gff-nostream 3.0.5 → 3.0.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +11 -5
- package/dist/api.d.ts +4 -2
- package/dist/api.js +65 -63
- package/dist/api.js.map +1 -1
- package/dist/util.d.ts +0 -15
- package/dist/util.js +33 -97
- package/dist/util.js.map +1 -1
- package/esm/api.d.ts +4 -2
- package/esm/api.js +65 -63
- package/esm/api.js.map +1 -1
- package/esm/util.d.ts +0 -15
- package/esm/util.js +33 -95
- package/esm/util.js.map +1 -1
- package/package.json +4 -4
- package/src/api.ts +67 -67
- package/src/util.ts +46 -120
package/README.md
CHANGED
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@@ -3,7 +3,8 @@
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[](https://npmjs.org/package/gff-nostream)
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[](https://github.com/GMOD/gff-nostream/actions?query=branch%3Amain+workflow%3APush+)
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Parse GFF3 data. A simplified version of
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Parse GFF3 data. A simplified version of
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[@gmod/gff](https://github.com/GMOD/gff-js) with no Node.js stream dependency.
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## Install
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@@ -21,7 +22,9 @@ const features = parseStringSync(stringOfGFF3)
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## Object format
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In GFF3, features can have more than one location. Features are returned as
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In GFF3, features can have more than one location. Features are returned as
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arrays of all lines sharing the same ID. Values that are `.` in GFF3 are `null`
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in the output.
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A simple feature located in one place:
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@@ -93,11 +96,13 @@ Synchronously parse a GFF3 string and return an array of features.
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### `parseStringSyncJBrowse(str: string): JBrowseFeature[]`
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Synchronously parse a GFF3 string and return features in JBrowse format (flat
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Synchronously parse a GFF3 string and return features in JBrowse format (flat
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objects with `subfeatures` instead of `child_features`).
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### `parseRecords(records: LineRecord[]): GFF3Feature[]`
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Parse an array of `LineRecord` objects. Useful when managing raw line data
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Parse an array of `LineRecord` objects. Useful when managing raw line data
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directly (e.g. from an indexed file with byte offsets).
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### `parseRecordsJBrowse(records: LineRecord[]): JBrowseFeature[]`
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@@ -105,7 +110,8 @@ Same as `parseRecords` but returns JBrowse-format features.
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## Publishing
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[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub
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[Trusted publishing](https://docs.npmjs.com/about-trusted-publishing) via GitHub
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Actions.
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```bash
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npm version patch # or minor/major
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package/dist/api.d.ts
CHANGED
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@@ -2,8 +2,10 @@ import type { GFF3Feature, JBrowseFeature } from './util.ts';
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export interface LineRecord {
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line: string;
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lineHash?: string | number;
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/** Optional passthrough byte offsets — not used by the parser */
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start?: number;
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/** Optional passthrough byte offsets — not used by the parser */
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end?: number;
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hasEscapes: boolean;
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}
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/**
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package/dist/api.js
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const lines = str.split(/\r?\n/);
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const records = [];
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for (const line of lines) {
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if (line.startsWith('##FASTA') || line.startsWith('>')) {
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break;
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}
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if (line.length === 0 || line.startsWith('#')) {
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if (line.startsWith('##FASTA')) {
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break;
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}
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continue;
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}
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if (line.startsWith('>')) {
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break;
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}
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records.push({
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line,
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start: 0,
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end: 0,
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hasEscapes: line.includes('%'),
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});
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}
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const parents = attrs?.Parent;
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if (!ids && !parents) {
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items.push([featureLine]);
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continue;
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}
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existing
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else {
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let feature;
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if (ids) {
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const id = ids[0];
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const existing = byId.get(id);
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if (existing) {
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// Multi-location continuation: share child_features/derived_features
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// with the first line so children remain visible across all lines
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// regardless of arrival order.
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featureLine.child_features = existing[0].child_features;
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featureLine.derived_features = existing[0].derived_features;
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existing.push(featureLine);
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feature = existing;
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}
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else {
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feature = [featureLine];
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if (!parents) {
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items.push(feature);
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}
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byId.set(id, feature);
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const waiting = orphans.get(id);
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if (waiting) {
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for (const w of waiting) {
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featureLine.child_features.push(w);
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}
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orphans.delete(id);
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}
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orphans.delete(id);
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}
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}
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else {
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feature = [featureLine];
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}
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if (parents) {
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for (const parentId of parents) {
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const parent = byId.get(parentId);
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if (parent) {
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// child_features is shared across all parent feature lines,
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// so push once via the first line.
