@gmod/bam 1.1.8 → 1.1.9

package/esm/sam.d.ts

@@ -0,0 +1,7 @@
+export declare function parseHeaderText(text: string): {
+    tag: string;
+    data: {
+        tag: string;
+        value: string;
+    }[];
+}[];

package/esm/sam.js

@@ -0,0 +1,16 @@
+export function parseHeaderText(text) {
+    const lines = text.split(/\r?\n/);
+    const data = [];
+    lines.forEach(line => {
+        const [tag, ...fields] = line.split(/\t/);
+        const parsedFields = fields.map(f => {
+            const [fieldTag, value] = f.split(':', 2);
+            return { tag: fieldTag, value };
+        });
+        if (tag) {
+            data.push({ tag: tag.substr(1), data: parsedFields });
+        }
+    });
+    return data;
+}
+//# sourceMappingURL=sam.js.map

package/esm/sam.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;QACnB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,MAAM,YAAY,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YAClC,MAAM,CAAC,QAAQ,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YACzC,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QACjC,CAAC,CAAC,CAAA;QACF,IAAI,GAAG,EAAE;YACP,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAA;SACtD;IACH,CAAC,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC"}

package/esm/util.d.ts

@@ -0,0 +1,35 @@
+import Chunk from './chunk';
+import VirtualOffset from './virtualOffset';
+export declare function timeout(ms: number): Promise<unknown>;
+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 interface BamOpts {
+    viewAsPairs?: boolean;
+    pairAcrossChr?: boolean;
+    maxInsertSize?: number;
+    signal?: AbortSignal;
+}
+export interface BaseOpts {
+    signal?: AbortSignal;
+}
+export declare function makeOpts(obj?: AbortSignal | BaseOpts): BaseOpts;
+export declare function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset): Chunk[];

package/esm/util.js

@@ -0,0 +1,92 @@
+export function timeout(ms) {
+    return new Promise(resolve => setTimeout(resolve, ms));
+}
+export function longToNumber(long) {
+    if (long.greaterThan(Number.MAX_SAFE_INTEGER) ||
+        long.lessThan(Number.MIN_SAFE_INTEGER)) {
+        throw new Error('integer overflow');
+    }
+    return long.toNumber();
+}
+/**
+ * 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 function checkAbortSignal(signal) {
+    if (!signal) {
+        return;
+    }
+    if (signal.aborted) {
+        // console.log('bam aborted!')
+        if (typeof DOMException !== 'undefined') {
+            throw new DOMException('aborted', 'AbortError');
+        }
+        else {
+            const e = new Error('aborted');
+            //@ts-ignore
+            e.code = 'ERR_ABORTED';
+            throw e;
+        }
+    }
+}
+/**
+ * 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 async function abortBreakPoint(signal) {
+    await Promise.resolve();
+    checkAbortSignal(signal);
+}
+export function canMergeBlocks(chunk1, chunk2) {
+    return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
+        chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000);
+}
+export function makeOpts(obj = {}) {
+    return 'aborted' in obj ? { signal: obj } : obj;
+}
+export function optimizeChunks(chunks, lowest) {
+    const mergedChunks = [];
+    let lastChunk = null;
+    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;
+        }
+    });
+    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;
+                }
+            }
+        }
+    });
+    return mergedChunks;
+}
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAGA,MAAM,UAAU,OAAO,CAAC,EAAU;IAChC,OAAO,IAAI,OAAO,CAAC,OAAO,CAAC,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC,CAAA;AACxD,CAAC;AAED,MAAM,UAAU,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC;QACA,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;KACpC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE;QACX,OAAM;KACP;IAED,IAAI,MAAM,CAAC,OAAO,EAAE;QAClB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE;YACvC,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;SAChD;aAAM;YACL,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,SAAS,CAAC,CAAA;YAC9B,YAAY;YACZ,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;SACR;KACF;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,CAAC,KAAK,UAAU,eAAe,CAAC,MAAoB;IACxD,MAAM,OAAO,CAAC,OAAO,EAAE,CAAA;IACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;AAC1B,CAAC;AAED,MAAM,UAAU,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;AAaD,MAAM,UAAU,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAE,GAAgB,CAAA;AAC7E,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,MAAe,EAAE,MAAqB;IACnE,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAAS,GAAiB,IAAI,CAAA;IAElC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;QACvB,OAAO,MAAM,CAAA;KACd;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,IAAI,GAAG,KAAK,CAAC,EAAE;YACb,OAAO,GAAG,CAAA;SACX;aAAM;YACL,OAAO,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;SACnD;IACH,CAAC,CAAC,CAAA;IAEF,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE;QACrB,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE;YAC/C,IAAI,SAAS,KAAK,IAAI,EAAE;gBACtB,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;aAClB;iBAAM;gBACL,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE;oBACpC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE;wBAC5C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;qBAC5B;iBACF;qBAAM;oBACL,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;iBAClB;aACF;SACF;IACH,CAAC,CAAC,CAAA;IAEF,OAAO,YAAY,CAAA;AACrB,CAAC"}

