@jbrowse/plugin-bed 1.6.9 → 1.7.0

package/dist/util.js

@@ -0,0 +1,124 @@
+"use strict";
+
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});
+exports.ucscProcessedTranscript = ucscProcessedTranscript;
+
+var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
+
+function ucscProcessedTranscript(feature) {
+  var children = feature.children(); // split the blocks into UTR, CDS, and exons
+
+  var thickStart = feature.get('thickStart');
+  var thickEnd = feature.get('thickEnd');
+
+  if (!thickStart && !thickEnd) {
+    return feature;
+  }
+
+  var blocks = children ? children.filter(function (child) {
+    return child.get('type') === 'block';
+  }).sort(function (a, b) {
+    return a.get('start') - b.get('start');
+  }) : []; // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+  var newChildren = [];
+  blocks.forEach(function (block) {
+    var start = block.get('start');
+    var end = block.get('end');
+
+    if (thickStart >= end) {
+      // left-side UTR
+      var prime = feature.get('strand') > 0 ? 'five' : 'three';
+      newChildren.push({
+        type: "".concat(prime, "_prime_UTR"),
+        start: start,
+        end: end
+      });
+    } else if (thickStart > start && thickStart < end && thickEnd >= end) {
+      // UTR | CDS
+      var _prime = feature.get('strand') > 0 ? 'five' : 'three';
+
+      newChildren.push({
+        type: "".concat(_prime, "_prime_UTR"),
+        start: start,
+        end: thickStart
+      }, {
+        type: 'CDS',
+        start: thickStart,
+        end: end
+      });
+    } else if (thickStart <= start && thickEnd >= end) {
+      // CDS
+      newChildren.push({
+        type: 'CDS',
+        start: start,
+        end: end
+      });
+    } else if (thickStart > start && thickStart < end && thickEnd < end) {
+      // UTR | CDS | UTR
+      var leftPrime = feature.get('strand') > 0 ? 'five' : 'three';
+      var rightPrime = feature.get('strand') > 0 ? 'three' : 'five';
+      newChildren.push({
+        type: "".concat(leftPrime, "_prime_UTR"),
+        start: start,
+        end: thickStart
+      }, {
+        type: "CDS",
+        start: thickStart,
+        end: thickEnd
+      }, {
+        type: "".concat(rightPrime, "_prime_UTR"),
+        start: thickEnd,
+        end: end
+      });
+    } else if (thickStart <= start && thickEnd > start && thickEnd < end) {
+      // CDS | UTR
+      var _prime2 = feature.get('strand') > 0 ? 'three' : 'five';
+
+      newChildren.push({
+        type: "CDS",
+        start: start,
+        end: thickEnd
+      }, {
+        type: "".concat(_prime2, "_prime_UTR"),
+        start: thickEnd,
+        end: end
+      });
+    } else if (thickEnd <= start) {
+      // right-side UTR
+      var _prime3 = feature.get('strand') > 0 ? 'three' : 'five';
+
+      newChildren.push({
+        type: "".concat(_prime3, "_prime_UTR"),
+        start: start,
+        end: end
+      });
+    }
+  }); // eslint-disable-next-line @typescript-eslint/no-explicit-any
+
+  var newData = {};
+  feature.tags().forEach(function (tag) {
+    newData[tag] = feature.get(tag);
+  });
+  newData.subfeatures = newChildren;
+  newData.type = 'mRNA';
+  newData.uniqueId = feature.id();
+  delete newData.chromStarts;
+  delete newData.chromStart;
+  delete newData.chromEnd;
+  delete newData.chrom;
+  delete newData.blockStarts;
+  delete newData.blockSizes;
+  delete newData.blockCount;
+  delete newData.thickStart;
+  delete newData.thickEnd;
+  var newFeature = new _simpleFeature["default"]({
+    data: newData,
+    id: feature.id()
+  });
+  return newFeature;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "1.6.9",
+  "version": "1.7.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -18,15 +18,12 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-bed.esm.js",
-  "module": "dist/plugin-bed.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/bed",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
@@ -47,5 +44,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "f6c3d4edfadc26f7ac635a2fa7259f50f0c7e5e3"
+  "gitHead": "cc13844074d11881d211342a6a7eea113561b70b"
 }