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parent[0].child_features.push(feature);
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}
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else {
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let arr = orphans.get(parentId);
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arr = [];
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orphans.set(parentId, arr);
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}
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arr.push(feature);
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}
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arr.push(feature);
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}
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}
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}
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if (record.lineHash !== undefined) {
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feature._lineHash = String(record.lineHash);
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}
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// attribute parsing collapses single-element arrays to scalars, so id can
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// be string | string[]; defensively take the first if multi-valued.
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const rawId = feature.id;
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const id = Array.isArray(rawId) ? rawId[0] : rawId;
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const parent = feature.parent;
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if (!id && !parent) {
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items.push(feature);
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continue;
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}
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if (id) {
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if (!existing) {
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else if (!id || !byId.has(id)) {
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if (id) {
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items.push(feature);
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}
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orphans.delete(id);
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}
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}
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if (parent) {
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const parents = Array.isArray(parent) ? parent : [parent];
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for (const parentId of parents) {
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const parentFeature = byId.get(parentId);
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if (parentFeature) {
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parentFeature.subfeatures.push(feature);
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}
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else {
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let arr = orphans.get(parentId);
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arr = [];
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orphans.set(parentId, arr);
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}
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arr.push(feature);
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arr.push(feature);
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}
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}
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package/dist/api.js.map
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{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":";;
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|
+
{"version":3,"file":"api.js","sourceRoot":"","sources":["../src/api.ts"],"names":[],"mappings":";;AA8BA,0CAEC;AAQD,wDAEC;AA2BD,oCA6EC;AASD,kDAyDC;AApND,uCAKkB;AAkBlB;;;;;;GAMG;AACH,SAAgB,eAAe,CAAC,GAAW;IACzC,OAAO,YAAY,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAA;AAC3C,CAAC;AAED;;;;;GAKG;AACH,SAAgB,sBAAsB,CAAC,GAAW;IAChD,OAAO,mBAAmB,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAA;AAClD,CAAC;AAED,SAAS,eAAe,CAAC,GAAW;IAClC,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IAChC,MAAM,OAAO,GAAiB,EAAE,CAAA;IAChC,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,IAAI,CAAC,UAAU,CAAC,SAAS,CAAC,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YACvD,MAAK;QACP,CAAC;QACD,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC9C,SAAQ;QACV,CAAC;QACD,OAAO,CAAC,IAAI,CAAC;YACX,IAAI;YACJ,UAAU,EAAE,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC;SAC/B,CAAC,CAAA;IACJ,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,YAAY,CAAC,OAAqB;IAChD,MAAM,KAAK,GAAkB,EAAE,CAAA;IAC/B,MAAM,IAAI,GAAG,IAAI,GAAG,EAAuB,CAAA;IAC3C,MAAM,OAAO,GAAG,IAAI,GAAG,EAAyB,CAAA;IAEhD,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,WAAW,GAAG,CAClB,MAAM,CAAC,UAAU;YACf,CAAC,CAAC,IAAA,sBAAY,EAAC,MAAM,CAAC,