gff-nostream 1.3.9 → 2.0.1

package/dist/util.d.ts

@@ -26,6 +26,14 @@ export declare function escapeColumn(rawVal: string | number): string;
  * @returns Parsed attributes
  */
 export declare function parseAttributes(attrString: string): GFF3Attributes;
+/**
+ * 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 declare function parseAttributesNoUnescape(attrString: string): GFF3Attributes;
 /**
  * Parse a GFF3 feature line
  *
@@ -33,6 +41,15 @@ export declare function parseAttributes(attrString: string): GFF3Attributes;
  * @returns The parsed feature
  */
 export declare function parseFeature(line: string): GFF3FeatureLine;
+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/dist/util.js

@@ -6,7 +6,10 @@ exports.unescape = unescape;
 exports.escape = escape;
 exports.escapeColumn = escapeColumn;
 exports.parseAttributes = parseAttributes;
+exports.parseAttributesNoUnescape = parseAttributesNoUnescape;
 exports.parseFeature = parseFeature;
+exports.parseFieldsArray = parseFieldsArray;
+exports.parseFieldsArrayNoUnescape = parseFieldsArrayNoUnescape;
 exports.parseDirective = parseDirective;
 exports.formatAttributes = formatAttributes;
 exports.formatFeature = formatFeature;
@@ -14,6 +17,15 @@ exports.formatDirective = formatDirective;
 exports.formatComment = formatComment;
 exports.formatSequence = formatSequence;
 exports.formatItem = formatItem;
+const escapeRegex = /%([0-9A-Fa-f]{2})/g;
+const directiveRegex = /^\s*##\s*(\S+)\s*(.*)/;
+const lineEndRegex = /\r?\n$/;
+const whitespaceRegex = /\s+/;
+const nonDigitRegex = /\D/g;
+// eslint-disable-next-line no-control-regex
+const attrEscapeRegex = /[\n;\r\t=%&,\u0000-\u001f\u007f-\u00ff]/g;
+// eslint-disable-next-line no-control-regex
+const columnEscapeRegex = /[\n\r\t%\u0000-\u001f\u007f-\u00ff]/g;
 /**
  * Unescape a string value used in a GFF3 attribute.
  *
@@ -21,7 +33,10 @@ exports.formatItem = formatItem;
  * @returns An unescaped string value
  */
 function unescape(stringVal) {
-    return stringVal.replaceAll(/%([0-9A-Fa-f]{2})/g, (_match, seq) => String.fromCharCode(parseInt(seq, 16)));
+    if (!stringVal.includes('%')) {
+        return stringVal;
+    }
+    return stringVal.replaceAll(escapeRegex, (_match, seq) => String.fromCharCode(parseInt(seq, 16)));
 }
 function _escape(regex, s) {
     return String(s).replace(regex, ch => {
@@ -36,7 +51,7 @@ function _escape(regex, s) {
  * @returns An escaped string value
  */
 function escape(rawVal) {
-    return _escape(/[\n;\r\t=%&,\u0000-\u001f\u007f-\u00ff]/g, rawVal);
+    return _escape(attrEscapeRegex, rawVal);
 }
 /**
  * Escape a value for use in a GFF3 column value.
@@ -45,7 +60,7 @@ function escape(rawVal) {
  * @returns An escaped column value
  */
 function escapeColumn(rawVal) {
-    return _escape(/[\n\r\t%\u0000-\u001f\u007f-\u00ff]/g, rawVal);
+    return _escape(columnEscapeRegex, rawVal);
 }
 /**
  * Parse the 9th column (attributes) of a GFF3 feature line.
@@ -58,26 +73,66 @@ function parseAttributes(attrString) {
         return {};
     }
     const attrs = {};
-    attrString
-        .replace(/\r?\n$/, '')
-        .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
+ */
+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;
 }
 /**
@@ -87,21 +142,67 @@ function parseAttributes(attrString) {
  * @returns The parsed feature
  */
 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;
+}
+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
+ */
+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.
@@ -110,8 +211,7 @@ function parseFeature(line) {
  * @returns The parsed directive
  */
 function parseDirective(line) {
-    var _a, _b;
-    const match = /^\s*##\s*(\S+)\s*(.*)/.exec(line);
+    const match = directiveRegex.exec(line);
     if (!match) {
         return null;
     }
@@ -119,18 +219,26 @@ function parseDirective(line) {
     let [, , contents] = match;
     const parsed = { directive: name };
     if (contents.length) {
-        contents = contents.replace(/\r?\n$/, '');
+        contents = contents.replace(lineEndRegex, '');
         parsed.value = contents;
     }
     // do a little additional parsing for sequence-region and genome-build directives
     if (name === 'sequence-region') {
-        const c = contents.split(/\s+/, 3);
-        return Object.assign(Object.assign({}, parsed), { seq_id: c[0], start: (_a = c[1]) === null || _a === void 0 ? void 0 : _a.replaceAll(/\D/g, ''), end: (_b = c[2]) === null || _b === void 0 ? void 0 : _b.replaceAll(/\D/g, '') });
+        const c = contents.split(whitespaceRegex, 3);
+        return {
+            ...parsed,
+            seq_id: c[0],
+            start: c[1]?.replaceAll(nonDigitRegex, ''),
+            end: c[2]?.replaceAll(nonDigitRegex, ''),
+        };
     }
     else if (name === 'genome-build') {
-        const [source, buildName] = contents.split(/\s+/, 2);
-        return Object.assign(Object.assign({}, parsed), { source,
-            buildName });
+        const [source, buildName] = contents.split(whitespaceRegex, 2);
+        return {
+            ...parsed,
+            source,
+            buildName,
+        };
     }
     return parsed;
 }
@@ -142,28 +250,18 @@ function parseDirective(line) {
  */
 function formatAttributes(attrs) {
     const attrOrder = [];
-    Object.entries(attrs).forEach(([tag, val]) => {
+    for (const [tag, val] of Object.entries(attrs)) {
         if (!val) {
-            return;
+            continue;
         }
-        let valstring;
-        if (val.hasOwnProperty('toString')) {
-            valstring = escape(val.toString());
-            // } else if (Array.isArray(val.values)) {
-            //   valstring = val.values.map(escape).join(',')
-        }
-        else if (Array.isArray(val)) {
-            valstring = val.map(escape).join(',');
-        }
-        else {
-            valstring = escape(val);
-        }
-        attrOrder.push(`${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 = [
@@ -268,7 +366,10 @@ 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

