gff-nostream 1.3.9 → 2.0.1

package/esm/util.js

@@ -1,5 +1,14 @@
 // Fast, low-level functions for parsing and formatting GFF3.
 // JavaScript port of Robert Buels's Bio::GFF3::LowLevel Perl module.
+const escapeRegex = /%([0-9A-Fa-f]{2})/g;
+const directiveRegex = /^\s*##\s*(\S+)\s*(.*)/;
+const lineEndRegex = /\r?\n$/;
+const whitespaceRegex = /\s+/;
+const nonDigitRegex = /\D/g;
+// eslint-disable-next-line no-control-regex
+const attrEscapeRegex = /[\n;\r\t=%&,\u0000-\u001f\u007f-\u00ff]/g;
+// eslint-disable-next-line no-control-regex
+const columnEscapeRegex = /[\n\r\t%\u0000-\u001f\u007f-\u00ff]/g;
 /**
  * Unescape a string value used in a GFF3 attribute.
  *
@@ -7,7 +16,10 @@
  * @returns An unescaped string value
  */
 export function unescape(stringVal) {
-    return stringVal.replaceAll(/%([0-9A-Fa-f]{2})/g, (_match, seq) => String.fromCharCode(parseInt(seq, 16)));
+    if (!stringVal.includes('%')) {
+        return stringVal;
+    }
+    return stringVal.replaceAll(escapeRegex, (_match, seq) => String.fromCharCode(parseInt(seq, 16)));
 }
 function _escape(regex, s) {
     return String(s).replace(regex, ch => {
@@ -22,7 +34,7 @@ function _escape(regex, s) {
  * @returns An escaped string value
  */
 export function escape(rawVal) {
-    return _escape(/[\n;\r\t=%&,\u0000-\u001f\u007f-\u00ff]/g, rawVal);
+    return _escape(attrEscapeRegex, rawVal);
 }
 /**
  * Escape a value for use in a GFF3 column value.
@@ -31,7 +43,7 @@ export function escape(rawVal) {
  * @returns An escaped column value
  */
 export function escapeColumn(rawVal) {
-    return _escape(/[\n\r\t%\u0000-\u001f\u007f-\u00ff]/g, rawVal);
+    return _escape(columnEscapeRegex, rawVal);
 }
 /**
  * Parse the 9th column (attributes) of a GFF3 feature line.
@@ -44,26 +56,66 @@ export function parseAttributes(attrString) {
         return {};
     }
     const attrs = {};
-    attrString
-        .replace(/\r?\n$/, '')
-        .split(';')
-        .forEach(a => {
-        var _a;
-        const nv = a.split('=', 2);
-        if (!((_a = nv[1]) === null || _a === void 0 ? void 0 : _a.length)) {
-            return;
+    let str = attrString;
+    if (str.endsWith('\n')) {
+        str = str.slice(0, str.endsWith('\r\n') ? -2 : -1);
+    }
+    for (const a of str.split(';')) {
+        const eqIdx = a.indexOf('=');
+        if (eqIdx === -1) {
+            continue;
+        }
+        const value = a.slice(eqIdx + 1);
+        if (!value.length) {
+            continue;
         }
-        nv[0] = nv[0].trim();
-        let arec = attrs[nv[0].trim()];
+        const tag = a.slice(0, eqIdx).trim();
+        let arec = attrs[tag];
         if (!arec) {
             arec = [];
-            attrs[nv[0]] = arec;
+            attrs[tag] = arec;
         }
-        arec.push(...nv[1]
-            .split(',')
-            .map(s => s.trim())
-            .map(unescape));
-    });
+        for (const s of value.split(',')) {
+            arec.push(unescape(s.trim()));
+        }
+    }
+    return attrs;
+}
+/**
+ * Parse the 9th column (attributes) of a GFF3 feature line without unescaping.
+ * Fast path for data known to contain no escaped characters.
+ *
+ * @param attrString - String of GFF3 9th column
+ * @returns Parsed attributes
+ */
+export function parseAttributesNoUnescape(attrString) {
+    if (!attrString.length || attrString === '.') {
+        return {};
+    }
+    const attrs = {};
+    let str = attrString;
+    if (str.endsWith('\n')) {
+        str = str.slice(0, str.endsWith('\r\n') ? -2 : -1);
+    }
+    for (const a of str.split(';')) {
+        const eqIdx = a.indexOf('=');
+        if (eqIdx === -1) {
+            continue;
+        }
+        const value = a.slice(eqIdx + 1);
+        if (!value.length) {
+            continue;
+        }
+        const tag = a.slice(0, eqIdx).trim();
+        let arec = attrs[tag];
+        if (!arec) {
+            arec = [];
+            attrs[tag] = arec;
+        }
+        for (const s of value.split(',')) {
+            arec.push(s.trim());
+        }
+    }
     return attrs;
 }
 /**
@@ -73,21 +125,67 @@ export function parseAttributes(attrString) {
  * @returns The parsed feature
  */
 export function parseFeature(line) {
-    // split the line into columns and replace '.' with null in each column
-    const f = line.split('\t').map(a => (a === '.' || a === '' ? null : a));
-    // unescape only the ref, source, and type columns
-    const parsed = {
-        seq_id: f[0] && unescape(f[0]),
-        source: f[1] && unescape(f[1]),
-        type: f[2] && unescape(f[2]),
-        start: f[3] === null ? null : parseInt(f[3], 10),
-        end: f[4] === null ? null : parseInt(f[4], 10),
-        score: f[5] === null ? null : parseFloat(f[5]),
-        strand: f[6],
-        phase: f[7],
-        attributes: f[8] === null ? null : parseAttributes(f[8]),
+    return parseFieldsArray(line.split('\t'));
+}
+/**
+ * Parse a GFF3 feature from a pre-split fields array
+ *
+ * @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
+ * @returns The parsed feature
+ */
