gff-nostream 3.0.4 → 3.0.6

package/esm/api.js

@@ -22,19 +22,14 @@ function stringToRecords(str) {
     const lines = str.split(/\r?\n/);
     const records = [];
     for (const line of lines) {
+        if (line.startsWith('##FASTA') || line.startsWith('>')) {
+            break;
+        }
         if (line.length === 0 || line.startsWith('#')) {
-            if (line.startsWith('##FASTA')) {
-                break;
-            }
             continue;
         }
-        if (line.startsWith('>')) {
-            break;
-        }
         records.push({
             line,
-            start: 0,
-            end: 0,
             hasEscapes: line.includes('%'),
         });
     }
@@ -66,49 +61,55 @@ export function parseRecords(records) {
         const parents = attrs?.Parent;
         if (!ids && !parents) {
             items.push([featureLine]);
-            continue;
         }
-        let feature;
-        if (ids) {
-            const id = ids[0];
-            const existing = byId.get(id);
-            if (existing) {
-                existing.push(featureLine);
-                feature = existing;
-            }
-            else {
-                feature = [featureLine];
-                if (!parents) {
-                    items.push(feature);
+        else {
+            let feature;
+            if (ids) {
+                const id = ids[0];
+                const existing = byId.get(id);
+                if (existing) {
+                    // Multi-location continuation: share child_features/derived_features
+                    // with the first line so children remain visible across all lines
+                    // regardless of arrival order.
+                    featureLine.child_features = existing[0].child_features;
+                    featureLine.derived_features = existing[0].derived_features;
+                    existing.push(featureLine);
+                    feature = existing;
                 }
-                byId.set(id, feature);
-                const waiting = orphans.get(id);
-                if (waiting) {
-                    for (const w of waiting) {
-                        featureLine.child_features.push(w);
+                else {
+                    feature = [featureLine];
+                    if (!parents) {
+                        items.push(feature);
+                    }
+                    byId.set(id, feature);
+                    const waiting = orphans.get(id);
+                    if (waiting) {
+                        for (const w of waiting) {
+                            featureLine.child_features.push(w);
+                        }
+                        orphans.delete(id);
                     }
-                    orphans.delete(id);
                 }
             }
-        }
-        else {
-            feature = [featureLine];
-        }
-        if (parents) {
-            for (const parentId of parents) {
-                const parent = byId.get(parentId);
-                if (parent) {
-                    for (const p of parent) {
-                        p.child_features.push(feature);
+            else {
+                feature = [featureLine];
+            }
+            if (parents) {
+                for (const parentId of parents) {
+                    const parent = byId.get(parentId);
+                    if (parent) {
+                        // child_features is shared across all parent feature lines,
+                        // so push once via the first line.
+                        parent[0].child_features.push(feature);
                     }
-                }
-                else {
-                    let arr = orphans.get(parentId);
-                    if (!arr) {
-                        arr = [];
-                        orphans.set(parentId, arr);
+                    else {
+                        let arr = orphans.get(parentId);
+                        if (!arr) {
+                            arr = [];
+                            orphans.set(parentId, arr);
+                        }
+                        arr.push(feature);
                     }
-                    arr.push(feature);
                 }
             }
         }
@@ -133,15 +134,16 @@ export function parseRecordsJBrowse(records) {
         if (record.lineHash !== undefined) {
             feature._lineHash = String(record.lineHash);
         }
-        const id = feature.id;
+        // attribute parsing collapses single-element arrays to scalars, so id can
+        // be string | string[]; defensively take the first if multi-valued.
+        const rawId = feature.id;
+        const id = Array.isArray(rawId) ? rawId[0] : rawId;
         const parent = feature.parent;
         if (!id && !parent) {
             items.push(feature);
-            continue;
         }
-        if (id) {
-            const existing = byId.get(id);
-            if (!existing) {
+        else if (!id || !byId.has(id)) {
+            if (id) {
                 if (!parent) {
                     items.push(feature);
                 }
@@ -154,21 +156,21 @@ export function parseRecordsJBrowse(records) {
                     orphans.delete(id);
                 }
             }
-        }
-        if (parent) {
-            const parents = Array.isArray(parent) ? parent : [parent];
-            for (const parentId of parents) {
-                const parentFeature = byId.get(parentId);
-                if (parentFeature) {
-                    parentFeature.subfeatures.push(feature);
-                }
-                else {
-                    let arr = orphans.get(parentId);
-                    if (!arr) {
-                        arr = [];
-                        orphans.set(parentId, arr);
+            if (parent) {
+                const parents = Array.isArray(parent) ? parent : [parent];
+                for (const parentId of parents) {
+                    const parentFeature = byId.get(parentId);
+                    if (parentFeature) {
+                        parentFeature.subfeatures.push(feature);
+                    }
+                    else {
+                        let arr = orphans.get(parentId);
+                        if (!arr) {
+                            arr = [];
+                            orphans.set(parentId, arr);
+                        }
+                        arr.push(feature);
                     }
-                    arr.push(feature);
                 }
             }
         }