IAAI,CAAC;YAC3B,CAAC,CAAC,IAAA,gCAAsB,EAAC,MAAM,CAAC,IAAI,CAAC,CACb,CAAA;QAC5B,WAAW,CAAC,cAAc,GAAG,EAAE,CAAA;QAC/B,WAAW,CAAC,gBAAgB,GAAG,EAAE,CAAA;QAEjC,IAAI,MAAM,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YAClC,WAAW,CAAC,UAAU,KAAK,EAAE,CAAA;YAC7B,WAAW,CAAC,UAAU,CAAC,SAAS,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,CAAA;QAC9D,CAAC;QAED,MAAM,KAAK,GAAG,WAAW,CAAC,UAAU,CAAA;QACpC,MAAM,GAAG,GAAG,KAAK,EAAE,EAAE,CAAA;QACrB,MAAM,OAAO,GAAG,KAAK,EAAE,MAAM,CAAA;QAE7B,IAAI,CAAC,GAAG,IAAI,CAAC,OAAO,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,CAAC,CAAA;QAC3B,CAAC;aAAM,CAAC;YACN,IAAI,OAAoB,CAAA;YACxB,IAAI,GAAG,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG,GAAG,CAAC,CAAC,CAAE,CAAA;gBAClB,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;gBAC7B,IAAI,QAAQ,EAAE,CAAC;oBACb,qEAAqE;oBACrE,kEAAkE;oBAClE,+BAA+B;oBAC/B,WAAW,CAAC,cAAc,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,cAAc,CAAA;oBACxD,WAAW,CAAC,gBAAgB,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,gBAAgB,CAAA;oBAC5D,QAAQ,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;oBAC1B,OAAO,GAAG,QAAQ,CAAA;gBACpB,CAAC;qBAAM,CAAC;oBACN,OAAO,GAAG,CAAC,WAAW,CAAC,CAAA;oBACvB,IAAI,CAAC,OAAO,EAAE,CAAC;wBACb,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;oBACrB,CAAC;oBACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;oBACrB,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;oBAC/B,IAAI,OAAO,EAAE,CAAC;wBACZ,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;4BACxB,WAAW,CAAC,cAAc,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;wBACpC,CAAC;wBACD,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;oBACpB,CAAC;gBACH,CAAC;YACH,CAAC;iBAAM,CAAC;gBACN,OAAO,GAAG,CAAC,WAAW,CAAC,CAAA;YACzB,CAAC;YAED,IAAI,OAAO,EAAE,CAAC;gBACZ,KAAK,MAAM,QAAQ,IAAI,OAAO,EAAE,CAAC;oBAC/B,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;oBACjC,IAAI,MAAM,EAAE,CAAC;wBACX,4DAA4D;wBAC5D,mCAAmC;wBACnC,MAAM,CAAC,CAAC,CAAE,CAAC,cAAc,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;oBACzC,CAAC;yBAAM,CAAC;wBACN,IAAI,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;wBAC/B,IAAI,CAAC,GAAG,EAAE,CAAC;4BACT,GAAG,GAAG,EAAE,CAAA;4BACR,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;wBAC5B,CAAC;wBACD,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;oBACnB,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAA;AACd,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,mBAAmB,CAAC,OAAqB;IACvD,MAAM,KAAK,GAAqB,EAAE,CAAA;IAClC,MAAM,IAAI,GAAG,IAAI,GAAG,EAA0B,CAAA;IAC9C,MAAM,OAAO,GAAG,IAAI,GAAG,EAA4B,CAAA;IAEnD,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;QAC7B,MAAM,OAAO,GAAG,MAAM,CAAC,UAAU;YAC/B,CAAC,CAAC,IAAA,6BAAmB,EAAC,MAAM,CAAC,IAAI,CAAC;YAClC,CAAC,CAAC,IAAA,uCAA6B,EAAC,MAAM,CAAC,IAAI,CAAC,CAAA;QAE9C,IAAI,MAAM,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;YAClC,OAAO,CAAC,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;QAC7C,CAAC;QAED,0EAA0E;QAC1E,oEAAoE;QACpE,MAAM,KAAK,GAAG,OAAO,CAAC,EAAmC,CAAA;QACzD,MAAM,EAAE,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;QAClD,MAAM,MAAM,GAAG,OAAO,CAAC,MAAuC,CAAA;QAE9D,IAAI,CAAC,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC;YACnB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;QACrB,CAAC;aAAM,IAAI,CAAC,EAAE,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;YAChC,IAAI,EAAE,EAAE,CAAC;gBACP,IAAI,CAAC,MAAM,EAAE,CAAC;oBACZ,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBACrB,CAAC;gBACD,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,OAAO,CAAC,CAAA;gBACrB,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;gBAC/B,IAAI,OAAO,EAAE,CAAC;oBACZ,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;wBACxB,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBAC7B,CAAC;oBACD,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;gBACpB,CAAC;YACH,CAAC;YAED,IAAI,MAAM,EAAE,CAAC;gBACX,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAA;gBACzD,KAAK,MAAM,QAAQ,IAAI,OAAO,EAAE,CAAC;oBAC/B,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;oBACxC,IAAI,aAAa,EAAE,CAAC;wBAClB,aAAa,CAAC,WAAW,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;oBACzC,CAAC;yBAAM,CAAC;wBACN,IAAI,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAA;wBAC/B,IAAI,CAAC,GAAG,EAAE,CAAC;4BACT,GAAG,GAAG,EAAE,CAAA;4BACR,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAA;wBAC5B,CAAC;wBACD,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;oBACnB,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAA;AACd,CAAC"}
|
package/dist/util.d.ts
CHANGED
|
@@ -35,21 +35,6 @@ export declare function parseFeature(line: string): GFF3FeatureLine;
|
|
|
35
35
|
* @returns The parsed feature
|
|
36
36
|
*/
|
|
37
37
|
export declare function parseFeatureNoUnescape(line: string): GFF3FeatureLine;
|
|
38
|
-
/**
|
|
39
|
-
* Parse a GFF3 feature from a pre-split fields array
|
|
40
|
-
*
|
|
41
|
-
* @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
|
|
42
|
-
* @returns The parsed feature
|
|
43
|
-
*/
|
|
44
|
-
export declare function parseFieldsArray(f: (string | null | undefined)[]): GFF3FeatureLine;
|
|
45
|
-
/**
|
|
46
|
-
* Parse a GFF3 feature from a pre-split fields array without unescaping.
