gff-nostream 3.0.10 → 4.0.0

package/README.md

@@ -19,92 +19,26 @@ import fs from 'fs'
 const features = parseStringSync(fs.readFileSync('my_annotations.gff3', 'utf8'))
 ```
 
-For browser or other non-Node environments, pass any GFF3 string directly — for
-example from `fetch`:
+In the browser or other non-Node environments, pass any GFF3 string directly —
+for example from `fetch`:
 
 ```js
-import { parseStringSyncJBrowse } from 'gff-nostream'
+import { parseStringSync } from 'gff-nostream'
 
 const text = await fetch('my_annotations.gff3').then(r => r.text())
-const features = parseStringSyncJBrowse(text)
+const features = parseStringSync(text)
 ```
 
 ## Object format
 
-### GFF3 format
-
-Features are returned as arrays of all lines sharing the same ID (to represent
-multi-location features). Values that are `.` in GFF3 are `null` in the output.
-
-A simple feature located in one place:
-
-```json
-[
-  {
-    "seq_id": "ctg123",
-    "source": null,
-    "type": "gene",
-    "start": 1000,
-    "end": 9000,
-    "score": null,
-    "strand": "+",
-    "phase": null,
-    "attributes": {
-      "ID": ["gene00001"],
-      "Name": ["EDEN"]
-    },
-    "child_features": [],
-    "derived_features": []
-  }
-]
-```
-
-A CDS called `cds00001` located in two places:
-
-```json
-[
-  {
-    "seq_id": "ctg123",
-    "source": null,
-    "type": "CDS",
-    "start": 1201,
-    "end": 1500,
-    "score": null,
-    "strand": "+",
-    "phase": "0",
-    "attributes": {
-      "ID": ["cds00001"],
-      "Parent": ["mRNA00001"]
-    },
-    "child_features": [],
-    "derived_features": []
-  },
-  {
-    "seq_id": "ctg123",
-    "source": null,
-    "type": "CDS",
-    "start": 3000,
-    "end": 3902,
-    "score": null,
-    "strand": "+",
-    "phase": "0",
-    "attributes": {
-      "ID": ["cds00001"],
-      "Parent": ["mRNA00001"]
-    },
-    "child_features": [],
-    "derived_features": []
-  }
-]
-```
-
-### JBrowse format
-
-The `JBrowse` variants return flat objects with coordinates converted to 0-based
+Features are returned as flat objects with coordinates converted to 0-based
 half-open, `strand` as a number (`1`/`-1`/`0`), attributes spread as lowercase
-top-level keys, and `subfeatures` instead of `child_features`.
+top-level keys, single-valued attributes unwrapped from their array, and child
+features nested under `subfeatures`. An attribute whose lowercased name collides
+with a built-in field (e.g. `Start`, `Type`) is suffixed with `2` (`start2`,
+`type2`).
 
-The same gene feature in JBrowse format:
+A gene with an mRNA child:
 
 ```json
 {
@@ -114,34 +48,44 @@ The same gene feature in JBrowse format:
   "start": 999,
   "end": 9000,
   "strand": 1,
-  "subfeatures": [],
   "id": "gene00001",
-  "name": "EDEN"
+  "name": "EDEN",
+  "subfeatures": [
+    {
+      "refName": "ctg123",
+      "source": null,
+      "type": "mRNA",
+      "start": 1049,
+      "end": 9000,
+      "strand": 1,
+      "id": "mRNA00001",
+      "parent": "gene00001",
+      "subfeatures": []
+    }
+  ]
 }
 ```
 
-Note: multi-location features (same ID on multiple lines) are not merged in
-JBrowse format — only the first occurrence is kept.
+Multi-location features (the same ID on multiple lines, such as a CDS spanning
+several segments) are not merged — each line is its own flat feature, attached
+to its parent (or kept as a top-level item) independently.
 
 ## API
 
-### `parseStringSync(str: string): GFF3Feature[]`
+### `parseStringSync(str: string): GffFeature[]`
 
 Synchronously parse a GFF3 string and return an array of features. Comments,
 directives, and `##FASTA` sections are ignored.
