Support htsget scheme. See samtools/hts-specs#581

igvteam · Jul 21, 2021 · e22aa85 · e22aa85
1 parent 69ab1d9
commit e22aa85
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Showing 2 changed files with 16 additions and 11 deletions.
diff --git a/dev/htsget.html b/dev/htsget.html
@@ -32,14 +32,14 @@ <h1>htsget server example</h1>
              //   name: 'giab.NA12878',
              //   sourceType: 'htsget',
              //   format: "VCF",
-                url: 'https://htsget.ga4gh.org/variants/giab.NA12878'
+                url: 'htsget://htsget.ga4gh.org/variants/giab.NA12878'
             },
             {
               //  type: 'alignment',
               //  name: 'giab.NA12878.NIST7086.1',
               //  sourceType: 'htsget',
               //  format: 'bam',
-                url: 'https://htsget.ga4gh.org/reads/giab.NA12878.NIST7086.1'
+                url: 'htsget://htsget.ga4gh.org/reads/giab.NA12878.NIST7086.1'
             }
         ]
     };

diff --git a/js/htsget/htsgetReader.js b/js/htsget/htsgetReader.js
@@ -77,7 +77,8 @@ class HtsgetReader {
 
     static async inferFormat(config) {
         try {
-            const headerURL = `${config.url}${config.url.includes("?") ? "&" : "?"}class=header`;
+            const url = getUrl(config);
+            const headerURL = `${url}${url.includes("?") ? "&" : "?"}class=header`;
             const ticket = await igvxhr.loadJson(headerURL, buildOptions(config))
             if (ticket.htsget) {
                 const format = ticket.htsget.format;
@@ -97,17 +98,21 @@ class HtsgetReader {
 }
 
 /**
- * Extract the full url from the config.  Striving for backward compatibility.
+ * Extract the full url from the config.  Striving for backward compatibility, "endpoint" and "id" are deprecated.
  *
  * @param config
  */
-function getUrl(config)  {
-    if(config.url && config.endpoint && config.id) {
-        return config.url + config.endpoint + config.id;
-    } else if(config.endpoint && config.id) {
-        return config.endpoint + config.id;
-    } else if(config.url) {
-        return config.url;
+function getUrl(config) {
+    if (config.url && config.endpoint && config.id) {
+        return config.url + config.endpoint + config.id;    // Deprecated
+    } else if (config.endpoint && config.id) {
+        return config.endpoint + config.id;                // Deprecated
+    } else if (config.url) {
+        if (config.url.startsWith("htsget://")) {
+            return config.url.replace("htsget://", "https://");    // htsget -> http not supported
+        } else {
+            return config.url;
+        }
     } else {
         throw Error("Must specify either 'url', or 'endpoint' and 'id");
     }