@gmod/bed 2.0.4 → 2.0.7

package/esm/autoSql.js.map

@@ -0,0 +1 @@
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package/esm/defaultTypes.d.ts

@@ -0,0 +1,4 @@
+declare var _default: {
+    [k: string]: {};
+};
+export default _default;

package/esm/defaultTypes.js

@@ -0,0 +1,6 @@
+import { parse } from './autoSql';
+import * as types from './as/autoSqlSchemas';
+export default Object.fromEntries(Object.entries(types).map(([key, val]) => {
+    return [key, parse(val.trim())];
+}));
+//# sourceMappingURL=defaultTypes.js.map

package/esm/defaultTypes.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"defaultTypes.js","sourceRoot":"","sources":["../src/defaultTypes.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,WAAW,CAAA;AACjC,OAAO,KAAK,KAAK,MAAM,qBAAqB,CAAA;AAE5C,eAAe,MAAM,CAAC,WAAW,CAC/B,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,EAAE;IACvC,OAAO,CAAC,GAAG,EAAE,KAAK,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;AACjC,CAAC,CAAC,CACH,CAAA"}

package/esm/index.d.ts

@@ -0,0 +1,2 @@
+export default BED;
+import BED from "./parser";

package/esm/index.js

@@ -0,0 +1,3 @@
+import BED from './parser';
+export default BED;
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,UAAU,CAAA;AAE1B,eAAe,GAAG,CAAA"}

package/esm/parser.d.ts

@@ -0,0 +1,13 @@
+export default class BED {
+    constructor(args?: {});
+    autoSql: any;
+    attemptDefaultBed: boolean | undefined;
+    parseLine(line: any, opts?: {}): {
+        chromStart: any;
+        chromEnd: any;
+        score: any;
+        strand: any;
+        uniqueId: any;
+        chrom: any;
+    };
+}

package/esm/parser.js

@@ -0,0 +1,95 @@
+import parser from './autoSql';
+import types from './defaultTypes';
+import { detectTypes } from './util';
+const strandMap = { '.': 0, '-': -1, '+': 1 };
+// heuristic that a BED file is BED12 like...the number in col 10 is blockCount-like
+function isBed12Like(fields) {
+    var _a;
+    return (fields.length >= 12 &&
+        !Number.isNaN(parseInt(fields[9], 10)) &&
+        ((_a = fields[10]) === null || _a === void 0 ? void 0 : _a.split(',').filter(f => !!f).length) === parseInt(fields[9], 10));
+}
+export default class BED {
+    constructor(args = {}) {
+        if (args.autoSql) {
+            this.autoSql = detectTypes(parser.parse(args.autoSql));
+        }
+        else if (args.type) {
+            if (!types[args.type]) {
+                throw new Error('Type not found');
+            }
+            this.autoSql = detectTypes(types[args.type]);
+        }
+        else {
+            this.autoSql = detectTypes(types.defaultBedSchema);
+            this.attemptDefaultBed = true;
+        }
+    }
+    /*
+     * parses a line of text as a BED line with the loaded autoSql schema
+     *
+     * @param line - a BED line as tab delimited text or array
+     * @param opts - supply opts.uniqueId
+     * @return a object representing a feature
+     */
+    parseLine(line, opts = {}) {
+        const { autoSql } = this;
+        const { uniqueId } = opts;
+        let fields = line;
+        if (!Array.isArray(line)) {
+            if (line.startsWith('track') || line.startsWith('browser')) {
+                throw new Error(`track and browser line parsing is not supported, please filter:\n${line}`);
+            }
+            fields = line.split('\t');
+        }
+        let feature = {};
+        if (!this.attemptDefaultBed ||
+            (this.attemptDefaultBed && isBed12Like(fields))) {
+            for (let i = 0; i < autoSql.fields.length; i++) {
+                const autoField = autoSql.fields[i];
+                let columnVal = fields[i];
+                const { isNumeric, isArray, arrayIsNumeric, name } = autoField;
+                if (columnVal === null || columnVal === undefined) {
+                    break;
+                }
+                if (columnVal !== '.') {
+                    if (isNumeric) {
+                        const num = Number(columnVal);
+                        columnVal = Number.isNaN(num) ? columnVal : num;
+                    }
+                    else if (isArray) {
+                        columnVal = columnVal.split(',');
+                        if (columnVal[columnVal.length - 1] === '') {
+                            columnVal.pop();
+                        }
+                        if (arrayIsNumeric) {
+                            columnVal = columnVal.map(str => Number(str));
+                        }
+                    }
+                    feature[name] = columnVal;
+                }
+            }
+        }
+        else {
+            const fieldNames = ['chrom', 'chromStart', 'chromEnd', 'name'];
+            feature = Object.fromEntries(fields.map((f, i) => [fieldNames[i] || 'field' + i, f]));
+            feature.chromStart = +feature.chromStart;
+            feature.chromEnd = +feature.chromEnd;
+            if (!Number.isNaN(Number.parseFloat(feature.field4))) {
+                feature.score = +feature.field4;
+                delete feature.field4;
+            }
+            if (feature.field5 === '+' || feature.field5 === '-') {
+                feature.strand = feature.field5;
+                delete feature.field5;
+            }
+        }
+        if (uniqueId) {
+            feature.uniqueId = uniqueId;
+        }
+        feature.strand = strandMap[feature.strand] || 0;
+        feature.chrom = decodeURIComponent(feature.chrom);
+        return feature;
+    }
+}
+//# sourceMappingURL=parser.js.map