 
-### `parseStringSyncJBrowse(str: string): JBrowseFeature[]`
-
-Synchronously parse a GFF3 string and return features in JBrowse format.
-
-### `parseRecords(records: LineRecord[]): GFF3Feature[]`
+### `parseRecords(records: LineRecord[]): GffFeature[]`
 
 Parse an array of `LineRecord` objects. Useful when managing raw line data
 directly (e.g. from a tabix-indexed file with byte offsets).
 
-### `parseRecordsJBrowse(records: LineRecord[]): JBrowseFeature[]`
+### `extractType(line: string): string`
 
-Same as `parseRecords` but returns JBrowse-format features.
+Extract the feature type (GFF3 column 3) from a raw line without fully splitting
+it.
 
 ### `LineRecord`
 
@@ -149,7 +93,7 @@ Same as `parseRecords` but returns JBrowse-format features.
 interface LineRecord {
   line: string
   hasEscapes: boolean // set true when line contains '%' to enable URL-decoding
-  lineHash?: string | number // propagated to attributes._lineHash on the parsed feature
+  lineHash?: string | number // propagated to the feature's _lineHash field
   start?: number // byte offset passthrough (not used by the parser)
   end?: number // byte offset passthrough (not used by the parser)
 }

package/dist/api.d.ts

@@ -1,4 +1,4 @@
-import type { GFF3Feature, JBrowseFeature } from './util.ts';
+import type { GffFeature } from './util.ts';
 interface ParseInput {
     line: string;
     lineHash?: string | number;
@@ -16,33 +16,18 @@ export interface LineRecord extends ParseInput {
 export declare function extractType(line: string): string;
 /**
  * Synchronously parse a string containing GFF3 and return an array of the
- * parsed items.
+ * parsed features. Comments, directives, and `##FASTA` sections are ignored.
  *
  * @param str - GFF3 string
  * @returns array of parsed features
  */
-export declare function parseStringSync(str: string): GFF3Feature[];
-/**
- * Synchronously parse a string containing GFF3 directly into JBrowse format.
- *
- * @param str - GFF3 string
- * @returns array of JBrowse-format features
- */
-export declare function parseStringSyncJBrowse(str: string): JBrowseFeature[];
+export declare function parseStringSync(str: string): GffFeature[];
 /**
  * Parse an array of LineRecord objects containing raw GFF3 lines.
- * Supports parent/child relationships.
- *
- * @param records - Array of LineRecord objects with raw line and metadata
- * @returns array of parsed features
- */
-export declare function parseRecords(records: ParseInput[]): GFF3Feature[];
-/**
- * Parse an array of LineRecord objects directly into JBrowse feature format.
  * Supports parent/child relationships via subfeatures.
  *
  * @param records - Array of LineRecord objects with raw line and metadata
- * @returns array of JBrowse-format features
+ * @returns array of parsed features
  */
-export declare function parseRecordsJBrowse(records: ParseInput[]): JBrowseFeature[];
-export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, JBrowseFeature, } from './util.ts';
+export declare function parseRecords(records: ParseInput[]): GffFeature[];
+export type { GffFeature } from './util.ts';

package/dist/api.js

@@ -2,9 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.extractType = extractType;
 exports.parseStringSync = parseStringSync;
-exports.parseStringSyncJBrowse = parseStringSyncJBrowse;
 exports.parseRecords = parseRecords;
-exports.parseRecordsJBrowse = parseRecordsJBrowse;
 const util_ts_1 = require("./util.js");
 /** Extract the GFF3 feature type (column 3) from a raw line without a full split. */
 function extractType(line) {
@@ -24,8 +22,8 @@ function appendOrphan(orphans, key, value) {
     }
 }
 /**
- * The JBrowse parser collapses single-element attribute arrays to scalars, so a
- * raw ID/Parent value can be a string, a string array, or absent. These coerce
+ * The parser collapses single-element attribute arrays to scalars, so a raw
+ * ID/Parent value can be a string, a string array, or absent. These coerce
  * those `unknown` values without typecasts.
  */
 function firstString(value) {
@@ -40,7 +38,7 @@ function toStringArray(value) {
 }
 /**
  * Synchronously parse a string containing GFF3 and return an array of the
- * parsed items.
