igv 2.13.6 → 2.13.7

package/dist/igv.js

@@ -7204,8 +7204,8 @@
     function encode(objectName) {
       let result = '';
       objectName.split('').forEach(function (letter) {
-        if (encodings$1.has(letter)) {
-          result += encodings$1.get(letter);
+        if (encodings$2.has(letter)) {
+          result += encodings$2.get(letter);
         } else {
           result += letter;
         }
@@ -7214,27 +7214,27 @@
     }
 
     //	%23	%24	%25	%26	%27	%28	%29	%2A	%2B	%2C	%2F	%3A	%3B	%3D	%3F	%40	%5B	%5D
-    const encodings$1 = new Map();
-    encodings$1.set("!", "%21");
-    encodings$1.set("#", "%23");
-    encodings$1.set("$", "%24");
-    encodings$1.set("%", "%25");
-    encodings$1.set("&", "%26");
-    encodings$1.set("'", "%27");
-    encodings$1.set("(", "%28");
-    encodings$1.set(")", "%29");
-    encodings$1.set("*", "%2A");
-    encodings$1.set("+", "%2B");
-    encodings$1.set(",", "%2C");
-    encodings$1.set("/", "%2F");
-    encodings$1.set(":", "%3A");
-    encodings$1.set(";", "%3B");
-    encodings$1.set("=", "%3D");
-    encodings$1.set("?", "%3F");
-    encodings$1.set("@", "%40");
-    encodings$1.set("[", "%5B");
-    encodings$1.set("]", "%5D");
-    encodings$1.set(" ", "%20");
+    const encodings$2 = new Map();
+    encodings$2.set("!", "%21");
+    encodings$2.set("#", "%23");
+    encodings$2.set("$", "%24");
+    encodings$2.set("%", "%25");
+    encodings$2.set("&", "%26");
+    encodings$2.set("'", "%27");
+    encodings$2.set("(", "%28");
+    encodings$2.set(")", "%29");
+    encodings$2.set("*", "%2A");
+    encodings$2.set("+", "%2B");
+    encodings$2.set(",", "%2C");
+    encodings$2.set("/", "%2F");
+    encodings$2.set(":", "%3A");
+    encodings$2.set(";", "%3B");
+    encodings$2.set("=", "%3D");
+    encodings$2.set("?", "%3F");
+    encodings$2.set("@", "%40");
+    encodings$2.set("[", "%5B");
+    encodings$2.set("]", "%5D");
+    encodings$2.set(" ", "%20");
 
     // Convenience functions for the gapi oAuth library.
     const FIVE_MINUTES = 5 * 60 * 1000;
@@ -17840,27 +17840,27 @@
     }
 
     //	%23	%24	%25	%26	%27	%28	%29	%2A	%2B	%2C	%2F	%3A	%3B	%3D	%3F	%40	%5B	%5D
-    const encodings = new Map();
-    encodings.set("!", "%21");
-    encodings.set("#", "%23");
-    encodings.set("$", "%24");
-    encodings.set("%", "%25");
-    encodings.set("&", "%26");
-    encodings.set("'", "%27");
-    encodings.set("(", "%28");
-    encodings.set(")", "%29");
-    encodings.set("*", "%2A");
-    encodings.set("+", "%2B");
-    encodings.set(",", "%2C");
-    encodings.set("/", "%2F");
-    encodings.set(":", "%3A");
-    encodings.set(";", "%3B");
-    encodings.set("=", "%3D");
-    encodings.set("?", "%3F");
-    encodings.set("@", "%40");
-    encodings.set("[", "%5B");
-    encodings.set("]", "%5D");
-    encodings.set(" ", "%20");
+    const encodings$1 = new Map();
+    encodings$1.set("!", "%21");
+    encodings$1.set("#", "%23");
+    encodings$1.set("$", "%24");
+    encodings$1.set("%", "%25");
+    encodings$1.set("&", "%26");
+    encodings$1.set("'", "%27");
+    encodings$1.set("(", "%28");
+    encodings$1.set(")", "%29");
+    encodings$1.set("*", "%2A");
+    encodings$1.set("+", "%2B");
+    encodings$1.set(",", "%2C");
+    encodings$1.set("/", "%2F");
+    encodings$1.set(":", "%3A");
+    encodings$1.set(";", "%3B");
+    encodings$1.set("=", "%3D");
+    encodings$1.set("?", "%3F");
+    encodings$1.set("@", "%40");
+    encodings$1.set("[", "%5B");
+    encodings$1.set("]", "%5D");
+    encodings$1.set(" ", "%20");
     if (typeof process === 'object' && typeof window === 'undefined') {
       global.atob = function (str) {
         return Buffer.from(str, 'base64').toString('binary');
@@ -21939,7 +21939,7 @@
       }
     };
 
-    const _version = "2.13.6";
+    const _version = "2.13.7";
     function version$1() {
       return _version;
     }
@@ -23469,7 +23469,7 @@
 
       const delim = 'gff3' === format ? '=' : ' ';
       return new GFFFeature({
-        source: tokens[1],
+        source: decodeGFFAttribute(tokens[1]),
         type: tokens[2],
         chr: tokens[0],
         start: parseInt(tokens[3]) - 1,
@@ -23570,7 +23570,7 @@
         const idx = kv.indexOf(keyValueDelim);
         if (idx > 0 && idx < kv.length - 1) {
           const key = kv.substring(0, idx);
-          let value = stripQuotes(decodeURIComponent(kv.substring(idx + 1).trim()));
+          let value = stripQuotes(decodeGFFAttribute(kv.substring(idx + 1).trim()));
           attributes.push([key, value]);
         }
       }
@@ -23583,6 +23583,42 @@
       return value;
     }
 
+    // GFF3 attributes have specific percent encoding rules, the list below are required, all others are forbidden
+    /*
+    tab (%09)
+    newline (%0A)
+    carriage return (%0D)
+    % percent (%25)
+    control characters (%00 through %1F, %7F)
+    In addition, the following characters have reserved meanings in column 9 and must be escaped when used in other contexts:
+    ; semicolon (%3B)
+    = equals (%3D)
+    & ampersand (%26)
+    , comma (%2C)
+     */
+
+    const encodings = new Map([["%09", "\t"], ["%0A", "\n"], ["%0D", "\r"], ["%25", "%"], ["%3B", ";"], ["%3D", "="], ["%26", "&"], ["%2C", ","]]);
+    function decodeGFFAttribute(str) {
+      if (!str.includes("%")) {
+        return str;
+      }
+      let decoded = "";
+      for (let i = 0; i < str.length; i++) {
+        if (str.charCodeAt(i) === 37 && i < str.length - 2) {
+          const key = str.substring(i, i + 3);
+          if (encodings.has(key)) {
+            decoded += encodings.get(key);
+          } else {
+            decoded += key;
+          }
+          i += 2;
+        } else {
+          decoded += str.charAt(i);
+        }
+      }
+      return decoded;
+    }
+
     /**
      * Wrapper class to record a decoding error.
      */
@@ -62872,10 +62908,7 @@
       setOauthToken,
       oauth,
       version: version$1,
-      setApiKey,
-      doAutoscale,
-      TrackView,
-      GenomeUtils
+      setApiKey
     };
 
     return index;