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package/esm/api.d.ts

@@ -1,4 +1,8 @@
-import { GFF3Feature } from './util';
+import type { GFF3Feature } from './util.ts';
+export interface LineRecord {
+    fields: string[];
+    lineHash?: string | number;
+}
 /**
  * Synchronously parse a string containing GFF3 and return an array of the
  * parsed items.
@@ -8,4 +12,31 @@ import { GFF3Feature } from './util';
  * @returns array of parsed features, directives, comments and/or sequences
  */
 export declare function parseStringSync(str: string): GFF3Feature[];
-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 declare function parseArraySync(arr: string[]): GFF3Feature[];
+/**
+ * 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 declare function parseRecordsSync(records: LineRecord[]): GFF3Feature[];
+/**
+ * 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 declare function parseRecordsSyncFast(records: LineRecord[], hasEscapes: boolean): GFF3Feature[];
+export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, } from './util.ts';

package/esm/api.js

@@ -1,4 +1,5 @@
-import Parser from './parse';
+import Parser from "./parse.js";
+import { parseFieldsArray, parseFieldsArrayNoUnescape } from "./util.js";
 /**
  * Synchronously parse a string containing GFF3 and return an array of the
  * parsed items.
@@ -13,7 +14,7 @@ export function parseStringSync(str) {
         featureCallback: arg => items.push(arg),
         disableDerivesFromReferences: true,
         errorCallback: err => {
-            throw err;
+            throw new Error(err);
         },
     });
     for (const line of str.split(/\r?\n/)) {
@@ -22,4 +23,88 @@ export function parseStringSync(str) {
     parser.finish();
     return items;
 }
+/**
+ * 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) {
+    const items = [];
+    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) {
+    const items = [];
+    const parser = new Parser({
+        featureCallback: arg => items.push(arg),
+        disableDerivesFromReferences: true,
+        errorCallback: err => {
+            throw new Error(err);
+        },
+    });
+    for (const record of records) {
+        const featureLine = 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, hasEscapes) {
+    const items = [];
+    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 = 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;
+}
 //# sourceMappingURL=api.js.map

