Changeset 5818

Timestamp:

Jan 31, 2020, 2:30:08 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1212: Enable filtering step for variant calling in auto-confirm mode

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/autoconfirm/HisatAlignAutoConfirmer.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/autoconfirm/HisatAlignAutoConfirmer.java

@@ -285 +285 @@
           VariantCallingJobCreator jobCreator = new VariantCallingJobCreator();
           jobCreator.setSkipRaw(false);
-          // TODO - to begin with we only do raw variant calling
-          jobCreator.setRawOnly(true);
+          jobCreator.setRawOnly(false);
           jobCreator.setSoftware(software);
           jobCreator.setAutoConfirm(true);