@jbrowse/plugin-gtf 1.6.9 → 1.7.3

package/dist/util.js

@@ -0,0 +1,87 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.featureData = featureData;
+
+var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+
+function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
+
+function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2["default"])(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
+
+function featureData(data) {
+  var f = _objectSpread({}, 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;
+  }
+
+  var defaultFields = ['start', 'end', 'seq_name', 'score', 'featureType', 'source', 'frame', 'strand'];
+  Object.keys(data.attributes).forEach(function (a) {
+    var 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) {
+      var attr = data.attributes[a];
+
+      if (Array.isArray(attr) && attr.length === 1) {
+        // gtf uses double quotes for text values in the attributes column, remove them
+        var 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(function (childLocs) {
+      return childLocs.map(function (childLoc) {
+        return 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;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gtf",
-  "version": "1.6.9",
+  "version": "1.7.3",
   "description": "JBrowse 2 gtf feature adapter",
   "keywords": [
     "jbrowse",
@@ -18,21 +18,19 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-gtf.esm.js",
-  "module": "dist/plugin-gtf.esm.js",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "start": "tsdx watch --verbose --noClean",
-    "build": "tsdx build",
+    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
     "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"
+    "useSrc": "node ../../scripts/useSrc.js",
+    "postbuild": "tsc --build tsconfig.build.json"
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^1.0.15",
@@ -52,5 +50,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "f6c3d4edfadc26f7ac635a2fa7259f50f0c7e5e3"
+  "gitHead": "09b13c85acf4ac68dd71ab23af87656c7552fdaf"
 }