@jbrowse/plugin-gtf 1.7.10 → 2.0.1

package/esm/util.js

@@ -0,0 +1,62 @@
+export function featureData(data) {
+    const f = { ...data };
+    f.start -= 1; // convert to interbase
+    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand]; // convert strand
+    f.phase = Number(data.frame);
+    f.refName = data.seq_name;
+    if (data.score === null) {
+        delete f.score;
+    }
+    if (data.frame === null) {
+        delete f.score;
+    }
+    const defaultFields = [
+        'start',
+        'end',
+        'seq_name',
+        'score',
+        'featureType',
+        'source',
+        'frame',
+        'strand',
+    ];
+    Object.keys(data.attributes).forEach(a => {
+        let b = a.toLowerCase();
+        if (defaultFields.includes(b)) {
+            // add "suffix" to tag name if it already exists
+            // reproduces behavior of NCList
+            b += '2';
+        }
+        if (data.attributes[a] !== null) {
+            let attr = data.attributes[a];
+            if (Array.isArray(attr) && attr.length === 1) {
+                // gtf uses double quotes for text values in the attributes column, remove them
+                const formattedAttr = attr[0].replace(/^"|"$/g, '');
+                attr = formattedAttr;
+            }
+            f[b] = attr;
+        }
+    });
+    f.refName = f.seq_name;
+    f.type = f.featureType;
+    // the SimpleFeature constructor takes care of recursively inflating subfeatures
+    if (data.child_features && data.child_features.length) {
+        f.subfeatures = data.child_features
+            .map(childLocs => childLocs.map(childLoc => featureData(childLoc)))
+            .flat();
+    }
+    delete f.child_features;
+    delete f.data;
+    delete f.derived_features;
+    // eslint-disable-next-line no-underscore-dangle
+    delete f._linehash;
+    delete f.attributes;
+    delete f.seq_name;
+    delete f.featureType;
+    delete f.frame;
+    if (f.transcript_id) {
+        f.name = f.transcript_id;
+    }
+    return f;
+}
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "1.7.10",
+  "version": "2.0.1",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -20,17 +20,21 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src"
+    "src",
+    "esm"
   ],
   "scripts": {
-    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/gtf --passWithNoTests",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
-    "postbuild": "tsc --build tsconfig.build.json"
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
     "@babel/runtime": "^7.17.9",
@@ -39,11 +43,12 @@
     "@gmod/gtf": "^0.0.6"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^1.0.0",
-    "@jbrowse/plugin-linear-genome-view": "^1.0.0",
-    "@material-ui/core": "^4.12.2",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "3.14.1",
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@mui/material": "^5.0.0",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "prop-types": "^15.0.0",
     "react": ">=16.8.0",
     "rxjs": "^6.0.0"
@@ -51,5 +56,8 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "02d8c1e88e5603ea5855faed4ccb814e28071b32"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "ed935bf5612af3818abdc8ef52d100d5d81d33a2"
 }

package/src/GtfAdapter/GtfAdapter.ts

@@ -23,11 +23,9 @@ export default class extends BaseFeatureDataAdapter {
     [key: string]: Promise<IntervalTree | undefined> | undefined
   } = {}
 
-  private async loadDataP() {
-    const buffer = await openLocation(
-      this.getConf('gtfLocation'),
-      this.pluginManager,
-    ).readFile()
+  private async loadDataP(opts: BaseOptions = {}) {
+    const gtfLoc = this.getConf('gtfLocation')
+    const buffer = await openLocation(gtfLoc, this.pluginManager).readFile(opts)
 
     const buf = isGzip(buffer) ? await unzip(buffer) : buffer
     // 512MB  max chrome string length is 512MB
@@ -39,7 +37,12 @@ export default class extends BaseFeatureDataAdapter {
     const lines = data.split('\n').filter(f => !!f && !f.startsWith('#'))
     const feats = {} as { [key: string]: string[] }
     for (let i = 0; i < lines.length; i++) {
-      const refName = lines[i].split('\t')[0]
+      const line = lines[i]
+      if (line.startsWith('#')) {
+        continue
+      }
+      const tab = line.indexOf('\t')
+      const refName = line.slice(0, tab)
       if (!feats[refName]) {
         feats[refName] = []
       }
@@ -49,9 +52,9 @@ export default class extends BaseFeatureDataAdapter {
     return { feats }
   }
 
-  private async loadData() {
+  private async loadData(opts: BaseOptions = {}) {
     if (!this.gtfFeatures) {
-      this.gtfFeatures = this.loadDataP().catch(e => {
+      this.gtfFeatures = this.loadDataP(opts).catch(e => {
         this.gtfFeatures = undefined
         throw e
       })
@@ -61,7 +64,7 @@ export default class extends BaseFeatureDataAdapter {
   }
 
   public async getRefNames(opts: BaseOptions = {}) {
-    const { feats } = await this.loadData()
+    const { feats } = await this.loadData(opts)
     return Object.keys(feats)
   }
 
@@ -83,7 +86,7 @@ export default class extends BaseFeatureDataAdapter {
       (f, i) =>
         new SimpleFeature({
           data: featureData(f),
-          id: `${this.id}-offset-${i}`,
+          id: `${this.id}-${refName}-${i}`,
         }),
     )