package/esm/api.js.map

@@ -1 +1 @@
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package/esm/util.d.ts

@@ -35,21 +35,6 @@ export declare function parseFeature(line: string): GFF3FeatureLine;
  * @returns The parsed feature
  */
 export declare function parseFeatureNoUnescape(line: string): GFF3FeatureLine;
-/**
- * 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
- */
-export declare function parseFieldsArray(f: (string | null | undefined)[]): GFF3FeatureLine;
-/**
- * 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 declare function parseFieldsArrayNoUnescape(f: (string | null | undefined)[]): GFF3FeatureLine;
 /**
  * Parse a GFF3 directive line.
  *

package/esm/util.js

@@ -1,7 +1,6 @@
 // Fast, low-level functions for parsing and formatting GFF3.
 // JavaScript port of Robert Buels's Bio::GFF3::LowLevel Perl module.
 const directiveRegex = /^\s*##\s*(\S+)\s*(.*)/;
-const lineEndRegex = /\r?\n$/;
 const whitespaceRegex = /\s+/;
 const nonDigitRegex = /\D/g;
 const HEX_LOOKUP = {};
@@ -106,30 +105,28 @@ export function parseAttributes(attrString) {
 export function parseAttributesNoUnescape(attrString) {
     return parseAttributesImpl(attrString, false);
 }
-function normImpl(s, shouldUnescape) {
-    if (s.length === 0 || s === '.') {
-        return null;
-    }
-    return shouldUnescape ? unescape(s) : s;
+function isEmpty(s) {
+    return s.length === 0 || s === '.';
+}
+function strField(s, shouldUnescape, empty) {
+    return isEmpty(s) ? empty : shouldUnescape ? unescape(s) : s;
+}
+function numField(s) {
+    return isEmpty(s) ? null : +s;
 }
 function parseFeatureImpl(line, shouldUnescape) {
     const f = line.split('\t');
-    const startStr = f[3];
-    const endStr = f[4];
-    const scoreStr = f[5];
-    const strand = f[6];
-    const phase = f[7];
     const attrString = f[8];
     return {
-        seq_id: normImpl(f[0], shouldUnescape),
-        source: normImpl(f[1], shouldUnescape),
-        type: normImpl(f[2], shouldUnescape),
-        start: startStr.length === 0 || startStr === '.' ? null : +startStr,
-        end: endStr.length === 0 || endStr === '.' ? null : +endStr,
-        score: scoreStr.length === 0 || scoreStr === '.' ? null : +scoreStr,
-        strand: normImpl(strand, false),
-        phase: normImpl(phase, false),
-        attributes: attrString.length === 0 || attrString === '.'
+        seq_id: strField(f[0], shouldUnescape, null),
+        source: strField(f[1], shouldUnescape, null),
+        type: strField(f[2], shouldUnescape, null),
+        start: numField(f[3]),
+        end: numField(f[4]),
+        score: numField(f[5]),
+        strand: strField(f[6], false, null),
+        phase: strField(f[7], false, null),
+        attributes: isEmpty(attrString)
             ? null
             : parseAttributesImpl(attrString, shouldUnescape),
     };
@@ -153,49 +150,6 @@ export function parseFeature(line) {
 export function parseFeatureNoUnescape(line) {
     return parseFeatureImpl(line, false);
 }
-function parseFieldsArrayImpl(f, shouldUnescape) {
-    const seq_id = f[0];
-    const source = f[1];
-    const type = f[2];
-    const startStr = f[3];
-    const endStr = f[4];
-    const scoreStr = f[5];
-    const strand = f[6];
-    const phase = f[7];
-    const attrString = f[8];
-    return {
-        seq_id: seq_id ? normImpl(seq_id, shouldUnescape) : null,
-        source: source ? normImpl(source, shouldUnescape) : null,
-        type: type ? normImpl(type, shouldUnescape) : null,
-        start: !startStr || startStr === '.' ? null : +startStr,
-        end: !endStr || endStr === '.' ? null : +endStr,
-        score: !scoreStr || scoreStr === '.' ? null : +scoreStr,
-        strand: strand && strand !== '.' ? strand : null,
-        phase: phase && phase !== '.' ? phase : null,
-        attributes: !attrString || attrString === '.'
-            ? null
-            : parseAttributesImpl(attrString, shouldUnescape),
-    };
-}
-/**
