@jbrowse/plugin-gff3 2.15.0 → 2.15.2

package/dist/Gff3Adapter/Gff3Adapter.js

@@ -9,7 +9,7 @@ const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-const gff_1 = __importDefault(require("@gmod/gff"));
+const gff_nostream_1 = require("gff-nostream");
 const util_1 = require("@jbrowse/core/util");
 const featureData_1 = require("../featureData");
 class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -60,14 +60,7 @@ class Gff3Adapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 if (!this.calculatedIntervalTreeMap[refName]) {
                     sc === null || sc === void 0 ? void 0 : sc('Parsing GFF data');
                     const intervalTree = new interval_tree_1.default();
-                    gff_1.default
-                        .parseStringSync(lines, {
-                        parseFeatures: true,
-                        parseComments: false,
-                        parseDirectives: false,
-                        parseSequences: false,
-                        disableDerivesFromReferences: true,
-                    })
+                    (0, gff_nostream_1.parseStringSync)(lines)
                         .flat()
                         .map((f, i) => new simpleFeature_1.default({
                         data: (0, featureData_1.featureData)(f),

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.d.ts

@@ -14,6 +14,5 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     private getFeaturesHelper;
     private parseLine;
-    private formatFeatures;
     freeResources(): void;
 }

package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -9,7 +9,7 @@ const io_1 = require("@jbrowse/core/util/io");
 const rxjs_1 = require("@jbrowse/core/util/rxjs");
 const simpleFeature_1 = __importDefault(require("@jbrowse/core/util/simpleFeature"));
 const tabix_1 = require("@gmod/tabix");
-const gff_1 = __importDefault(require("@gmod/gff"));
+const gff_nostream_1 = require("gff-nostream");
 const configuration_1 = require("@jbrowse/core/configuration");
 const featureData_1 = require("../featureData");
 class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
@@ -45,6 +45,7 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         }, opts.signal);
     }
     async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
+        var _a, _b;
         try {
             const lines = [];
             await this.gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
@@ -53,7 +54,7 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             if (allowRedispatch && lines.length) {
                 let minStart = Number.POSITIVE_INFINITY;
                 let maxEnd = Number.NEGATIVE_INFINITY;
-                lines.forEach(line => {
+                for (const line of lines) {
                     const featureType = line.fields[2];
                     // only expand redispatch range if feature is not a "dontRedispatch"
                     // type skips large regions like chromosome,region
@@ -66,7 +67,7 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                             maxEnd = line.end;
                         }
                     }
-                });
+                }
                 if (maxEnd > query.end || minStart < query.start) {
                     // make a new feature callback to only return top-level features
                     // in the original query range
@@ -75,7 +76,7 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 }
             }
             const gff3 = lines
-                .map((lineRecord) => {
+                .map(lineRecord => {
                 if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
                     if (!lineRecord.fields[8].includes('_lineHash')) {
                         lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`;
@@ -87,20 +88,17 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 return lineRecord.fields.join('\t');
             })
                 .join('\n');
-            const features = gff_1.default.parseStringSync(gff3, {
-                parseFeatures: true,
-                parseComments: false,
-                parseDirectives: false,
-                parseSequences: false,
-                disableDerivesFromReferences: true,
-            });
-            features.forEach(featureLocs => {
-                this.formatFeatures(featureLocs).forEach(f => {
+            for (const featureLocs of (0, gff_nostream_1.parseStringSync)(gff3)) {
+                for (const featureLoc of featureLocs) {
+                    const f = new simpleFeature_1.default({
+                        data: (0, featureData_1.featureData)(featureLoc),
+                        id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
+                    });
                     if ((0, range_1.doesIntersect2)(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
                         observer.next(f);
                     }
-                });
-            });
+                }
+            }
             observer.complete();
         }
         catch (e) {
@@ -117,15 +115,6 @@ class Gff3TabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             fields,
         };
     }
-    formatFeatures(featureLocs) {
-        return featureLocs.map(featureLoc => {
-            var _a, _b;
-            return new simpleFeature_1.default({
-                data: (0, featureData_1.featureData)(featureLoc),
-                id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
-            });
-        });
-    }
     freeResources( /* { region } */) { }
 }
 exports.default = Gff3TabixAdapter;

