@gmod/bed - npm Package Compare versions

Comparing version 2.1.2 to 2.1.3

CHANGELOG.md

@@ -1,5 +0,9 @@
-## [2.1.2](https://github.com/GMOD/bed-js/compare/v2.1.1...v2.1.2) (2022-07-24)
+## [2.1.3](https://github.com/GMOD/bed-js/compare/v2.1.2...v2.1.3) (2024-3-25)
 
 
 
+- Fix autoSql with comments in column names
+
+## [2.1.2](https://github.com/GMOD/bed-js/compare/v2.1.1...v2.1.2) (2022-07-24)
+
 - Add comment string to autoSql types
@@ -33,3 +37,4 @@
 
-- Allow for badly formatted comments not entirely within a quote, was exhibited by https://hgdownload.soe.ucsc.edu/gbdb/hg19/gnomAD/pLI/pliByGene.bb
+- Allow for badly formatted comments not entirely within a quote, was exhibited
+  by https://hgdownload.soe.ucsc.edu/gbdb/hg19/gnomAD/pLI/pliByGene.bb
 
@@ -44,3 +49,4 @@ ## [2.0.3](https://github.com/GMOD/bed-js/compare/v2.0.2...v2.0.3) (2020-07-09)
 
-- Small autoSql grammar improvements e.g. allow \_ in autoSql names (for `_mouseover` from ucsc)
+- Small autoSql grammar improvements e.g. allow \_ in autoSql names (for
+  `_mouseover` from ucsc)
 
@@ -59,9 +65,13 @@ <a name="2.0.1"></a>
 - Remove snake case of results
-- Returned values match autoSql very faithfully and uses the naming from UCSC e.g. exact strings from autoSql {chrom, chromStart, chromEnd}
-- Accepts a opts.uniqueId for the parseLine method which adds this to the featureData
-- Parses the default BED schema with a defaultBedSchema.as autoSql definition instead of a separate method
+- Returned values match autoSql very faithfully and uses the naming from UCSC
+  e.g. exact strings from autoSql {chrom, chromStart, chromEnd}
+- Accepts a opts.uniqueId for the parseLine method which adds this to the
+  featureData
+- Parses the default BED schema with a defaultBedSchema.as autoSql definition
+  instead of a separate method
 
 ## [1.0.4](https://github.com/GMOD/bed-js/compare/v1.0.3...v1.0.4) (2019-04-14)
 
-- Changed parseBedText to accept an Options argument with offset and optionally a uniqueId
+- Changed parseBedText to accept an Options argument with offset and optionally
+  a uniqueId
 
@@ -68,0 +78,0 @@ ## [1.0.3](https://github.com/GMOD/bed-js/compare/v1.0.2...v1.0.3) (2019-04-02)

dist/index.d.ts

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

dist/index.js

@@ -6,4 +6,5 @@ "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var parser_1 = __importDefault(require("./parser"));
-exports.default = parser_1.default;
+exports.default = void 0;
+var parser_1 = require("./parser");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(parser_1).default; } });
 //# sourceMappingURL=index.js.map

dist/parser.d.ts

@@ -11,5 +11,3 @@ import { AutoSqlSchema } from './util';
         uniqueId?: string;
-    }): {
-        [key: string]: any;
-    };
+    }): Record<string, any>;
 }

dist/parser.js

@@ -67,3 +67,3 @@ "use strict";
                         if (arrayIsNumeric) {
-                            columnVal = columnVal.map(function (str) { return Number(str); });
+                            columnVal = columnVal.map(Number);
                         }
@@ -70,0 +70,0 @@ }

dist/util.d.ts

@@ -20,2 +20,2 @@ export interface AutoSqlPreSchema {
 };
-export declare type AutoSqlSchema = ReturnType<typeof detectTypes>;
+export type AutoSqlSchema = ReturnType<typeof detectTypes>;

