gff-nostream 3.0.11 → 5.0.0

package/esm/api.js

@@ -1,4 +1,4 @@
-import { parseFeature, parseFeatureJBrowse, parseFeatureJBrowseNoUnescape, parseFeatureNoUnescape, } from "./util.js";
+import { parseFeature } from "./util.js";
 /** Extract the GFF3 feature type (column 3) from a raw line without a full split. */
 export function extractType(line) {
     const t1 = line.indexOf('\t');
@@ -17,8 +17,8 @@ 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) {
@@ -32,174 +32,82 @@ function toStringArray(value) {
     return typeof value === 'string' ? [value] : [];
 }
 /**
- * Synchronously parse a string containing GFF3 and return an array of the
- * parsed items.
- *
- * @param str - GFF3 string
- * @returns array of parsed features
- */
-export 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
+ * Register a feature's ID and attach it to its parent(s), building the
+ * subfeature tree in `byId`/`orphans`. Returns true when the feature is
+ * top-level (has no Parent) and the caller should collect it.
  */
-export function parseStringSyncJBrowse(str) {
-    return parseRecordsJBrowse(stringToRecords(str));
-}
-function stringToRecords(str) {
-    const lines = str.split(/\r?\n/);
-    const records = [];
-    for (const line of lines) {
-        if (line.startsWith('##FASTA') || line.startsWith('>')) {
-            break;
+function linkFeature(feature, byId, orphans) {
+    const id = firstString(feature.id);
+    const parents = toStringArray(feature.parent);
+    // 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);
         }
-        if (line.length === 0 || line.startsWith('#')) {
-            continue;
+    }
+    for (const parentId of parents) {
+        const parentFeature = byId.get(parentId);
+        if (parentFeature) {
+            parentFeature.subfeatures.push(feature);
+        }
+        else {
+            appendOrphan(orphans, parentId, feature);
         }
-        records.push({
-            line,
-            hasEscapes: line.includes('%'),
-        });
     }
-    return records;
+    // Every line of a top-level discontinuous feature (e.g. cDNA_match spanning
+    // several segments under one shared ID, with no Parent) is its own top-level
+    // item, so this is independent of whether the id was just registered.
+    return parents.length === 0;
 }
 /**
- * Parse an array of LineRecord objects containing raw GFF3 lines.
- * Supports parent/child relationships.
+ * Synchronously parse a string containing GFF3 and return an array of the
+ * parsed features. Comments, directives, and `##FASTA` sections are ignored.
  *
- * @param records - Array of LineRecord objects with raw line and metadata
+ * @param str - GFF3 string
  * @returns array of parsed features
  */
-export function parseRecords(records) {
+export function parseStringSync(str) {
     const items = [];
     const byId = new Map();
     const orphans = new Map();
-    for (const record of records) {
-        const parsed = record.hasEscapes
-            ? parseFeature(record.line)
-            : 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]);
+    for (const line of str.split(/\r?\n/)) {
+        if (line.startsWith('##FASTA') || line.startsWith('>')) {
+            break;
         }
-        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);
-                    }
-                }
+        if (line.length !== 0 && !line.startsWith('#')) {
+            const feature = parseFeature(line);
+            if (linkFeature(feature, byId, orphans)) {
+                items.push(feature);
             }
         }
     }
     return items;
 }
 /**
- * Parse an array of LineRecord objects directly into JBrowse feature format.
- * Supports parent/child relationships via subfeatures.
+ * Parse an array of records wrapping raw GFF3 lines, resolving parent/child
+ * relationships into `subfeatures`. Returns each top-level feature paired with
+ * the record it came from, so callers can attach their own identity (e.g. a
+ * byte offset) without the parser stamping anything onto the feature.
  *
- * @param records - Array of LineRecord objects with raw line and metadata
- * @returns array of JBrowse-format features
+ * @param records - Array of records, each carrying a raw GFF3 `line`
+ * @returns top-level features, each paired with its originating record
  */
-export function parseRecordsJBrowse(records) {
+export function parseRecords(records) {
     const items = [];
     const byId = new Map();
     const orphans = new Map();
     for (const record of records) {
-        const feature = record.hasEscapes
-            ? parseFeatureJBrowse(record.line)
-            : parseFeatureJBrowseNoUnescape(record.line);
-        if (record.lineHash !== undefined) {
-            feature._lineHash = String(record.lineHash);
-        }
-        const id = firstString(feature.id);
-        const parents = toStringArray(feature.parent);
-        if (!id && parents.length === 0) {
-            items.push(feature);
-        }
-        else {
-            // 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 here regardless of whether the id is already registered.
-            if (parents.length === 0) {
-                items.push(feature);
-            }
-            // 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);
-                }
-            }
+        const feature = parseFeature(record.line);
+        if (linkFeature(feature, byId, orphans)) {
+            items.push({ feature, record });
         }
     }
     return items;

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package/esm/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, ParsedRecord } from './api.ts';

package/esm/index.js

@@ -1,2 +1,2 @@
-export { extractType, parseRecords, parseRecordsJBrowse, parseStringSync, parseStringSyncJBrowse, } from "./api.js";
+export { extractType, parseRecords, parseStringSync } from "./api.js";
 //# 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,EACL,WAAW,EACX,YAAY,EACZ,mBAAmB,EACnB,eAAe,EACf,sBAAsB,GACvB,MAAM,UAAU,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,eAAe,EAAE,MAAM,UAAU,CAAA"}

package/esm/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 +19,20 @@ 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. Unescaping is skipped entirely for lines with no
+ * '%' character, which is the common case.
+ *
+ * @param line - GFF3 feature line
+ * @returns The parsed feature
+ */
+export declare function parseFeature(line: string): GffFeature;