package/dist/featureData.d.ts

@@ -1,2 +1,16 @@
-import { GFF3FeatureLineWithRefs } from '@gmod/gff';
-export declare function featureData(data: GFF3FeatureLineWithRefs): Record<string, unknown>;
+import { GFF3FeatureLineWithRefs } from 'gff-nostream';
+interface GFF3Feature {
+    start: number;
+    end: number;
+    strand?: number;
+    type: string | null;
+    source: string | null;
+    refName: string;
+    derived_features: unknown[] | null;
+    phase?: number;
+    score?: number;
+    subfeatures: GFF3Feature[] | undefined;
+    [key: string]: unknown;
+}
+export declare function featureData(data: GFF3FeatureLineWithRefs): GFF3Feature;
+export {};

package/dist/featureData.js

@@ -2,24 +2,16 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.featureData = featureData;
 function featureData(data) {
-    const f = { ...data };
-    f.start -= 1; // convert to interbase
-    if (data.strand === '+') {
-        f.strand = 1;
+    const { end, start, child_features, derived_features, attributes, type, source, phase, seq_id, score, strand, } = data;
+    let strand2;
+    if (strand === '+') {
+        strand2 = 1;
     }
-    else if (data.strand === '-') {
-        f.strand = -1;
+    else if (strand === '-') {
+        strand2 = -1;
     }
-    else if (data.strand === '.') {
-        f.strand = 0;
-    }
-    else {
-        f.strand = undefined;
-    }
-    f.phase = data.phase === null ? undefined : Number(data.phase);
-    f.refName = data.seq_id;
-    if (data.score === null) {
-        f.score = undefined;
+    else if (strand === '.') {
+        strand2 = 0;
     }
     const defaultFields = new Set([
         'start',
@@ -31,7 +23,8 @@ function featureData(data) {
         'phase',
         'strand',
     ]);
-    const dataAttributes = data.attributes || {};
+    const dataAttributes = attributes || {};
+    const resultAttributes = {};
     for (const a of Object.keys(dataAttributes)) {
         let b = a.toLowerCase();
         if (defaultFields.has(b)) {
@@ -39,26 +32,26 @@ function featureData(data) {
             // reproduces behavior of NCList
             b += '2';
         }
-        if (dataAttributes[a]) {
+        if (dataAttributes[a] && a !== '_lineHash') {
             let attr = dataAttributes[a];
             if (Array.isArray(attr) && attr.length === 1) {
                 ;
                 [attr] = attr;
             }
-            f[b] = attr;
+            resultAttributes[b] = attr;
         }
     }
-    f.refName = f.seq_id;
-    // the SimpleFeature constructor takes care of recursively inflating
-    // subfeatures
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-    if (data.child_features && data.child_features.length > 0) {
-        f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc)));
-    }
-    f.child_features = undefined;
-    f.data = undefined;
-    // delete f.derived_features
-    f.attributes = undefined;
-    f.seq_id = undefined;
-    return f;
+    return {
+        ...resultAttributes,
+        start: start - 1,
+        end: end,
+        strand: strand2,
+        type,
+        source,
+        refName: seq_id,
+        derived_features,
+        phase: phase === null ? undefined : Number(phase),
+        score: score === null ? undefined : score,
+        subfeatures: child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc))),
+    };
 }