package/esm/parser.js.map

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package/esm/util.d.ts

@@ -0,0 +1 @@
+export function detectTypes(autoSql: any): any;

package/esm/util.js

@@ -0,0 +1,27 @@
+/*
+ * adds some type annotations to the autoSql schema
+ * for numeric fields ['uint', 'int', 'float', 'long'] "isNumeric" is added
+ * for array types "isArray" is added
+ * for numeric array types "isArray" and "arrayIsNumeric" is set
+ *
+ * @param autoSql - an autoSql schema from the peg parser
+ * @return autoSql with type annotations added
+ */
+export function detectTypes(autoSql) {
+    const numericTypes = ['uint', 'int', 'float', 'long'];
+    const fields = autoSql.fields.map(autoField => {
+        const type = {};
+        if (!autoField.size && numericTypes.includes(autoField.type)) {
+            type.isNumeric = true;
+        }
+        if (autoField.size && autoField.type !== 'char') {
+            type.isArray = true;
+        }
+        if (autoField.size && numericTypes.includes(autoField.type)) {
+            type.arrayIsNumeric = true;
+        }
+        return { ...autoField, ...type };
+    });
+    return { ...autoSql, fields };
+}
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,8 +1,9 @@
 {
   "name": "@gmod/bed",
-  "version": "2.0.4",
+  "version": "2.0.7",
   "description": "A BED file format parser with autoSql support",
-  "main": "dist/main.js",
+  "main": "dist/index.js",
+  "module": "esm/index.js",
   "repository": "github:GMOD/bed-js",
   "author": {
     "name": "Colin Diesh",
@@ -15,51 +16,42 @@
     "url": "https://github.com/GMOD/bed-js/issues"
   },
   "files": [
-    "dist"
+    "dist",
+    "esm"
   ],
   "engines": {
     "node": ">=6"
   },
   "scripts": {
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts src test",
     "test": "jest",
     "coverage": "npm test -- --coverage",
-    "lint": "eslint src test",
-    "clean": "rimraf dist",
+    "clean": "rimraf dist esm",
     "generate": "pegjs -o src/autoSql.js autoSql.pegjs",
-    "prebuild": "npm run clean && npm run lint",
-    "build": "npm run generate && webpack",
-    "preversion": "npm run lint && npm test && npm run build",
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --target es2018 --outDir esm",
+    "build:es5": "tsc --target es5 --outDir dist",
+    "build": "npm run generate && npm run build:esm && npm run build:es5",
+    "preversion": "npm test && npm run build",
     "version": "standard-changelog && git add CHANGELOG.md",
-    "postpublish": "git push origin master --follow-tags"
+    "postversion": "git push --follow-tags"
   },
   "devDependencies": {
-    "@babel/cli": "^7.2.3",
-    "@babel/core": "^7.2.2",
-    "@babel/plugin-proposal-class-properties": "^7.4.0",
-    "@babel/plugin-proposal-throw-expressions": "^7.2.0",
-    "@babel/plugin-transform-runtime": "^7.2.0",
-    "@babel/preset-env": "^7.3.1",
-    "@babel/runtime": "^7.3.1",
-    "babel-eslint": "^10.0.1",
-    "babel-loader": "^8.0.5",
-    "documentation": "^13.0.0",
-    "eslint": "^7.1.0",
-    "eslint-config-airbnb-base": "^14.1.0",
-    "eslint-config-prettier": "^6.11.0",
-    "eslint-plugin-import": "^2.10.0",
-    "eslint-plugin-prettier": "^3.0.1",
-    "jest": "^26.0.1",
-    "jest-raw-loader": "^1.0.1",
+    "@types/jest": "^27.0.3",
+    "@typescript-eslint/eslint-plugin": "^5.7.0",
+    "@typescript-eslint/parser": "^5.7.0",
+    "eslint": "^7.0.0",
+    "eslint-config-prettier": "^8.3.0",
+    "eslint-plugin-import": "^2.25.3",
+    "eslint-plugin-prettier": "^4.0.0",
+    "jest": "^27.4.5",
     "pegjs": "^0.10.0",
-    "prettier": "^2.0.5",
-    "raw-loader": "^4.0.1",
-    "regenerator-runtime": "^0.13.5",
+    "prettier": "^2.5.1",
     "rimraf": "^3.0.2",
     "standard-changelog": "^2.0.24",
-    "webpack": "^4.29.5",
-    "webpack-cli": "^3.2.3"
+    "ts-jest": "^27.1.2",
+    "typescript": "^4.5.4"
   },
-  "dependencies": {},
   "keywords": [
     "bed",
     "autosql",
@@ -69,11 +61,5 @@
   ],
   "publishConfig": {
     "access": "public"
-  },
-  "jest": {
-    "transform": {
-      "\\.as$": "jest-raw-loader",
-      "\\.js$": "babel-jest"
-    }
   }
 }