- * 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
- */
-export function parseFieldsArray(f) {
-    return parseFieldsArrayImpl(f, true);
-}
-/**
- * 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) {
-    return parseFieldsArrayImpl(f, false);
-}
 /**
  * Parse a GFF3 directive line.
  *
@@ -207,28 +161,27 @@ export function parseDirective(line) {
     if (!match) {
         return null;
     }
-    const [, name] = match;
-    let [, , contents] = match;
+    const name = match[1];
+    const contents = match[2];
     const parsed = { directive: name };
     if (contents.length) {
-        contents = contents.replace(lineEndRegex, '');
-        parsed.value = contents;
+        parsed.value = contents.trimEnd();
     }
     if (name === 'sequence-region') {
         const c = contents.split(whitespaceRegex, 3);
         return {
             ...parsed,
             seq_id: c[0],
-            start: c[1]?.replaceAll(nonDigitRegex, ''),
-            end: c[2]?.replaceAll(nonDigitRegex, ''),
+            start: c[1].replaceAll(nonDigitRegex, ''),
+            end: c[2].replaceAll(nonDigitRegex, ''),
         };
     }
     else if (name === 'genome-build') {
         const [source, buildName] = contents.split(whitespaceRegex, 2);
         return {
             ...parsed,
-            source,
-            buildName,
+            source: source,
+            buildName: buildName,
         };
     }
     return parsed;
@@ -286,10 +239,6 @@ function parseAttributesJBrowseImpl(attrString, result, shouldUnescape) {
             const eqIdx = attrString.indexOf('=', start);
             if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
                 const tag = attrString.slice(start, eqIdx);
-                if (tag === '_lineHash') {
-                    start = semiIdx + 1;
-                    continue;
-                }
                 let key = COMMON_ATTRS[tag];
                 if (key === undefined) {
                     key = tag.toLowerCase();
@@ -322,38 +271,27 @@ export function parseAttributesJBrowse(attrString, result) {
 export function parseAttributesJBrowseNoUnescape(attrString, result) {
     parseAttributesJBrowseImpl(attrString, result, false);
 }
+const STRAND_MAP = {
+    '+': 1,
+    '-': -1,
+    '.': 0,
+};
 function parseFeatureJBrowseImpl(line, shouldUnescape) {
     const f = line.split('\t');
-    const seq_id = f[0];
-    const source = f[1];
-    const type = f[2];
     const startStr = f[3];
     const endStr = f[4];
     const scoreStr = f[5];
-    const strand = f[6];
     const phase = f[7];
     const attrString = f[8];
     const result = {
-        refName: seq_id.length === 0 || seq_id === '.'
-            ? ''
-            : shouldUnescape
-                ? unescape(seq_id)
-                : seq_id,
-        source: source.length === 0 || source === '.'
-            ? null
-            : shouldUnescape
-                ? unescape(source)
-                : source,
-        type: type.length === 0 || type === '.'
-            ? null
-            : shouldUnescape
-                ? unescape(type)
-                : type,
-        start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
-        end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
-        score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
-        strand: strand === '+' ? 1 : strand === '-' ? -1 : strand === '.' ? 0 : undefined,
-        phase: phase.length === 0 || phase === '.' ? undefined : +phase,
+        refName: strField(f[0], shouldUnescape, ''),
+        source: strField(f[1], shouldUnescape, null),
+        type: strField(f[2], shouldUnescape, null),
+        start: isEmpty(startStr) ? 0 : +startStr - 1,
+        end: isEmpty(endStr) ? 0 : +endStr,
+        score: isEmpty(scoreStr) ? undefined : +scoreStr,
+        strand: STRAND_MAP[f[6]],
+        phase: isEmpty(phase) ? undefined : +phase,
         subfeatures: [],
     };
     parseAttributesJBrowseImpl(attrString, result, shouldUnescape);