dist/util.js

@@ -25,6 +25,9 @@ "use strict";
 function detectTypes(autoSql) {
-    var numericTypes = ['uint', 'int', 'float', 'long'];
-    return __assign(__assign({}, autoSql), { fields: autoSql.fields.map(function (autoField) { return (__assign(__assign({}, autoField), { isArray: autoField.size && autoField.type !== 'char', arrayIsNumeric: autoField.size && numericTypes.includes(autoField.type), isNumeric: !autoField.size && numericTypes.includes(autoField.type) })); }) });
+    var numericTypes = new Set(['uint', 'int', 'float', 'long']);
+    return __assign(__assign({}, autoSql), { fields: autoSql.fields
+            .map(function (autoField) { return (__assign(__assign({}, autoField), { isArray: autoField.size && autoField.type !== 'char', arrayIsNumeric: autoField.size && numericTypes.has(autoField.type), isNumeric: !autoField.size && numericTypes.has(autoField.type) })); })
+            // this is needed because the autoSql doesn't properly parse comments in the autoSql
+            .filter(function (f) { return !!f.name; }) });
 }
 exports.detectTypes = detectTypes;
 //# sourceMappingURL=util.js.map

esm/index.d.ts

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

esm/index.js

@@ -1,3 +0,2 @@
-import BED from './parser';
-export default BED;
+export { default } from './parser';
 //# sourceMappingURL=index.js.map

esm/parser.d.ts

@@ -11,5 +11,3 @@ import { AutoSqlSchema } from './util';
         uniqueId?: string;
-    }): {
-        [key: string]: any;
-    };
+    }): Record<string, any>;
 }

esm/parser.js

@@ -60,3 +60,3 @@ import parser from './autoSql';
                         if (arrayIsNumeric) {
-                            columnVal = columnVal.map((str) => Number(str));
+                            columnVal = columnVal.map(Number);
                         }
@@ -63,0 +63,0 @@ }

esm/util.d.ts

@@ -20,2 +20,2 @@ export interface AutoSqlPreSchema {
 };
-export declare type AutoSqlSchema = ReturnType<typeof detectTypes>;
+export type AutoSqlSchema = ReturnType<typeof detectTypes>;

esm/util.js

@@ -11,13 +11,16 @@ /*
 export function detectTypes(autoSql) {
-    const numericTypes = ['uint', 'int', 'float', 'long'];
+    const numericTypes = new Set(['uint', 'int', 'float', 'long']);
     return {
         ...autoSql,
-        fields: autoSql.fields.map(autoField => ({
+        fields: autoSql.fields
+            .map(autoField => ({
             ...autoField,
             isArray: autoField.size && autoField.type !== 'char',
-            arrayIsNumeric: autoField.size && numericTypes.includes(autoField.type),
-            isNumeric: !autoField.size && numericTypes.includes(autoField.type),
-        })),
+            arrayIsNumeric: autoField.size && numericTypes.has(autoField.type),
+            isNumeric: !autoField.size && numericTypes.has(autoField.type),
+        }))
+            // this is needed because the autoSql doesn't properly parse comments in the autoSql
+            .filter(f => !!f.name),
     };
 }
 //# sourceMappingURL=util.js.map

package.json

 {
   "name": "@gmod/bed",
-  "version": "2.1.2",
+  "version": "2.1.3",
   "description": "A BED file format parser with autoSql support",
@@ -41,16 +41,17 @@ "main": "dist/index.js",
   "devDependencies": {
-    "@types/jest": "^28.1.6",
-    "@typescript-eslint/eslint-plugin": "^5.30.7",
-    "@typescript-eslint/parser": "^5.30.7",
-    "eslint": "^8.20.0",
-    "eslint-config-prettier": "^8.3.0",
-    "eslint-plugin-import": "^2.26.0",
-    "eslint-plugin-prettier": "^4.2.1",
-    "jest": "^28.1.3",
+    "@types/jest": "^29.5.1",
+    "@typescript-eslint/eslint-plugin": "^7.3.1",
+    "@typescript-eslint/parser": "^7.3.1",
+    "eslint": "^8.40.0",
+    "eslint-config-prettier": "^9.1.0",
+    "eslint-plugin-import": "^2.27.5",
+    "eslint-plugin-prettier": "^5.1.3",
+    "eslint-plugin-unicorn": "^51.0.1",
+    "jest": "^29.5.0",
     "pegjs": "^0.10.0",
-    "prettier": "^2.7.1",
-    "rimraf": "^3.0.2",
-    "standard-changelog": "^2.0.24",
-    "ts-jest": "^28.0.7",
-    "typescript": "^4.7.4"
+    "prettier": "^3.2.5",
+    "rimraf": "^5.0.0",
+    "standard-changelog": "^5.0.0",
+    "ts-jest": "^29.1.0",
+    "typescript": "^5.0.4"
   },
@@ -57,0 +58,0 @@ "keywords": [

