 ? 10000000 : _b, _c = _a.chunkSize, chunkSize = _c === void 0 ? 32768 : _c;
-        if (!fetch) {
-            throw new Error('fetch function required');
-        }
-        this.fetch = fetch;
-        this.chunkSize = chunkSize;
-        this.lruCache = new quick_lru_1.default({ maxSize: Math.floor(size / chunkSize) });
-    }
-    BufferCache.prototype.get = function (outputBuffer, offset, length, position) {
-        return __awaiter(this, void 0, void 0, function () {
-            var firstChunk, lastChunk, fetches, _loop_1, this_1, chunk, chunks, chunksOffset;
-            var _this = this;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0:
-                        if (outputBuffer.length < offset + length) {
-                            throw new Error('output buffer not big enough for request');
-                        }
-                        firstChunk = Math.floor(position / this.chunkSize);
-                        lastChunk = Math.floor((position + length) / this.chunkSize);
-                        fetches = new Array(lastChunk - firstChunk + 1);
-                        _loop_1 = function (chunk) {
-                            fetches[chunk - firstChunk] = this_1._getChunk(chunk).then(function (data) { return ({
-                                data: data,
-                                chunkNumber: chunk,
-                            }); });
-                        };
-                        this_1 = this;
-                        for (chunk = firstChunk; chunk <= lastChunk; chunk += 1) {
-                            _loop_1(chunk);
-                        }
-                        return [4 /*yield*/, Promise.all(fetches)];
-                    case 1:
-                        chunks = _a.sent();
-                        chunksOffset = position - chunks[0].chunkNumber * this.chunkSize;
-                        chunks.forEach(function (_a) {
-                            var data = _a.data, chunkNumber = _a.chunkNumber;
-                            var chunkPositionStart = chunkNumber * _this.chunkSize;
-                            var copyStart = 0;
-                            var copyEnd = _this.chunkSize;
-                            var copyOffset = offset + (chunkNumber - firstChunk) * _this.chunkSize - chunksOffset;
-                            if (chunkNumber === firstChunk) {
-                                copyOffset = offset;
-                                copyStart = chunksOffset;
-                            }
-                            if (chunkNumber === lastChunk) {
-                                copyEnd = position + length - chunkPositionStart;
-                            }
-                            data.copy(outputBuffer, copyOffset, copyStart, copyEnd);
-                        });
-                        return [2 /*return*/];
-                }
-            });
-        });
-    };
-    BufferCache.prototype._getChunk = function (chunkNumber) {
-        var cachedPromise = this.lruCache.get(chunkNumber);
-        if (cachedPromise) {
-            return cachedPromise;
-        }
-        var freshPromise = this.fetch(chunkNumber * this.chunkSize, this.chunkSize);
-        this.lruCache.set(chunkNumber, freshPromise);
-        return freshPromise;
-    };
-    return BufferCache;
-}());
-exports.default = BufferCache;
-//# sourceMappingURL=bufferCache.js.map

package/dist/io/bufferCache.js.map

@@ -1 +0,0 @@
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package/dist/io/localFile.d.ts

@@ -1,10 +0,0 @@
-export default class LocalFile {
-    constructor(source: any);
-    position: number;
-    filename: any;
-    fd: any;
-    read(buffer: any, offset: number | undefined, length: any, position: any): Promise<any>;
-    readFile(): Promise<any>;
-    stat(): Promise<any>;
-    _stat: any;
-}

package/dist/io/localFile.js

@@ -1,108 +0,0 @@
-"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 __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-var es6_promisify_1 = require("es6-promisify");
-var fs_1 = __importDefault(require("fs"));
-var fsOpen = fs_1.default && (0, es6_promisify_1.promisify)(fs_1.default.open);
-var fsRead = fs_1.default && (0, es6_promisify_1.promisify)(fs_1.default.read);
-var fsFStat = fs_1.default && (0, es6_promisify_1.promisify)(fs_1.default.fstat);
-var fsReadFile = fs_1.default && (0, es6_promisify_1.promisify)(fs_1.default.readFile);
-var LocalFile = /** @class */ (function () {
-    function LocalFile(source) {
-        this.position = 0;
-        this.filename = source;
-        this.fd = fsOpen(this.filename, 'r');
-    }
-    LocalFile.prototype.read = function (buffer, offset, length, position) {
-        if (offset === void 0) { offset = 0; }
-        return __awaiter(this, void 0, void 0, function () {
-            var readPosition, _a;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        readPosition = position;
-                        if (readPosition === null) {
-                            readPosition = this.position;
-                            this.position += length;
-                        }
-                        _a = fsRead;
-                        return [4 /*yield*/, this.fd];
-                    case 1: return [2 /*return*/, _a.apply(void 0, [_b.sent(), buffer, offset, length, position])];
-                }
-            });
-        });
-    };
-    LocalFile.prototype.readFile = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var _a;
-            return __generator(this, function (_b) {
-                switch (_b.label) {
-                    case 0:
-                        _a = fsReadFile;
-                        return [4 /*yield*/, this.fd];
-                    case 1: return [2 /*return*/, _a.apply(void 0, [_b.sent()])];
-                }
-            });
-        });
-    };
-    LocalFile.prototype.stat = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var _a, _b;
-            return __generator(this, function (_c) {
-                switch (_c.label) {
-                    case 0:
-                        if (!!this._stat) return [3 /*break*/, 3];
-                        _a = this;
-                        _b = fsFStat;
-                        return [4 /*yield*/, this.fd];
-                    case 1: return [4 /*yield*/, _b.apply(void 0, [_c.sent()])];
-                    case 2:
-                        _a._stat = _c.sent();
-                        _c.label = 3;
-                    case 3: return [2 /*return*/, this._stat];
-                }
-            });
-        });
-    };
-    return LocalFile;
-}());
-exports.default = LocalFile;
-//# sourceMappingURL=localFile.js.map

package/dist/io/localFile.js.map

@@ -1 +0,0 @@
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package/dist/io/remoteFile.d.ts

@@ -1,16 +0,0 @@
-export default class RemoteFile {
-    constructor(source: any);
-    position: number;
-    url: any;
-    cache: BufferCache;
-    _fetch(position: any, length: any): Promise<Buffer>;
-    _stat: {
-        size: number;
-    } | undefined;
-    read(buffer: any, offset?: number, length?: number, position?: number): Promise<void>;
-    readFile(): Promise<Buffer>;
-    stat(): Promise<{
-        size: number;
-    }>;
-}
-import BufferCache from "./bufferCache";