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gff-nostream",
-  "version": "3.0.4",
+  "version": "3.0.6",
   "description": "utilities to read GFF3 data",
   "license": "MIT",
   "repository": {
@@ -8,7 +8,7 @@
     "url": "https://github.com/GMOD/gff-nostream.git"
   },
   "type": "module",
-  "types": "./dist/index.d.ts",
+  "main": "dist/index.js",
   "exports": {
     "import": "./esm/index.js",
     "require": "./dist/index.js"
@@ -25,18 +25,19 @@
   ],
   "scripts": {
     "test": "vitest",
-    "benchonly": "vitest bench",
-    "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
-    "clean": "rm -rf dist esm",
-    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
+    "clean": "rimraf dist esm",
     "format": "prettier --write .",
-    "prebuild": "yarn clean",
-    "build:esm": "tsc --target esnext --outDir esm",
-    "build:es5": "tsc --target es2020 --module commonjs --moduleResolution bundler --outDir dist",
+    "lint": "eslint --report-unused-disable-directives --max-warnings 0",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc --outDir esm",
+    "build:es5": "tsc --module commonjs --moduleResolution bundler --outDir dist",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
-    "build": "yarn build:es5 && yarn build:esm",
-    "prepublishOnly": "yarn test --run && yarn build",
-    "postversion": "git push --follow-tags"
+    "preversion": "pnpm lint && pnpm test --run && pnpm build",
+    "postversion": "git push --follow-tags",
+    "build": "pnpm build:esm && pnpm build:es5",
+    "benchonly": "vitest bench",
+    "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
+    "prepublishOnly": "pnpm test --run && pnpm build"
   },
   "keywords": [
     "bionode",
@@ -46,12 +47,14 @@
     "genomics"
   ],
   "devDependencies": {
-    "@types/node": "^25.6.0",
-    "eslint": "^10.2.1",
-    "eslint-plugin-import": "^2.32.0",
+    "@eslint/js": "^10.0.1",
+    "@types/node": "^25.6.2",
+    "eslint": "^10.3.0",
+    "eslint-plugin-import-x": "^4.16.2",
     "prettier": "^3.8.3",
+    "rimraf": "^6.1.3",
     "typescript": "^6.0.3",
-    "typescript-eslint": "^8.59.0",
+    "typescript-eslint": "^8.59.2",
     "vitest": "^4.1.5"
   }
 }