Changeset 5736

Timestamp:

Nov 19, 2019, 3:43:51 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1199: Implement Variant calling pipeline

Fixed some documentation and changes the auto-confirmation from Hisat to start raw-only variant calling.

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie

Files:

• autoconfirm/HisatAlignAutoConfirmer.java (modified) (1 diff)
• grid/VariantCallingJobCreator.java (modified) (2 diffs)

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

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

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantCallingJobCreator.java

@@ -397 +397 @@
         script.newLine();
       
-        script.comment("Calculate GC content and DNA strengt using custom script");
+        script.comment("Calculate GC content and DNA strength using custom script");
         script.comment("We need to get the reference sequence within 50 base-pairs of each entry in the VCF");
         script.comment("and run that through gc_stat.py which produces a VCF file that vcfanno can use");
@@ -499 +499 @@
   /**
     Job completion handler for Variant call jobs. The handler downloads the
-    'files.out' file and create links to the files and ....
-    TODO
+    'files.out' and 'stats.out' files. Links are created to the listed files
+    and some information is added as annotations to either the alignment or
+    raw bioassay.
   */
   public static class VariantCallJobCompletionHandler