igv 2.13.6 → 2.13.7

package/README.md

@@ -12,19 +12,19 @@ Below are examples and a quickstart guide.  See the [Wiki](https://github.com/ig
 
 # Examples
  
-***[Alignments](https://igv.org/web/release/2.13.6/examples/cram-vcf.html)***
+***[Alignments](https://igv.org/web/release/2.13.7/examples/cram-vcf.html)***
 
-***[Interactions](https://igv.org/web/release/2.13.6/examples/interact.html)***
+***[Interactions](https://igv.org/web/release/2.13.7/examples/interact.html)***
 
-***[Copy number](https://igv.org/web/release/2.13.6/examples/copyNumber.html)***
+***[Copy number](https://igv.org/web/release/2.13.7/examples/copyNumber.html)***
 
-***[Multiple regions](https://igv.org/web/release/2.13.6/examples/multi-locus.html)***
+***[Multiple regions](https://igv.org/web/release/2.13.7/examples/multi-locus.html)***
 
-***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.13.6/examples/maf-tcga.html)***
+***[Mutation Annotation Format (MAF)](https://igv.org/web/release/2.13.7/examples/maf-tcga.html)***
 
-***[Variant color options](https://igv.org/web/release/2.13.6/examples/variant-colors.html)***
+***[Variant color options](https://igv.org/web/release/2.13.7/examples/variant-colors.html)***
 
-***[More](https://igv.org/web/release/2.13.6/examples/)***
+***[More](https://igv.org/web/release/2.13.7/examples/)***
 
  
 # Quickstart
@@ -33,18 +33,18 @@ Below are examples and a quickstart guide.  See the [Wiki](https://github.com/ig
 igv.js consists of a single javascript file with no external dependencies.  
 
 Pre-built files for ES5 (igv.min.js) and ES6 (igv.esm.min.js)
-can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.13.6/dist/](https://cdn.jsdelivr.net/npm/igv@2.13.6/dist/). 
+can be downloaded from [https://cdn.jsdelivr.net/npm/igv@2.13.7/dist/](https://cdn.jsdelivr.net/npm/igv@2.13.7/dist/). 
 
 To import igv as an ES6 module
 
 ```javascript
-import igv from "https://cdn.jsdelivr.net/npm/igv@2.13.6/dist/igv.esm.min.js"
+import igv from "https://cdn.jsdelivr.net/npm/igv@2.13.7/dist/igv.esm.min.js"
 ``` 
 
 Or as a script include (defines the "igv" global)
 
 ```html
-<script src="https://cdn.jsdelivr.net/npm/igv@2.13.6/dist/igv.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/igv@2.13.7/dist/igv.min.js"></script>
 ```   
  
 Alternatively you can install with npm  

package/dist/igv.esm.js

@@ -8482,8 +8482,8 @@ 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;
         }
@@ -8492,27 +8492,27 @@ function encode(objectName) {
 }
 
 //	%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.
 
@@ -19700,27 +19700,27 @@ function createMenuElements$1(itemList, popover) {
 }
 
 //	%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) {
@@ -24215,7 +24215,7 @@ const Cytoband = function (start, end, name, typestain) {
     }
 };
 
-const _version = "2.13.6";
+const _version = "2.13.7";
 function version() {
     return _version
 }
@@ -25949,7 +25949,7 @@ function decode(tokens, header) {
 
     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,
@@ -26060,7 +26060,7 @@ function parseAttributeString(attributeString, keyValueDelim) {
         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]);
         }
     }
@@ -26074,6 +26074,55 @@ function stripQuotes(value) {
     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.
  */
@@ -54209,10 +54258,7 @@ var index = {
     setOauthToken,
     oauth,
     version,
-    setApiKey,
-    doAutoscale,
-    TrackView,
-    GenomeUtils
+    setApiKey
 };
 
 export { index as default };