+ * parsed features. Comments, directives, and `##FASTA` sections are ignored.
  *
  * @param str - GFF3 string
  * @returns array of parsed features
@@ -48,15 +46,6 @@ function toStringArray(value) {
 function parseStringSync(str) {
     return parseRecords(stringToRecords(str));
 }
-/**
- * Synchronously parse a string containing GFF3 directly into JBrowse format.
- *
- * @param str - GFF3 string
- * @returns array of JBrowse-format features
- */
-function parseStringSyncJBrowse(str) {
-    return parseRecordsJBrowse(stringToRecords(str));
-}
 function stringToRecords(str) {
     const lines = str.split(/\r?\n/);
     const records = [];
@@ -76,7 +65,7 @@ function stringToRecords(str) {
 }
 /**
  * Parse an array of LineRecord objects containing raw GFF3 lines.
- * Supports parent/child relationships.
+ * Supports parent/child relationships via subfeatures.
  *
  * @param records - Array of LineRecord objects with raw line and metadata
  * @returns array of parsed features
@@ -86,122 +75,40 @@ function parseRecords(records) {
     const byId = new Map();
     const orphans = new Map();
     for (const record of records) {
-        const parsed = record.hasEscapes
-            ? (0, util_ts_1.parseFeature)(record.line)
-            : (0, util_ts_1.parseFeatureNoUnescape)(record.line);
-        const featureLine = {
-            ...parsed,
-            child_features: [],
-            derived_features: [],
-        };
-        if (record.lineHash !== undefined) {
-            featureLine.attributes ??= {};
-            featureLine.attributes._lineHash = [String(record.lineHash)];
-        }
-        const attrs = featureLine.attributes;
-        const ids = attrs?.ID;
-        const parents = attrs?.Parent;
-        if (!ids && !parents) {
-            items.push([featureLine]);
-        }
-        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;
-                }
-                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);
-                    }
-                }
-            }
-            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 {
-                        appendOrphan(orphans, parentId, feature);
-                    }
-                }
-            }
-        }
-    }
-    return items;
-}
-/**
- * Parse an array of LineRecord objects directly into JBrowse feature format.
- * Supports parent/child relationships via subfeatures.
- *
- * @param records - Array of LineRecord objects with raw line and metadata
- * @returns array of JBrowse-format features
- */
-function parseRecordsJBrowse(records) {
-    const items = [];
-    const byId = new Map();
-    const orphans = new Map();
-    for (const record of records) {
-        const feature = record.hasEscapes
-            ? (0, util_ts_1.parseFeatureJBrowse)(record.line)
-            : (0, util_ts_1.parseFeatureJBrowseNoUnescape)(record.line);
+        const feature = (0, util_ts_1.parseFeature)(record.line, record.hasEscapes);
         if (record.lineHash !== undefined) {
             feature._lineHash = String(record.lineHash);
         }
         const id = firstString(feature.id);
         const parents = toStringArray(feature.parent);
-        if (!id && parents.length === 0) {
+        // A parentless line is a top-level item. Every line of a top-level
+        // discontinuous feature (e.g. cDNA_match/EST_match spanning several
+        // segments under one shared ID, with no Parent) is its own top-level
+        // item, so push regardless of whether the id is already registered.
+        if (parents.length === 0) {
             items.push(feature);
         }
-        else {
-            // Register the id only the first time it is seen. Continuation lines
-            // (multi-location features such as a CDS spanning several segments share
-            // one ID across lines) skip registration but must still be attached to
-            // their parent below, so this is independent of the parent handling.
-            if (id && !byId.has(id)) {
-                if (parents.length === 0) {
-                    items.push(feature);
-                }
-                byId.set(id, feature);
-                const waiting = orphans.get(id);
-                if (waiting) {
-                    for (const w of waiting) {
-                        feature.subfeatures.push(w);
-                    }
-                    orphans.delete(id);
+        // Register the id only the first time it is seen. Continuation lines
+        // (multi-location features such as a CDS spanning several segments share
+        // one ID across lines) skip registration but must still be attached to
+        // their parent below, so this is independent of the parent handling.