+function norm(a) {
+    return a === '.' || a === '' || a === undefined ? null : a;
+}
+export function parseFieldsArray(f) {
+    const seq_id = norm(f[0]);
+    const source = norm(f[1]);
+    const type = norm(f[2]);
+    const start = norm(f[3]);
+    const end = norm(f[4]);
+    const score = norm(f[5]);
+    const strand = norm(f[6]);
+    const phase = norm(f[7]);
+    const attrString = norm(f[8]);
+    return {
+        seq_id: seq_id ? unescape(seq_id) : null,
+        source: source ? unescape(source) : null,
+        type: type ? unescape(type) : null,
+        start: start === null ? null : parseInt(start, 10),
+        end: end === null ? null : parseInt(end, 10),
+        score: score === null ? null : parseFloat(score),
+        strand,
+        phase,
+        attributes: attrString === null ? null : parseAttributes(attrString),
+    };
+}
+/**
+ * Parse a GFF3 feature from a pre-split fields array without unescaping.
+ * Fast path for data known to contain no escaped characters.
+ *
+ * @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
+ * @returns The parsed feature
+ */
+export function parseFieldsArrayNoUnescape(f) {
+    const seq_id = norm(f[0]);
+    const source = norm(f[1]);
+    const type = norm(f[2]);
+    const start = norm(f[3]);
+    const end = norm(f[4]);
+    const score = norm(f[5]);
+    const strand = norm(f[6]);
+    const phase = norm(f[7]);
+    const attrString = norm(f[8]);
+    return {
+        seq_id,
+        source,
+        type,
+        start: start === null ? null : parseInt(start, 10),
+        end: end === null ? null : parseInt(end, 10),
+        score: score === null ? null : parseFloat(score),
+        strand,
+        phase,
+        attributes: attrString === null ? null : parseAttributesNoUnescape(attrString),
     };
-    return parsed;
 }
 /**
  * Parse a GFF3 directive line.
@@ -96,8 +194,7 @@ export function parseFeature(line) {
  * @returns The parsed directive
  */
 export function parseDirective(line) {
-    var _a, _b;
-    const match = /^\s*##\s*(\S+)\s*(.*)/.exec(line);
+    const match = directiveRegex.exec(line);
     if (!match) {
         return null;
     }
@@ -105,21 +202,21 @@ export function parseDirective(line) {
     let [, , contents] = match;
     const parsed = { directive: name };
     if (contents.length) {
-        contents = contents.replace(/\r?\n$/, '');
+        contents = contents.replace(lineEndRegex, '');
         parsed.value = contents;
     }
     // do a little additional parsing for sequence-region and genome-build directives
     if (name === 'sequence-region') {
-        const c = contents.split(/\s+/, 3);
+        const c = contents.split(whitespaceRegex, 3);
         return {
             ...parsed,
             seq_id: c[0],
-            start: (_a = c[1]) === null || _a === void 0 ? void 0 : _a.replaceAll(/\D/g, ''),
-            end: (_b = c[2]) === null || _b === void 0 ? void 0 : _b.replaceAll(/\D/g, ''),
+            start: c[1]?.replaceAll(nonDigitRegex, ''),
+            end: c[2]?.replaceAll(nonDigitRegex, ''),
         };
     }
     else if (name === 'genome-build') {
-        const [source, buildName] = contents.split(/\s+/, 2);
+        const [source, buildName] = contents.split(whitespaceRegex, 2);
         return {
             ...parsed,
             source,
@@ -136,28 +233,18 @@ export function parseDirective(line) {
  */
 export function formatAttributes(attrs) {
     const attrOrder = [];
-    Object.entries(attrs).forEach(([tag, val]) => {
+    for (const [tag, val] of Object.entries(attrs)) {
         if (!val) {
-            return;
+            continue;
         }
-        let valstring;
-        if (val.hasOwnProperty('toString')) {
-            valstring = escape(val.toString());
-            // } else if (Array.isArray(val.values)) {
-            //   valstring = val.values.map(escape).join(',')
-        }
-        else if (Array.isArray(val)) {
-            valstring = val.map(escape).join(',');
-        }
-        else {
-            valstring = escape(val);
-        }
-        attrOrder.push(`${escape(tag)}=${valstring}`);
-    });
+        attrOrder.push(`${escape(tag)}=${val.map(escape).join(',')}`);
+    }
     return attrOrder.length ? attrOrder.join(';') : '.';
 }
 function _formatSingleFeature(f, seenFeature) {
-    const attrString = f.attributes === null || f.attributes === undefined
+    const attrString = 
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    f.attributes === null || f.attributes === undefined
         ? '.'
         : formatAttributes(f.attributes);
     const fields = [
@@ -262,7 +349,10 @@ export function formatItem(itemOrItems) {
     return formatSingleItem(itemOrItems);
 }
 function _isFeatureLineWithRefs(featureLine) {
-    return (featureLine.child_features !== undefined &&
+    return (
+    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    featureLine.child_features !== undefined &&
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         featureLine.derived_features !== undefined);
 }
 //# sourceMappingURL=util.js.map

