@gmod/tabix 1.5.0 → 1.5.1

package/esm/util.d.ts

@@ -0,0 +1,25 @@
+/// <reference types="long" />
+import Chunk from './chunk';
+import VirtualOffset from './virtualOffset';
+export declare function longToNumber(long: Long): number;
+/**
+ * Properly check if the given AbortSignal is aborted.
+ * Per the standard, if the signal reads as aborted,
+ * this function throws either a DOMException AbortError, or a regular error
+ * with a `code` attribute set to `ERR_ABORTED`.
+ *
+ * For convenience, passing `undefined` is a no-op
+ *
+ * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted` attribute
+ * @returns nothing
+ */
+export declare function checkAbortSignal(signal?: AbortSignal): void;
+/**
+ * Skips to the next tick, then runs `checkAbortSignal`.
+ * Await this to inside an otherwise synchronous loop to
+ * provide a place to break when an abort signal is received.
+ * @param {AbortSignal} signal
+ */
+export declare function abortBreakPoint(signal?: AbortSignal): Promise<void>;
+export declare function canMergeBlocks(chunk1: Chunk, chunk2: Chunk): boolean;
+export declare function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset): Chunk[];

package/esm/util.js

@@ -0,0 +1,98 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.optimizeChunks = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = void 0;
+function longToNumber(long) {
+    if (long.greaterThan(Number.MAX_SAFE_INTEGER) ||
+        long.lessThan(Number.MIN_SAFE_INTEGER)) {
+        throw new Error('integer overflow');
+    }
+    return long.toNumber();
+}
+exports.longToNumber = longToNumber;
+class AbortError extends Error {
+}
+/**
+ * Properly check if the given AbortSignal is aborted.
+ * Per the standard, if the signal reads as aborted,
+ * this function throws either a DOMException AbortError, or a regular error
+ * with a `code` attribute set to `ERR_ABORTED`.
+ *
+ * For convenience, passing `undefined` is a no-op
+ *
+ * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted` attribute
+ * @returns nothing
+ */
+function checkAbortSignal(signal) {
+    if (!signal) {
+        return;
+    }
+    if (signal.aborted) {
+        // console.log('bam aborted!')
+        if (typeof DOMException !== 'undefined') {
+            // eslint-disable-next-line  no-undef
+            throw new DOMException('aborted', 'AbortError');
+        }
+        else {
+            const e = new AbortError('aborted');
+            e.code = 'ERR_ABORTED';
+            throw e;
+        }
+    }
+}
+exports.checkAbortSignal = checkAbortSignal;
+/**
+ * Skips to the next tick, then runs `checkAbortSignal`.
+ * Await this to inside an otherwise synchronous loop to
+ * provide a place to break when an abort signal is received.
+ * @param {AbortSignal} signal
+ */
+async function abortBreakPoint(signal) {
+    await Promise.resolve();
+    checkAbortSignal(signal);
+}
+exports.abortBreakPoint = abortBreakPoint;
+function canMergeBlocks(chunk1, chunk2) {
+    return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
+        chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000);
+}
+exports.canMergeBlocks = canMergeBlocks;
+function optimizeChunks(chunks, lowest) {
+    const mergedChunks = [];
+    let lastChunk = null;
+    if (chunks.length === 0) {
+        return chunks;
+    }
+    chunks.sort(function (c0, c1) {
+        const dif = c0.minv.blockPosition - c1.minv.blockPosition;
+        if (dif !== 0) {
+            return dif;
+        }
+        else {
+            return c0.minv.dataPosition - c1.minv.dataPosition;
+        }
+    });
+    chunks.forEach(chunk => {
+        if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
+            if (lastChunk === null) {
+                mergedChunks.push(chunk);
+                lastChunk = chunk;
+            }
+            else {
+                if (canMergeBlocks(lastChunk, chunk)) {
+                    if (chunk.maxv.compareTo(lastChunk.maxv) > 0) {
+                        lastChunk.maxv = chunk.maxv;
+                    }
+                }
+                else {
+                    mergedChunks.push(chunk);
+                    lastChunk = chunk;
+                }
+            }
+        }
+        // else {
+        //   console.log(`skipping chunk ${chunk}`)
+        // }
+    });
+    return mergedChunks;
+}
+exports.optimizeChunks = optimizeChunks;

package/esm/virtualOffset.d.ts

@@ -0,0 +1,10 @@
+/// <reference types="node" />
+export default 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: Buffer, offset?: number, bigendian?: boolean): VirtualOffset;

package/esm/virtualOffset.js

@@ -0,0 +1,41 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fromBytes = void 0;
+class VirtualOffset {
+    constructor(blockPosition, dataPosition) {
+        this.blockPosition = blockPosition; // < offset of the compressed data block
+        this.dataPosition = dataPosition; // < offset into the uncompressed data
+    }
+    toString() {
+        return `${this.blockPosition}:${this.dataPosition}`;
+    }
+    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;
+function fromBytes(bytes, offset = 0, bigendian = false) {
+    if (bigendian) {
+        throw new Error('big-endian virtual file offsets not implemented');
+    }
+    return new VirtualOffset(bytes[offset + 7] * 0x10000000000 +
+        bytes[offset + 6] * 0x100000000 +
+        bytes[offset + 5] * 0x1000000 +
+        bytes[offset + 4] * 0x10000 +
+        bytes[offset + 3] * 0x100 +
+        bytes[offset + 2], (bytes[offset + 1] << 8) | bytes[offset]);
+}
+exports.fromBytes = fromBytes;