|
|
47
|
-
* Fast path for data known to contain no escaped characters.
|
|
48
|
-
*
|
|
49
|
-
* @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
|
|
50
|
-
* @returns The parsed feature
|
|
51
|
-
*/
|
|
52
|
-
export declare function parseFieldsArrayNoUnescape(f: (string | null | undefined)[]): GFF3FeatureLine;
|
|
53
38
|
/**
|
|
54
39
|
* Parse a GFF3 directive line.
|
|
55
40
|
*
|
package/dist/util.js
CHANGED
|
@@ -7,15 +7,12 @@ exports.parseAttributes = parseAttributes;
|
|
|
7
7
|
exports.parseAttributesNoUnescape = parseAttributesNoUnescape;
|
|
8
8
|
exports.parseFeature = parseFeature;
|
|
9
9
|
exports.parseFeatureNoUnescape = parseFeatureNoUnescape;
|
|
10
|
-
exports.parseFieldsArray = parseFieldsArray;
|
|
11
|
-
exports.parseFieldsArrayNoUnescape = parseFieldsArrayNoUnescape;
|
|
12
10
|
exports.parseDirective = parseDirective;
|
|
13
11
|
exports.parseAttributesJBrowse = parseAttributesJBrowse;
|
|
14
12
|
exports.parseAttributesJBrowseNoUnescape = parseAttributesJBrowseNoUnescape;
|
|
15
13
|
exports.parseFeatureJBrowse = parseFeatureJBrowse;
|
|
16
14
|
exports.parseFeatureJBrowseNoUnescape = parseFeatureJBrowseNoUnescape;
|
|
17
15
|
const directiveRegex = /^\s*##\s*(\S+)\s*(.*)/;
|
|
18
|
-
const lineEndRegex = /\r?\n$/;
|
|
19
16
|
const whitespaceRegex = /\s+/;
|
|
20
17
|
const nonDigitRegex = /\D/g;
|
|
21
18
|
const HEX_LOOKUP = {};
|
|
@@ -120,30 +117,28 @@ function parseAttributes(attrString) {
|
|
|
120
117
|
function parseAttributesNoUnescape(attrString) {
|
|
121
118
|
return parseAttributesImpl(attrString, false);
|
|
122
119
|
}
|
|
123
|
-
function
|
|
124
|
-
|
|
125
|
-
|
|
126
|
-
|
|
127
|
-
return shouldUnescape ? unescape(s) : s;
|
|
120
|
+
function isEmpty(s) {
|
|
121
|
+
return s.length === 0 || s === '.';
|
|
122
|
+
}
|
|
123
|
+
function strField(s, shouldUnescape, empty) {
|
|
124
|
+
return isEmpty(s) ? empty : shouldUnescape ? unescape(s) : s;
|
|
125
|
+
}
|
|
126
|
+
function numField(s) {
|
|
127
|
+
return isEmpty(s) ? null : +s;
|
|
128
128
|
}
|
|
129
129
|
function parseFeatureImpl(line, shouldUnescape) {
|
|
130
130
|
const f = line.split('\t');
|
|
131
|
-
const startStr = f[3];
|
|
132
|
-
const endStr = f[4];
|
|
133
|
-
const scoreStr = f[5];
|
|
134
|
-
const strand = f[6];
|
|
135
|
-
const phase = f[7];
|
|
136
131
|
const attrString = f[8];
|
|
137
132
|
return {
|
|
138
|
-
seq_id:
|
|
139
|
-
source:
|
|
140
|
-
type:
|
|
141
|
-
start:
|
|
142
|
-
end:
|
|
143
|
-
score:
|
|
144
|
-
strand:
|
|
145
|
-
phase:
|
|
146
|
-
attributes: attrString
|
|
133
|
+