package/esm/util.js.map

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package/package.json

@@ -1,11 +1,19 @@
 {
   "name": "gff-nostream",
-  "version": "1.3.9",
+  "version": "2.0.1",
   "description": "utilities to read GFF3 data",
   "license": "MIT",
   "repository": "cmdcolin/gff-nostream",
-  "main": "dist/index.js",
-  "module": "esm/index.js",
+  "type": "module",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    "import": {
+      "import": "./esm/index.js"
+    },
+    "require": {
+      "require": "./dist/index.js"
+    }
+  },
   "author": {
     "name": "Colin Diesh",
     "email": "colin.diesh@gmail.com",
@@ -18,13 +26,15 @@
   ],
   "scripts": {
     "test": "vitest",
+    "benchonly": "vitest bench",
+    "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
     "clean": "rimraf dist esm",
-    "lint": "eslint src test",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
     "docs": "documentation readme src/api.ts --section=API  --shallow && yarn format",
     "format": "prettier --write .",
     "prebuild": "yarn clean",
-    "build:esm": "tsc --target es2018 --outDir esm",
-    "build:es5": "tsc --target es2015 --module commonjs --outDir dist",
+    "build:esm": "tsc --target esnext --outDir esm",
+    "build:es5": "tsc --target es2020 --module commonjs --outDir dist",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
     "build": "yarn build:es5 && yarn build:esm",
     "prepublishOnly": "yarn test --run && yarn build",
@@ -38,16 +48,17 @@
     "genomics"
   ],
   "devDependencies": {
-    "@types/node": "^22.15.17",
-    "@typescript-eslint/eslint-plugin": "^8.4.0",
-    "@typescript-eslint/parser": "^8.4.0",
-    "@vitest/coverage-v8": "^3.0.1",
+    "@types/node": "^24.10.1",
+    "@typescript-eslint/eslint-plugin": "^8.48.0",
+    "@typescript-eslint/parser": "^8.48.0",
+    "@vitest/coverage-v8": "^4.0.14",
     "documentation": "^14.0.1",
-    "eslint": "^9.9.1",
-    "prettier": "^3.3.3",
-    "rimraf": "^6.0.1",
-    "typescript": "^5.5.4",
-    "typescript-eslint": "^8.4.0",
-    "vitest": "^3.0.1"
+    "eslint": "^9.39.1",
+    "eslint-plugin-import": "^2.32.0",
+    "prettier": "^3.6.2",
+    "rimraf": "^6.1.2",
+    "typescript": "^5.9.3",
+    "typescript-eslint": "^8.48.0",
+    "vitest": "^4.0.14"
   }
 }

package/src/api.ts

@@ -1,5 +1,12 @@
-import Parser from './parse'
-import { GFF3Feature } from './util'
+import Parser from './parse.ts'
+import { parseFieldsArray, parseFieldsArrayNoUnescape } from './util.ts'
+
+import type { GFF3Feature, GFF3FeatureLine } from './util.ts'
+
+export interface LineRecord {
+  fields: string[]
+  lineHash?: string | number
+}
 
