Changeset 5735

Timestamp:

Nov 19, 2019, 3:42:48 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1199: Implement Variant calling pipeline

Removed version number from variant annotations. This was used on Cosmic and dbSnp annotations but would make it harder to write code in a future-proof way. For example, we already display the Cosmic ID in one dialog and it is better to have that under a generic name.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/analysis/view_variants.js (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/VariantCallingServlet.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/trunk/resources/analysis/view_variants.js

@@ -27 +27 @@
       var snp = snpData[snpNo];
       var info = snp.info;
-      var cosmicId = info['CCv87_ID'];
+      var cosmicId = info['cosmic_ID'];
       html += '<tr class="snp highlight">';
       html += '<td>'+Strings.encodeTags(snp.chromosome+':'+snp.position)+'</td>';

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/VariantCallingServlet.java

@@ -213 +213 @@
           parser.setUseLineNoAsId(true);
           parser.setInfoFactory(new VariantCallingInfoFactory(
-              Arrays.asList("CCv87_ID"),
+              Arrays.asList("cosmic_ID"),
               Arrays.asList("Gene_Name")
               ));