seq_id: strField(f[0], shouldUnescape, null),
|
|
134
|
+
source: strField(f[1], shouldUnescape, null),
|
|
135
|
+
type: strField(f[2], shouldUnescape, null),
|
|
136
|
+
start: numField(f[3]),
|
|
137
|
+
end: numField(f[4]),
|
|
138
|
+
score: numField(f[5]),
|
|
139
|
+
strand: strField(f[6], false, null),
|
|
140
|
+
phase: strField(f[7], false, null),
|
|
141
|
+
attributes: isEmpty(attrString)
|
|
147
142
|
? null
|
|
148
143
|
: parseAttributesImpl(attrString, shouldUnescape),
|
|
149
144
|
};
|
|
@@ -167,49 +162,6 @@ function parseFeature(line) {
|
|
|
167
162
|
function parseFeatureNoUnescape(line) {
|
|
168
163
|
return parseFeatureImpl(line, false);
|
|
169
164
|
}
|
|
170
|
-
function parseFieldsArrayImpl(f, shouldUnescape) {
|
|
171
|
-
const seq_id = f[0];
|
|
172
|
-
const source = f[1];
|
|
173
|
-
const type = f[2];
|
|
174
|
-
const startStr = f[3];
|
|
175
|
-
const endStr = f[4];
|
|
176
|
-
const scoreStr = f[5];
|
|
177
|
-
const strand = f[6];
|
|
178
|
-
const phase = f[7];
|
|
179
|
-
const attrString = f[8];
|
|
180
|
-
return {
|
|
181
|
-
seq_id: seq_id ? normImpl(seq_id, shouldUnescape) : null,
|
|
182
|
-
source: source ? normImpl(source, shouldUnescape) : null,
|
|
183
|
-
type: type ? normImpl(type, shouldUnescape) : null,
|
|
184
|
-
start: !startStr || startStr === '.' ? null : +startStr,
|
|
185
|
-
end: !endStr || endStr === '.' ? null : +endStr,
|
|
186
|
-
score: !scoreStr || scoreStr === '.' ? null : +scoreStr,
|
|
187
|
-
strand: strand && strand !== '.' ? strand : null,
|
|
188
|
-
phase: phase && phase !== '.' ? phase : null,
|
|
189
|
-
attributes: !attrString || attrString === '.'
|
|
190
|
-
? null
|
|
191
|
-
: parseAttributesImpl(attrString, shouldUnescape),
|
|
192
|
-
};
|
|
193
|
-
}
|
|
194
|
-
/**
|
|
195
|
-
* Parse a GFF3 feature from a pre-split fields array
|
|
196
|
-
*
|
|
197
|
-
* @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
|
|
198
|
-
* @returns The parsed feature
|
|
199
|
-
*/
|
|
200
|
-
function parseFieldsArray(f) {
|
|
201
|
-
return parseFieldsArrayImpl(f, true);
|
|
202
|
-
}
|
|
203
|
-
/**
|
|
204
|
-
* Parse a GFF3 feature from a pre-split fields array without unescaping.
|
|
205
|
-
* Fast path for data known to contain no escaped characters.
|
|
206
|
-
*
|
|
207
|
-
* @param f - Array of 9 GFF3 column values (use null or '.' for empty values)
|
|
208
|
-
* @returns The parsed feature
|
|
209
|
-
*/
|
|
210
|
-
function parseFieldsArrayNoUnescape(f) {
|
|
211
|
-
return parseFieldsArrayImpl(f, false);
|
|
212
|
-
}
|
|
213
165
|
/**
|
|
214
166
|
* Parse a GFF3 directive line.