 /**
  * Synchronously parse a string containing GFF3 and return an array of the
@@ -15,7 +22,7 @@ export function parseStringSync(str: string): GFF3Feature[] {
     featureCallback: arg => items.push(arg),
     disableDerivesFromReferences: true,
     errorCallback: err => {
-      throw err
+      throw new Error(err)
     },
   })
 
@@ -27,12 +34,106 @@ export function parseStringSync(str: string): GFF3Feature[] {
   return items
 }
 
-export {
-  type GFF3FeatureLine,
-  type GFF3Comment,
-  type GFF3FeatureLineWithRefs,
-  type GFF3Directive,
-  type GFF3Sequence,
-  type GFF3Feature,
-  type GFF3Item,
-} from './util'
+/**
+ * Synchronously parse an array of strings containing GFF3 and return an array of the
+ * parsed items.
+ *
+ * @param arr - GFF3 array of strings
+ * @param inputOptions - Parsing options
+ * @returns array of parsed features, directives, comments and/or sequences
+ */
+export function parseArraySync(arr: string[]): GFF3Feature[] {
+  const items: GFF3Feature[] = []
+  const parser = new Parser({
+    featureCallback: arg => items.push(arg),
+    disableDerivesFromReferences: true,
+    errorCallback: err => {
+      throw new Error(err)
+    },
+  })
+
+  for (const line of arr) {
+    parser.addLine(line)
+  }
+  parser.finish()
+
+  return items
+}
+
+/**
+ * Synchronously parse an array of LineRecord objects containing pre-split GFF3
+ * fields and return an array of the parsed items.
+ *
+ * @param records - Array of LineRecord objects with fields array and optional lineHash
+ * @returns array of parsed features
+ */
+export function parseRecordsSync(records: LineRecord[]): GFF3Feature[] {
+  const items: GFF3Feature[] = []
+  const parser = new Parser({
+    featureCallback: arg => items.push(arg),
+    disableDerivesFromReferences: true,
+    errorCallback: err => {
+      throw new Error(err)
+    },
+  })
+
+  for (const record of records) {
+    const featureLine: GFF3FeatureLine = parseFieldsArray(record.fields)
+    if (record.lineHash !== undefined) {
+      if (!featureLine.attributes) {
+        featureLine.attributes = {}
+      }
+      featureLine.attributes._lineHash = [String(record.lineHash)]
+    }
+    parser.addParsedFeatureLine(featureLine)
+  }
+  parser.finish()
+
+  return items
+}
+
+/**
+ * Synchronously parse an array of LineRecord objects containing pre-split GFF3
+ * fields and return an array of the parsed items. Uses a fast path that skips
+ * unescaping when hasEscapes is false.
+ *
+ * @param records - Array of LineRecord objects with fields array and optional lineHash
+ * @param hasEscapes - Whether the records contain percent-encoded characters
+ * @returns array of parsed features
+ */
+export function parseRecordsSyncFast(records: LineRecord[], hasEscapes: boolean): GFF3Feature[] {
+  const items: GFF3Feature[] = []
+  const parser = new Parser({
+    featureCallback: arg => items.push(arg),
+    disableDerivesFromReferences: true,
+    errorCallback: err => {
+      throw new Error(err)
+    },
+  })
+
+  const parseFunc = hasEscapes ? parseFieldsArray : parseFieldsArrayNoUnescape
+
+  for (const record of records) {
+    const featureLine: GFF3FeatureLine = parseFunc(record.fields)
+    if (record.lineHash !== undefined) {
+      if (!featureLine.attributes) {
+        featureLine.attributes = {}
+      }
+      featureLine.attributes._lineHash = [String(record.lineHash)]
+    }
+    parser.addParsedFeatureLine(featureLine)
+  }
+  parser.finish()
+
+  return items
+}
+
+export type {
+  GFF3Comment,
+  GFF3Directive,
+  GFF3Feature,
+  GFF3FeatureLine,
+  GFF3FeatureLineWithRefs,
+  GFF3Item,
+  GFF3Sequence,
+} from './util.ts'

package/src/index.ts

@@ -1,12 +1,13 @@
-import { parseStringSync } from './api'
-export { parseStringSync }
+import { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync } from './api.ts'
+export { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync }
 
 export type {
   GFF3Comment,
-  GFF3Feature,
   GFF3Directive,
-  GFF3FeatureLineWithRefs,
+  GFF3Feature,
   GFF3FeatureLine,
+  GFF3FeatureLineWithRefs,
   GFF3Item,
   GFF3Sequence,
-} from './api'
+  LineRecord,
+} from './api.ts'