package/esm/api.js.map

@@ -1 +1 @@
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+{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,YAAY,CAAA;AAC/B,OAAO,EAAE,gBAAgB,EAAE,0BAA0B,EAAE,MAAM,WAAW,CAAA;AASxE;;;;;;;GAOG;AACH,MAAM,UAAU,eAAe,CAAC,GAAW;IACzC,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC;QACxB,eAAe,EAAE,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC;QACvC,4BAA4B,EAAE,IAAI;QAClC,aAAa,EAAE,GAAG,CAAC,EAAE;YACnB,MAAM,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACtB,CAAC;KACF,CAAC,CAAA;IAEF,KAAK,MAAM,IAAI,IAAI,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,CAAC;QACtC,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IACtB,CAAC;IACD,MAAM,CAAC,MAAM,EAAE,CAAA;IAEf,OAAO,KAAK,CAAA;AACd,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,cAAc,CAAC,GAAa;IAC1C,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC;QACxB,eAAe,EAAE,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC;QACvC,4BAA4B,EAAE,IAAI;QAClC,aAAa,EAAE,GAAG,CAAC,EAAE;YACnB,MAAM,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACtB,CAAC;KACF,CAAC,CAAA;IAEF,KAAK,MAAM,IAAI,IAAI,GAAG,EAAE,CAAC;QACvB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAA;IACtB,CAAC;IACD,MAAM,CAAC,MAAM,EAAE,CAAA;IAEf,OAAO,KAAK,CAAA;AACd,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,gBAAgB,CAAC,OAAqB;IACpD,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC;QACxB,eAAe,EAAE,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC;QACvC,4BAA4B,EAAE,IAAI;QAClC,aAAa,EAAE,GAAG,CAAC,EAAE;YACnB,MAAM,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACtB,CAAC;KACF,CAAC,CAAA;IAEF,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,WAAW,GAAoB,gBAAgB,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACpE,IAAI,MAAM,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YAClC,IAAI,CAAC,WAAW,CAAC,UAAU,EAAE,CAAC;gBAC5B,WAAW,CAAC,UAAU,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,WAAW,CAAC,UAAU,CAAC,SAAS,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,CAAC;QACD,MAAM,CAAC,oBAAoB,CAAC,WAAW,CAAC,CAAA;IAC1C,CAAC;IACD,MAAM,CAAC,MAAM,EAAE,CAAA;IAEf,OAAO,KAAK,CAAA;AACd,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,oBAAoB,CAAC,OAAqB,EAAE,UAAmB;IAC7E,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC;QACxB,eAAe,EAAE,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC;QACvC,4BAA4B,EAAE,IAAI;QAClC,aAAa,EAAE,GAAG,CAAC,EAAE;YACnB,MAAM,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACtB,CAAC;KACF,CAAC,CAAA;IAEF,MAAM,SAAS,GAAG,UAAU,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,0BAA0B,CAAA;IAE5E,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,WAAW,GAAoB,SAAS,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QAC7D,IAAI,MAAM,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YAClC,IAAI,CAAC,WAAW,CAAC,UAAU,EAAE,CAAC;gBAC5B,WAAW,CAAC,UAAU,GAAG,EAAE,CAAA;YAC7B,CAAC;YACD,WAAW,CAAC,UAAU,CAAC,SAAS,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,CAAC;QACD,MAAM,CAAC,oBAAoB,CAAC,WAAW,CAAC,CAAA;IAC1C,CAAC;IACD,MAAM,CAAC,MAAM,EAAE,CAAA;IAEf,OAAO,KAAK,CAAA;AACd,CAAC"}

package/esm/index.d.ts

@@ -1,3 +1,3 @@
-import { parseStringSync } from './api';
-export { parseStringSync };
-export type { GFF3Comment, GFF3Feature, GFF3Directive, GFF3FeatureLineWithRefs, GFF3FeatureLine, GFF3Item, GFF3Sequence, } from './api';
+import { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync } from './api.ts';
+export { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync };
+export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, LineRecord, } from './api.ts';

package/esm/index.js

@@ -1,3 +1,3 @@
-import { parseStringSync } from './api';
-export { parseStringSync };
+import { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync } from "./api.js";
+export { parseArraySync, parseRecordsSync, parseRecordsSyncFast, parseStringSync };
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAE,eAAe,EAAE,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,eAAe,EAAE,MAAM,UAAU,CAAA;AAClG,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,oBAAoB,EAAE,eAAe,EAAE,CAAA"}

package/esm/parse.d.ts

@@ -1,23 +1,10 @@
-import * as GFF3 from './util';
-export declare class FASTAParser {
-    seqCallback: (sequence: GFF3.GFF3Sequence) => void;
-    currentSequence: {
-        id: string;
-        sequence: string;
-        description?: string;
-    } | undefined;
-    constructor(seqCallback: (sequence: GFF3.GFF3Sequence) => void);
-    addLine(line: string): void;
-    private _flush;
-    finish(): void;
-}
+import * as GFF3 from './util.ts';
 interface ParserArgs {
     featureCallback?(feature: GFF3.GFF3Feature): void;
     endCallback?(): void;
     commentCallback?(comment: GFF3.GFF3Comment): void;
     errorCallback?(error: string): void;
     directiveCallback?(directive: GFF3.GFF3Directive): void;
-    sequenceCallback?(sequence: GFF3.GFF3Sequence): void;
     bufferSize?: number;
     disableDerivesFromReferences?: boolean;
 }
@@ -28,9 +15,7 @@ export default class Parser {
     errorCallback: (error: string) => void;
     disableDerivesFromReferences: boolean;
     directiveCallback: (directive: GFF3.GFF3Directive) => void;
-    sequenceCallback: (sequence: GFF3.GFF3Sequence) => void;
     bufferSize: number;
-    fastaParser: FASTAParser | undefined;
     eof: boolean;
     lineNumber: number;
     private _underConstructionTopLevel;
@@ -39,6 +24,7 @@ export default class Parser {
     private _underConstructionOrphans;
     constructor(args: ParserArgs);
     addLine(line: string): void;
+    addParsedFeatureLine(featureLine: GFF3.GFF3FeatureLine): void;
     finish(): void;
     private _emitItem;
     private _enforceBufferSizeLimit;
@@ -48,6 +34,7 @@ export default class Parser {
      */
     private _emitAllUnderConstructionFeatures;
     private _bufferLine;
+    private _bufferParsedLine;
     private _resolveReferencesTo;
     private _parseError;
     private _resolveReferencesFrom;