|
|
215
167
|
*
|
|
@@ -221,12 +173,11 @@ function parseDirective(line) {
|
|
|
221
173
|
if (!match) {
|
|
222
174
|
return null;
|
|
223
175
|
}
|
|
224
|
-
const
|
|
225
|
-
|
|
176
|
+
const name = match[1];
|
|
177
|
+
const contents = match[2];
|
|
226
178
|
const parsed = { directive: name };
|
|
227
179
|
if (contents.length) {
|
|
228
|
-
|
|
229
|
-
parsed.value = contents;
|
|
180
|
+
parsed.value = contents.trimEnd();
|
|
230
181
|
}
|
|
231
182
|
if (name === 'sequence-region') {
|
|
232
183
|
const c = contents.split(whitespaceRegex, 3);
|
|
@@ -300,10 +251,6 @@ function parseAttributesJBrowseImpl(attrString, result, shouldUnescape) {
|
|
|
300
251
|
const eqIdx = attrString.indexOf('=', start);
|
|
301
252
|
if (eqIdx !== -1 && eqIdx < semiIdx && eqIdx + 1 < semiIdx) {
|
|
302
253
|
const tag = attrString.slice(start, eqIdx);
|
|
303
|
-
if (tag === '_lineHash') {
|
|
304
|
-
start = semiIdx + 1;
|
|
305
|
-
continue;
|
|
306
|
-
}
|
|
307
254
|
let key = COMMON_ATTRS[tag];
|
|
308
255
|
if (key === undefined) {
|
|
309
256
|
key = tag.toLowerCase();
|
|
@@ -336,38 +283,27 @@ function parseAttributesJBrowse(attrString, result) {
|
|
|
336
283
|
function parseAttributesJBrowseNoUnescape(attrString, result) {
|
|
337
284
|
parseAttributesJBrowseImpl(attrString, result, false);
|
|
338
285
|
}
|
|
286
|
+
const STRAND_MAP = {
|
|
287
|
+
'+': 1,
|
|
288
|
+
'-': -1,
|
|
289
|
+
'.': 0,
|
|
290
|
+
};
|
|
339
291
|
function parseFeatureJBrowseImpl(line, shouldUnescape) {
|
|
340
292
|
const f = line.split('\t');
|
|
341
|
-
const seq_id = f[0];
|
|
342
|
-
const source = f[1];
|
|
343
|
-
const type = f[2];
|
|
344
293
|
const startStr = f[3];
|
|
345
294
|
const endStr = f[4];
|
|
346
295
|
const scoreStr = f[5];
|
|
347
|
-
const strand = f[6];
|
|
348
296
|
const phase = f[7];
|
|
349
297
|
const attrString = f[8];
|
|
350
298
|
const result = {
|
|
351
|
-
refName:
|
|
352
|
-
|
|
353
|
-
|
|
354
|
-
|
|
355
|
-
|
|
356
|
-
|
|
357
|
-
|
|
358
|
-
|
|
359
|
-
? unescape(source)
|
|
360
|
-
: source,
|
|
361
|
-
type: type.length === 0 || type === '.'
|
|
362
|
-
? null
|
|
363
|
-
: shouldUnescape
|
|
364
|
-
? unescape(type)
|
|
365
|
-
: type,
|
|
366
|
-
start: startStr.length === 0 || startStr === '.' ? 0 : +startStr - 1,
|
|
367
|
-
end: endStr.length === 0 || endStr === '.' ? 0 : +endStr,
|
|
368
|
-
score: scoreStr.length === 0 || scoreStr === '.' ? undefined : +scoreStr,
|
|
369
|
-
strand: strand === '+' ? 1 : strand === '-' ? -1 : strand === '.' ? 0 : undefined,
|
|
370
|
-
phase: phase.length === 0 || phase === '.' ? undefined : +phase,
|
|
299
|
+
refName: strField(f[0], shouldUnescape, ''),
|
|
300
|
+
source: strField(f[1], shouldUnescape, null),
|
|
301
|
+
type: strField(f[2], shouldUnescape, null),
|
|
302
|
+
start: isEmpty(startStr) ? 0 : +startStr - 1,
|
|
303
|
+
end: isEmpty(endStr) ? 0 : +endStr,
|
|
304
|
+
score: isEmpty(scoreStr) ? undefined : +scoreStr,
|
|
305
|
+
strand: STRAND_MAP[f[6]],