README.md

 # bed-js
 
 [![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/bed-js/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/bed-js/branch/master)
-[![Build Status](https://img.shields.io/github/workflow/status/GMOD/bed-js/Push/master?logo=github&style=flat-query)](https://github.com/GMOD/bed-js/actions?query=branch%3Amaster+workflow%3APush+)
+[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/bed-js/push.yml?branch=master)](https://github.com/GMOD/bed-js/actions)
 
@@ -46,3 +46,4 @@ Performs parsing of BED files including autoSql
 
-If neither autoSql or type is specified, the default BED schema is used (see [here](src/as/defaultBedSchema.as))
+If neither autoSql or type is specified, the default BED schema is used (see
+[here](src/as/defaultBedSchema.as))
 
@@ -59,7 +60,9 @@ ### parseLine(line, opts)
 
-- opts.uniqueId - an indication of a uniqueId that is not encoded by the BED line itself
+- opts.uniqueId - an indication of a uniqueId that is not encoded by the BED
+  line itself
 
 The default instantiation of the parser with new BED() simply parses lines
-assuming the fields come from the standard BED schema.
-Your line can just contain just a subset of the fields e.g. `chrom, chromStart, chromEnd, name, score`
+assuming the fields come from the standard BED schema. Your line can just
+contain just a subset of the fields e.g.
+`chrom, chromStart, chromEnd, name, score`
 
@@ -79,3 +82,4 @@ ## Examples
 
-If you have a BED format that corresponds to a different schema, you can specify from the list of default built in schemas
+If you have a BED format that corresponds to a different schema, you can specify
+from the list of default built in schemas
 
@@ -130,4 +134,4 @@ Specify this in the opts.type for the BED constructor
 
-- Does not parse "browser" or "track" lines and will throw an error if
-  parseLine receives one of these
+- Does not parse "browser" or "track" lines and will throw an error if parseLine
+  receives one of these
 - By default, parseLine parses only tab delimited text, if you want to use
@@ -149,4 +153,6 @@ spaces as is allowed by UCSC then pass an array to `line` for parseLine
 
-based on https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/autoSql/autoSql.doc
+based on
+https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/autoSql/autoSql.doc
 
-also see http://genomewiki.ucsc.edu/index.php/AutoSql and https://www.linuxjournal.com/article/5949
+also see http://genomewiki.ucsc.edu/index.php/AutoSql and
+https://www.linuxjournal.com/article/5949

src/index.ts

@@ -1,3 +0,1 @@
-import BED from './parser'
-
-export default BED
+export { default } from './parser'

src/parser.ts

@@ -46,3 +46,3 @@ import parser from './autoSql'
 
-    let feature = {} as { [key: string]: any }
+    let feature = {} as Record<string, any>
     if (
@@ -69,3 +69,3 @@ !this.attemptDefaultBed ||
             if (arrayIsNumeric) {
-              columnVal = columnVal.map((str: string) => Number(str))
+              columnVal = columnVal.map(Number)
             }
@@ -72,0 +72,0 @@ }

src/util.ts

@@ -15,11 +15,15 @@ export interface AutoSqlPreSchema {
 export function detectTypes(autoSql: AutoSqlPreSchema) {
-  const numericTypes = ['uint', 'int', 'float', 'long']
+  const numericTypes = new Set(['uint', 'int', 'float', 'long'])
   return {
     ...autoSql,
-    fields: autoSql.fields.map(autoField => ({
-      ...autoField,
-      isArray: autoField.size && autoField.type !== 'char',
-      arrayIsNumeric: autoField.size && numericTypes.includes(autoField.type),
-      isNumeric: !autoField.size && numericTypes.includes(autoField.type),
-    })),
+    fields: autoSql.fields
+      .map(autoField => ({
+        ...autoField,
+        isArray: autoField.size && autoField.type !== 'char',
+        arrayIsNumeric: autoField.size && numericTypes.has(autoField.type),
+        isNumeric: !autoField.size && numericTypes.has(autoField.type),
+      }))
+
+      // this is needed because the autoSql doesn't properly parse comments in the autoSql
+      .filter(f => !!f.name),
   }
@@ -26,0 +30,0 @@ }

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Improved metrics

Total package byte prevSize

354438

increased by2.42%

Lines of code

5412

increased by0.02%

Number of lines in readme file

154

increased by4.05%

Worsened metrics

Dev dependency count

15

increased by7.14%

No dependency changes