package/package.json

@@ -1,10 +1,11 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.0",
+  "version": "1.5.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",
   "main": "dist/index.js",
+  "module": "esm/index.js",
   "author": {
     "name": "Robert Buels",
     "email": "rbuels@gmail.com",
@@ -14,30 +15,22 @@
     "node": ">=6"
   },
   "files": [
-    "dist"
+    "dist",
+    "esm"
   ],
   "scripts": {
     "test": "jest",
     "coverage": "npm test -- --coverage",
     "lint": "eslint --ext .js,.ts src test",
-    "clean": "rimraf dist",
+    "clean": "rimraf dist esm",
     "prebuild": "npm run clean && npm run lint",
-    "build:types": "tsc --emitDeclarationOnly",
-    "build:js": "babel src --out-dir dist --extensions \".ts,.tsx\" --source-maps inline",
-    "build": "npm run build:types && npm run build:js",
+    "build:esm": "tsc --target es2018 --outDir esm",
+    "build:es5": "tsc --target es5 --outDir dist",
+    "build": "npm run build:esm && npm run build:es5",
     "preversion": "npm run lint && npm test && npm run build",
-    "watch": "npm-watch",
     "prepublishOnly": "npm run lint && npm test && npm run build",
-    "postpublish": "git push origin master --follow-tags",
-    "version": "standard-changelog && git add CHANGELOG.md"
-  },
-  "watch": {
-    "test": "{src,test}/*.js",
-    "lint": "{src,test}/*.js",
-    "build": "src"
-  },
-  "jest": {
-    "testEnvironment": "node"
+    "version": "standard-changelog && git add CHANGELOG.md",
+    "postversion": "git push --follow-tags"
   },
   "keywords": [
     "bionode",
@@ -45,41 +38,31 @@
     "genomics"
   ],
   "dependencies": {
-    "@babel/runtime-corejs2": "^7.3.1",
     "@gmod/bgzf-filehandle": "^1.3.3",
-    "abortable-promise-cache": "^1.0.1",
+    "abortable-promise-cache": "^1.4.1",
     "es6-promisify": "^6.0.1",
     "generic-filehandle": "^2.0.1",
     "long": "^4.0.0",
-    "quick-lru": "^2.0.0"
+    "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@babel/cli": "^7.2.3",
-    "@babel/core": "^7.3.3",
-    "@babel/plugin-transform-runtime": "^7.2.0",
-    "@babel/preset-env": "^7.3.1",
-    "@babel/preset-flow": "^7.0.0",
-    "@babel/preset-typescript": "^7.6.0",
+    "@types/jest": "^27.0.3",
     "@types/long": "^4.0.0",
     "@types/node": "^12.7.11",
     "@types/quick-lru": "2.0.0",
-    "@typescript-eslint/eslint-plugin": "^2.3.3",
-    "@typescript-eslint/parser": "^2.3.3",
-    "babel-eslint": "^10.0.1",
-    "babel-jest": "^24.1.0",
+    "@typescript-eslint/eslint-plugin": "^5.7.0",
+    "@typescript-eslint/parser": "^5.7.0",
     "documentation": "^9.1.1",
-    "eslint": "^5.12.0",
-    "eslint-config-airbnb-base": "^13.1.0",
-    "eslint-config-prettier": "^5.0.0",
-    "eslint-plugin-import": "^2.10.0",
-    "eslint-plugin-jest": "^22.17.0",
-    "eslint-plugin-prettier": "^3.0.1",
-    "jest": "^24.1.0",
-    "npm-watch": "^0.5.0",
-    "prettier": "^1.11.1",
+    "eslint": "^7.0.0",
+    "eslint-config-prettier": "^8.3.0",
+    "eslint-plugin-import": "^2.25.3",
+    "eslint-plugin-prettier": "^4.0.0",
+    "jest": "^27.4.3",
+    "prettier": "^2.5.1",
     "rimraf": "^2.6.2",
     "standard-changelog": "^1.0.0",
-    "typescript": "^3.6.3"
+    "ts-jest": "^27.0.7",
+    "typescript": "^4.5.2"
   },
   "publishConfig": {
     "access": "public"

package/dist/declare.d.js

@@ -1,2 +0,0 @@
-"use strict";
-//# sourceMappingURL=data:application/json;charset=utf-8;base64,eyJ2ZXJzaW9uIjozLCJzb3VyY2VzIjpbXSwibmFtZXMiOltdLCJtYXBwaW5ncyI6IiIsInNvdXJjZXNDb250ZW50IjpbXX0=