|
|
306
|
+
phase: isEmpty(phase) ? undefined : +phase,
|
|
371
307
|
subfeatures: [],
|
|
372
308
|
};
|
|
373
309
|
parseAttributesJBrowseImpl(attrString, result, shouldUnescape);
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";AAAA,6DAA6D;AAC7D,qEAAqE;;AAoBrE,4BA4BC;AA4DD,0CAEC;AASD,8DAEC;AA6CD,oCAEC;AASD,wDAEC;AAQD,wCAsCC;AAoMD,wDAKC;AAED,4EAKC;AAmCD,kDAEC;AAED,sEAEC;AAxdD,MAAM,cAAc,GAAG,uBAAuB,CAAA;AAC9C,MAAM,eAAe,GAAG,KAAK,CAAA;AAC7B,MAAM,aAAa,GAAG,KAAK,CAAA;AAE3B,MAAM,UAAU,GAAuC,EAAE,CAAA;AACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;IAC7B,MAAM,GAAG,GAAG,CAAC,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;IACzD,UAAU,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;IACxC,UAAU,CAAC,GAAG,CAAC,WAAW,EAAE,CAAC,GAAG,MAAM,CAAC,YAAY,CAAC,CAAC,CAAC,CAAA;AACxD,CAAC;AAED;;;;;GAKG;AAEH,SAAgB,QAAQ,CAAC,SAAiB;IACxC,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;IAClC,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE,CAAC;QACf,OAAO,SAAS,CAAA;IAClB,CAAC;IAED,IAAI,MAAM,GAAG,EAAE,CAAA;IACf,IAAI,OAAO,GAAG,CAAC,CAAA;IACf,IAAI,CAAC,GAAG,GAAG,CAAA;IAEX,OAAO,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC;QAC5B,IAAI,SAAS,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC;YACrD,MAAM,IAAI,SAAS,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,CAAA;YACrC,MAAM,GAAG,GAAG,SAAS,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;YACzC,MAAM,IAAI,GAAG,UAAU,CAAC,GAAG,CAAC,CAAA;YAC5B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,MAAM,IAAI,IAAI,CAAA;YAChB,CAAC;iBAAM,CAAC;gBACN,MAAM,IAAI,SAAS,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAA;YACrC,CAAC;YACD,CAAC,IAAI,CAAC,CAAA;YACN,OAAO,GAAG,CAAC,CAAA;QACb,CAAC;aAAM,CAAC;YACN,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IAED,OAAO,MAAM,GAAG,SAAS,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;AAC1C,CAAC;AAED,SAAS,mBAAmB,CAC1B,UAAkB,EAClB,cAAuB;IAEvB,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,IAAI,UAAU,KAAK,GAAG,EAAE,CAAC;QAClD,OAAO,EAAE,CAAA;IACX,CAAC;IAED,MAAM,KAAK,GAAmB,EAAE,CAAA;IAChC,IAAI,GAAG,GAAG,UAAU,CAAC,MAAM,CAAA;IAE3B,IAAI,UAAU,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC;QACjC,GAAG,GAAG,UAAU,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAA;QACtD,UAAU,GAAG,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;IACvC,CAAC;IAED,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,OAAO,KAAK,GAAG,GAAG,EAAE,CAAC;QACnB,IAAI,OAAO,GAAG,UAAU,CAAC,OAAO,CAAC,GAAG,EAAE,KAAK,CAAC,CAAA;QAC5C,IAAI,OAAO,KAAK,CAAC,CAAC,EAAE,CAAC;YACnB,OAAO,GAAG,GAAG,CAAA;QACf,CAAC;QAED,IAAI,OAAO,GAAG,KAAK,EAAE,CAAC;YACpB,MAAM,KAAK,GAAG,UAAU,CAAC,OAAO,CAAC,GAAG,EAAE,KAAK,CAAC,CAAA;YAC5C,IAAI,KAAK,KAAK,CAAC,CAAC,IAAI,KAAK,GAAG,OAAO,IAAI,KAAK,GAAG,CAAC,GAAG,OAAO,EAAE,CAAC;gBAC3D,MAAM,GAAG,GAAG,UAAU,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;gBAC1C,IAAI,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;gBACrB,IAAI,CAAC,IAAI,EAAE,CAAC;oBACV,IAAI,GAAG,EAAE,CAAA;oBACT,KAAK,CAAC,GAAG,CAAC,GAAG,IAAI,CAAA;gBACnB