+        if (id && !byId.has(id)) {
+            byId.set(id, feature);
+            const waiting = orphans.get(id);
+            if (waiting) {
+                for (const w of waiting) {
+                    feature.subfeatures.push(w);
                 }
+                orphans.delete(id);
             }
-            for (const parentId of parents) {
-                const parentFeature = byId.get(parentId);
-                if (parentFeature) {
-                    parentFeature.subfeatures.push(feature);
-                }
-                else {
-                    appendOrphan(orphans, parentId, feature);
-                }
+        }
+        for (const parentId of parents) {
+            const parentFeature = byId.get(parentId);
+            if (parentFeature) {
+                parentFeature.subfeatures.push(feature);
+            }
+            else {
+                appendOrphan(orphans, parentId, feature);
             }
         }
     }

package/dist/api.js.map

@@ -1 +1 @@
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package/dist/index.d.ts

@@ -1,2 +1,2 @@
-export { extractType, parseRecords, parseRecordsJBrowse, parseStringSync, parseStringSyncJBrowse, } from './api.ts';
-export type { GFF3Comment, GFF3Directive, GFF3Feature, GFF3FeatureLine, GFF3FeatureLineWithRefs, GFF3Item, GFF3Sequence, JBrowseFeature, LineRecord, } from './api.ts';
+export { extractType, parseRecords, parseStringSync } from './api.ts';
+export type { GffFeature, LineRecord } from './api.ts';

package/dist/index.js

@@ -1,10 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseStringSyncJBrowse = exports.parseStringSync = exports.parseRecordsJBrowse = exports.parseRecords = exports.extractType = void 0;
+exports.parseStringSync = exports.parseRecords = exports.extractType = void 0;
 var api_ts_1 = require("./api.js");
 Object.defineProperty(exports, "extractType", { enumerable: true, get: function () { return api_ts_1.extractType; } });
 Object.defineProperty(exports, "parseRecords", { enumerable: true, get: function () { return api_ts_1.parseRecords; } });
-Object.defineProperty(exports, "parseRecordsJBrowse", { enumerable: true, get: function () { return api_ts_1.parseRecordsJBrowse; } });
 Object.defineProperty(exports, "parseStringSync", { enumerable: true, get: function () { return api_ts_1.parseStringSync; } });
-Object.defineProperty(exports, "parseStringSyncJBrowse", { enumerable: true, get: function () { return api_ts_1.parseStringSyncJBrowse; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,mCAMiB;AALf,qGAAA,WAAW,OAAA;AACX,sGAAA,YAAY,OAAA;AACZ,6GAAA,mBAAmB,OAAA;AACnB,yGAAA,eAAe,OAAA;AACf,gHAAA,sBAAsB,OAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;AAAA,mCAAqE;AAA5D,qGAAA,WAAW,OAAA;AAAE,sGAAA,YAAY,OAAA;AAAE,yGAAA,eAAe,OAAA"}

package/dist/util.d.ts

@@ -6,122 +6,11 @@
  */
 export declare function unescape(stringVal: string): string;
 /**
- * Parse the 9th column (attributes) of a GFF3 feature line.
- *
- * @param attrString - String of GFF3 9th column
- * @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
- *
- * @param line - GFF3 feature line
- * @returns The parsed feature
+ * A parsed GFF3 feature: a flat object with 0-based half-open coordinates,
+ * numeric strand (`1`/`-1`/`0`), attributes spread as lowercase top-level keys,
+ * and child features nested under `subfeatures`.
  */
-export declare function parseFeature(line: string): GFF3FeatureLine;
-/**
- * Parse a GFF3 feature line without unescaping.
- * Fast path for data known to contain no escaped characters.
- *
- * @param line - GFF3 feature line
- * @returns The parsed feature
- */
-export declare function parseFeatureNoUnescape(line: string): GFF3FeatureLine;
-/**
- * Parse a GFF3 directive line.