package/esm/Gff3Adapter/Gff3Adapter.js

@@ -4,7 +4,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import IntervalTree from '@flatten-js/interval-tree';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { unzip } from '@gmod/bgzf-filehandle';
-import gff from '@gmod/gff';
+import { parseStringSync } from 'gff-nostream';
 import { isGzip, updateStatus } from '@jbrowse/core/util';
 import { featureData } from '../featureData';
 export default class Gff3Adapter extends BaseFeatureDataAdapter {
@@ -55,14 +55,7 @@ export default class Gff3Adapter extends BaseFeatureDataAdapter {
                 if (!this.calculatedIntervalTreeMap[refName]) {
                     sc === null || sc === void 0 ? void 0 : sc('Parsing GFF data');
                     const intervalTree = new IntervalTree();
-                    gff
-                        .parseStringSync(lines, {
-                        parseFeatures: true,
-                        parseComments: false,
-                        parseDirectives: false,
-                        parseSequences: false,
-                        disableDerivesFromReferences: true,
-                    })
+                    parseStringSync(lines)
                         .flat()
                         .map((f, i) => new SimpleFeature({
                         data: featureData(f),

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.d.ts

@@ -14,6 +14,5 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
     getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     private getFeaturesHelper;
     private parseLine;
-    private formatFeatures;
     freeResources(): void;
 }

package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js

@@ -4,7 +4,7 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { TabixIndexedFile } from '@gmod/tabix';
-import gff from '@gmod/gff';
+import { parseStringSync } from 'gff-nostream';
 import { readConfObject, } from '@jbrowse/core/configuration';
 import { featureData } from '../featureData';
 export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
@@ -40,6 +40,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
         }, opts.signal);
     }
     async getFeaturesHelper(query, opts, metadata, observer, allowRedispatch, originalQuery = query) {
+        var _a, _b;
         try {
             const lines = [];
             await this.gff.getLines(query.refName, query.start, query.end, (line, fileOffset) => {
@@ -48,7 +49,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
             if (allowRedispatch && lines.length) {
                 let minStart = Number.POSITIVE_INFINITY;
                 let maxEnd = Number.NEGATIVE_INFINITY;
-                lines.forEach(line => {
+                for (const line of lines) {
                     const featureType = line.fields[2];
                     // only expand redispatch range if feature is not a "dontRedispatch"
                     // type skips large regions like chromosome,region
@@ -61,7 +62,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
                             maxEnd = line.end;
                         }
                     }
-                });
+                }
                 if (maxEnd > query.end || minStart < query.start) {
                     // make a new feature callback to only return top-level features
                     // in the original query range
@@ -70,7 +71,7 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
                 }
             }
             const gff3 = lines
-                .map((lineRecord) => {
+                .map(lineRecord => {
                 if (lineRecord.fields[8] && lineRecord.fields[8] !== '.') {
                     if (!lineRecord.fields[8].includes('_lineHash')) {
                         lineRecord.fields[8] += `;_lineHash=${lineRecord.lineHash}`;
@@ -82,20 +83,17 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
                 return lineRecord.fields.join('\t');
             })
                 .join('\n');
-            const features = gff.parseStringSync(gff3, {
-                parseFeatures: true,
-                parseComments: false,
-                parseDirectives: false,
-                parseSequences: false,
-                disableDerivesFromReferences: true,
-            });
-            features.forEach(featureLocs => {
-                this.formatFeatures(featureLocs).forEach(f => {
+            for (const featureLocs of parseStringSync(gff3)) {
+                for (const featureLoc of featureLocs) {
+                    const f = new SimpleFeature({
+                        data: featureData(featureLoc),
+                        id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
+                    });
                     if (doesIntersect2(f.get('start'), f.get('end'), originalQuery.start, originalQuery.end)) {
                         observer.next(f);
                     }
-                });
-            });
+                }
+            }
             observer.complete();
         }
         catch (e) {
@@ -112,14 +110,5 @@ export default class Gff3TabixAdapter extends BaseFeatureDataAdapter {
             fields,
         };
     }
-    formatFeatures(featureLocs) {
-        return featureLocs.map(featureLoc => {
-            var _a, _b;
-            return new SimpleFeature({
-                data: featureData(featureLoc),
-                id: `${this.id}-offset-${(_b = (_a = featureLoc.attributes) === null || _a === void 0 ? void 0 : _a._lineHash) === null || _b === void 0 ? void 0 : _b[0]}`,
-            });
-        });
-    }
     freeResources( /* { region } */) { }
 }