,CAAC;gBAED,IAAI,QAAQ,GAAG,KAAK,GAAG,CAAC,CAAA;gBACxB,OAAO,QAAQ,GAAG,OAAO,EAAE,CAAC;oBAC1B,IAAI,QAAQ,GAAG,UAAU,CAAC,OAAO,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;oBAChD,IAAI,QAAQ,KAAK,CAAC,CAAC,IAAI,QAAQ,GAAG,OAAO,EAAE,CAAC;wBAC1C,QAAQ,GAAG,OAAO,CAAA;oBACpB,CAAC;oBACD,IAAI,QAAQ,GAAG,QAAQ,EAAE,CAAC;wBACxB,MAAM,GAAG,GAAG,UAAU,CAAC,KAAK,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAA;wBAChD,IAAI,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;oBACjD,CAAC;oBACD,QAAQ,GAAG,QAAQ,GAAG,CAAC,CAAA;gBACzB,CAAC;YACH,CAAC;QACH,CAAC;QACD,KAAK,GAAG,OAAO,GAAG,CAAC,CAAA;IACrB,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC;AAED;;;;;GAKG;AACH,SAAgB,eAAe,CAAC,UAAkB;IAChD,OAAO,mBAAmB,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;AAC9C,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,yBAAyB,CAAC,UAAkB;IAC1D,OAAO,mBAAmB,CAAC,UAAU,EAAE,KAAK,CAAC,CAAA;AAC/C,CAAC;AAED,SAAS,OAAO,CAAC,CAAS;IACxB,OAAO,CAAC,CAAC,MAAM,KAAK,CAAC,IAAI,CAAC,KAAK,GAAG,CAAA;AACpC,CAAC;AAED,SAAS,QAAQ,CACf,CAAS,EACT,cAAuB,EACvB,KAAQ;IAER,OAAO,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAC9D,CAAC;AAED,SAAS,QAAQ,CAAC,CAAS;IACzB,OAAO,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAC/B,CAAC;AAED,SAAS,gBAAgB,CACvB,IAAY,EACZ,cAAuB;IAEvB,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC1B,MAAM,UAAU,GAAG,CAAC,CAAC,CAAC,CAAE,CAAA;IACxB,OAAO;QACL,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAE,EAAE,cAAc,EAAE,IAAI,CAAC;QAC7C,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAE,EAAE,cAAc,EAAE,IAAI,CAAC;QAC7C,IAAI,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAE,EAAE,cAAc,EAAE,IAAI,CAAC;QAC3C,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC;QACtB,GAAG,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC;QACpB,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAE,CAAC;QACtB,MAAM,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAE,EAAE,KAAK,EAAE,IAAI,CAAC;QACpC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAE,EAAE,KAAK,EAAE,IAAI,CAAC;QACnC,UAAU,EAAE,OAAO,CAAC,UAAU,CAAC;YAC7B,CAAC,CAAC,IAAI;YACN,CAAC,CAAC,mBAAmB,CAAC,UAAU,EAAE,cAAc,CAAC;KACpD,CAAA;AACH,CAAC;AAED;;;;;GAKG;AACH,SAAgB,YAAY,CAAC,IAAY;IACvC,OAAO,gBAAgB,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;AACrC,CAAC;AAED;;;;;;GAMG;AACH,SAAgB,sBAAsB,CAAC,IAAY;IACjD,OAAO,gBAAgB,CAAC,IAAI,EAAE,KAAK,CAAC,CAAA;AACtC,CAAC;AAED;;;;;GAKG;AACH,SAAgB,cAAc,CAC5B,IAAY;IAMZ,MAAM,KAAK,GAAG,cAAc,CAAC,IAAI,CA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|
package/esm/api.d.ts
CHANGED
|
@@ -2,8 +2,10 @@ import type { GFF3Feature, JBrowseFeature } from './util.ts';
|
|
|
2
2
|
export interface LineRecord {
|
|
3
3
|
line: string;
|
|
4
4
|
lineHash?: string | number;
|
|
5
|
-
|
|
6
|
-
|
|
5
|
+
/** Optional passthrough byte offsets — not used by the parser */
|
|
6
|
+
start?: number;
|
|
7
|
+
/** Optional passthrough byte offsets — not used by the parser */
|
|
8
|
+
end?: number;
|
|
7
9
|
hasEscapes: boolean;
|
|
8
10
|
}
|
|
9
11
|
/**
|