- *
- * @param line - GFF3 directive line
- * @returns The parsed directive
- */
-export declare function parseDirective(line: string): GFF3Directive | GFF3SequenceRegionDirective | GFF3GenomeBuildDirective | null;
-/** A record of GFF3 attribute identifiers and the values of those identifiers */
-export type GFF3Attributes = Record<string, string[] | undefined>;
-/** A representation of a single line of a GFF3 file */
-export interface GFF3FeatureLine {
-    /** The ID of the landmark used to establish the coordinate system for the current feature */
-    seq_id: string | null;
-    /** A free text qualifier intended to describe the algorithm or operating procedure that generated this feature */
-    source: string | null;
-    /** The type of the feature */
-    type: string | null;
-    /** The start coordinates of the feature */
-    start: number | null;
-    /** The end coordinates of the feature */
-    end: number | null;
-    /** The score of the feature */
-    score: number | null;
-    /** The strand of the feature */
-    strand: string | null;
-    /** For features of type "CDS", the phase indicates where the next codon begins relative to the 5' end of the current CDS feature */
-    phase: string | null;
-    /** Feature attributes */
-    attributes: GFF3Attributes | null;
-}
-/**
- * A GFF3 Feature line that includes references to other features defined in
- * their "Parent" or "Derives_from" attributes
- */
-export interface GFF3FeatureLineWithRefs extends GFF3FeatureLine {
-    /** An array of child features */
-    child_features: GFF3Feature[];
-    /** An array of features derived from this feature */
-    derived_features: GFF3Feature[];
-}
-/**
- * A GFF3 feature, which may include multiple individual feature lines
- */
-export type GFF3Feature = GFF3FeatureLineWithRefs[];
-/** A GFF3 directive */
-export interface GFF3Directive {
-    /** The name of the directive */
-    directive: string;
-    /** The string value of the directive */
-    value?: string;
-}
-/** A GFF3 sequence-region directive */
-export interface GFF3SequenceRegionDirective extends GFF3Directive {
-    /** The string value of the directive */
-    value: string;
-    /** The sequence ID parsed from the directive */
-    seq_id: string;
-    /** The sequence start parsed from the directive */
-    start: string;
-    /** The sequence end parsed from the directive */
-    end: string;
-}
-/** A GFF3 genome-build directive */
-export interface GFF3GenomeBuildDirective extends GFF3Directive {
-    /** The string value of the directive */
-    value: string;
-    /** The genome build source parsed from the directive */
-    source: string;
-    /** The genome build name parsed from the directive */
-    buildName: string;
-}
-/** A GFF3 comment */
-export interface GFF3Comment {
-    /** The text of the comment */
-    comment: string;
-}
-/** A GFF3 FASTA single sequence */
-export interface GFF3Sequence {
-    /** The ID of the sequence */
-    id: string;
-    /** The description of the sequence */
-    description?: string;
-    /** The sequence */
-    sequence: string;
-}
-export type GFF3Item = GFF3Feature | GFF3Directive | GFF3Comment | GFF3Sequence;
-export interface JBrowseFeature {
+export interface GffFeature {
     start: number;
     end: number;
     strand?: number;
@@ -130,10 +19,21 @@ export interface JBrowseFeature {
     refName: string;
     phase?: number;
     score?: number;
-    subfeatures: JBrowseFeature[];
+    subfeatures: GffFeature[];
     [key: string]: unknown;
 }
-export declare function parseAttributesJBrowse(attrString: string, result: Record<string, unknown>): void;
-export declare function parseAttributesJBrowseNoUnescape(attrString: string, result: Record<string, unknown>): void;
-export declare function parseFeatureJBrowse(line: string): JBrowseFeature;
-export declare function parseFeatureJBrowseNoUnescape(line: string): JBrowseFeature;
+/**
+ * Parse the 9th column (attributes) of a GFF3 feature line into `result`,
+ * lowercasing keys and suffixing any that collide with a default field name.
+ * Pass shouldUnescape=false as a fast path for data with no escaped characters.
+ */
+export declare function parseAttributes(attrString: string, result: Record<string, unknown>, shouldUnescape: boolean): void;
+/**
+ * Parse a GFF3 feature line. Pass shouldUnescape=false as a fast path for data
+ * known to contain no escaped characters.
+ *
+ * @param line - GFF3 feature line
+ * @param shouldUnescape - whether to unescape percent-encoded values
+ * @returns The parsed feature
+ */
+export declare function parseFeature(line: string, shouldUnescape: boolean): GffFeature;