package/esm/featureData.d.ts

@@ -1,2 +1,16 @@
-import { GFF3FeatureLineWithRefs } from '@gmod/gff';
-export declare function featureData(data: GFF3FeatureLineWithRefs): Record<string, unknown>;
+import { GFF3FeatureLineWithRefs } from 'gff-nostream';
+interface GFF3Feature {
+    start: number;
+    end: number;
+    strand?: number;
+    type: string | null;
+    source: string | null;
+    refName: string;
+    derived_features: unknown[] | null;
+    phase?: number;
+    score?: number;
+    subfeatures: GFF3Feature[] | undefined;
+    [key: string]: unknown;
+}
+export declare function featureData(data: GFF3FeatureLineWithRefs): GFF3Feature;
+export {};

package/esm/featureData.js

@@ -1,22 +1,14 @@
 export function featureData(data) {
-    const f = { ...data };
-    f.start -= 1; // convert to interbase
-    if (data.strand === '+') {
-        f.strand = 1;
+    const { end, start, child_features, derived_features, attributes, type, source, phase, seq_id, score, strand, } = data;
+    let strand2;
+    if (strand === '+') {
+        strand2 = 1;
     }
-    else if (data.strand === '-') {
-        f.strand = -1;
+    else if (strand === '-') {
+        strand2 = -1;
     }
-    else if (data.strand === '.') {
-        f.strand = 0;
-    }
-    else {
-        f.strand = undefined;
-    }
-    f.phase = data.phase === null ? undefined : Number(data.phase);
-    f.refName = data.seq_id;
-    if (data.score === null) {
-        f.score = undefined;
+    else if (strand === '.') {
+        strand2 = 0;
     }
     const defaultFields = new Set([
         'start',
@@ -28,7 +20,8 @@ export function featureData(data) {
         'phase',
         'strand',
     ]);
-    const dataAttributes = data.attributes || {};
+    const dataAttributes = attributes || {};
+    const resultAttributes = {};
     for (const a of Object.keys(dataAttributes)) {
         let b = a.toLowerCase();
         if (defaultFields.has(b)) {
@@ -36,26 +29,26 @@ export function featureData(data) {
             // reproduces behavior of NCList
             b += '2';
         }
-        if (dataAttributes[a]) {
+        if (dataAttributes[a] && a !== '_lineHash') {
             let attr = dataAttributes[a];
             if (Array.isArray(attr) && attr.length === 1) {
                 ;
                 [attr] = attr;
             }
-            f[b] = attr;
+            resultAttributes[b] = attr;
         }
     }
-    f.refName = f.seq_id;
-    // the SimpleFeature constructor takes care of recursively inflating
-    // subfeatures
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
-    if (data.child_features && data.child_features.length > 0) {
-        f.subfeatures = data.child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc)));
-    }
-    f.child_features = undefined;
-    f.data = undefined;
-    // delete f.derived_features
-    f.attributes = undefined;
-    f.seq_id = undefined;
-    return f;
+    return {
+        ...resultAttributes,
+        start: start - 1,
+        end: end,
+        strand: strand2,
+        type,
+        source,
+        refName: seq_id,
+        derived_features,
+        phase: phase === null ? undefined : Number(phase),
+        score: score === null ? undefined : score,
+        subfeatures: child_features.flatMap(childLocs => childLocs.map(childLoc => featureData(childLoc))),
+    };
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "2.15.0",
+  "version": "2.15.2",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",
@@ -38,8 +38,8 @@
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
     "@gmod/bgzf-filehandle": "^1.4.3",
-    "@gmod/gff": "^1.3.0",
-    "@gmod/tabix": "^1.5.6"
+    "@gmod/tabix": "^1.5.6",
+    "gff-nostream": "^1.3.3"
   },
   "peerDependencies": {
     "@jbrowse/core": "^2.0.0",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "87eeb1fbf8311dbf88d5e75b5a265f03beffdda8"
+  "gitHead": "8a58cefbfe39af4c97bcb6ead354d72c9fef9224"
 }