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 +1,37 @@
+export default 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;
+    }
+}
+export 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]);
+}
+//# sourceMappingURL=virtualOffset.js.map

package/esm/virtualOffset.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,OAAO,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;AACD,MAAM,UAAU,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"}

package/package.json

@@ -1,10 +1,11 @@
 {
   "name": "@gmod/bam",
-  "version": "1.1.8",
+  "version": "1.1.9",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
   "main": "dist/index.js",
+  "module": "esm/index.js",
   "author": {
     "name": "Colin Diesh",
     "email": "colin.diesh@gmail.com",
@@ -14,24 +15,22 @@
     "node": ">=6"
   },
   "files": [
-    "dist"
+    "dist",
+    "esm"
   ],
   "scripts": {
     "test": "jest",
     "coverage": "npm test -- --coverage",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts src test",
-    "clean": "rimraf dist",
+    "clean": "rimraf dist esm",
+    "build:esm": "tsc --target es2018 --outDir esm",
+    "build:es5": "tsc --target es5 --outDir dist",
+    "build": "npm run build:esm && npm run build:es5",
     "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",
     "preversion": "npm run lint && npm test && npm run build",
     "version": "standard-changelog && git add CHANGELOG.md",
     "postversion": "git push --follow-tags"
   },
-  "jest": {
-    "testEnvironment": "node"
-  },
   "keywords": [
     "bionode",
     "biojs",
@@ -39,7 +38,6 @@
     "genomics"
   ],
   "dependencies": {
-    "@babel/runtime-corejs3": "^7.5.5",
     "@gmod/bgzf-filehandle": "^1.3.3",
     "abortable-promise-cache": "^1.4.0",
     "buffer-crc32": "^0.2.13",
@@ -52,30 +50,24 @@
     "range-parser": "^1.2.1"
   },
   "devDependencies": {
-    "@babel/cli": "^7.2.3",
-    "@babel/core": "^7.3.3",
-    "@babel/plugin-proposal-class-properties": "^7.5.5",
-    "@babel/plugin-transform-runtime": "^7.2.0",
-    "@babel/preset-env": "^7.3.1",
-    "@babel/preset-typescript": "^7.6.0",
     "@types/buffer-crc32": "^0.2.0",
+    "@types/jest": "^27.0.2",
     "@types/long": "^4.0.0",
     "@types/node": "^12.7.8",
     "@types/range-parser": "^1.2.3",
-    "@typescript-eslint/eslint-plugin": "^2.3.1",
-    "@typescript-eslint/parser": "^2.3.1",
-    "babel-jest": "^24.1.0",
-    "eslint": "^5.12.0",
-    "eslint-config-airbnb-base": "^13.1.0",
-    "eslint-config-prettier": "^4.1.0",
-    "eslint-plugin-import": "^2.10.0",
-    "eslint-plugin-jest": "^22.17.0",
-    "eslint-plugin-prettier": "^3.0.1",
-    "jest": "^24.3.1",
-    "prettier": "^1.11.1",
-    "rimraf": "^2.6.2",
+    "@typescript-eslint/eslint-plugin": "^5.7.0",
+    "@typescript-eslint/parser": "^5.7.0",
+    "eslint": "^7.0.0",
+    "eslint-config-airbnb-base": "^15.0.0",
+    "eslint-config-prettier": "^8.3.0",
+    "eslint-plugin-import": "^2.25.3",
+    "eslint-plugin-prettier": "^4.0.0",
+    "jest": "^27.3.1",
+    "prettier": "^2.4.1",
+    "rimraf": "^3.0.2",
     "standard-changelog": "^1.0.0",
-    "typescript": "^3.6.3"
+    "ts-jest": "^27.0.7",
+    "typescript": "^4.4.4"
   },
   "publishConfig": {
     "access": "public"

package/dist/declare.d.js

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