0cc6f12b82336610b9250bd5df050ebde29f314c
braney
  Fri Sep 3 14:34:14 2010 -0700
update to reflect reality,  apparently these haven't been used for a while
diff --git src/hg/lib/gencodeGeneClass.sql src/hg/lib/gencodeGeneClass.sql
index 026786c..09f631f 100644
--- src/hg/lib/gencodeGeneClass.sql
+++ src/hg/lib/gencodeGeneClass.sql
@@ -1,12 +1,17 @@
 # gencodeGeneClass.sql was originally generated by the autoSql program, which also 
 # generated gencodeGeneClass.c and gencodeGeneClass.h.  This creates the database representation of
 # an object which can be loaded and saved from RAM in a fairly 
 # automatic way.
 
 #Class for Gencode genes
 CREATE TABLE gencodeGeneClass (
+    geneId varchar(255) not null,	# Gene ID for Gencode gene
     name varchar(255) not null,	# Transcript ID for Gencode gene
-    class enum('Novel_transcript', 'Novel_transcript_gencode_conf', 'Artifact', 'Known', 'Novel_CDS', 'Novel_transcript', 'Novel_transcript_gencode_conf', 'Putative', 'Putative_gencode_conf', 'TEC', 'Processed_pseudogene', 'Unprocessed_pseudogene') not null,
+    transcriptType varchar(255) not null,	# Transcript type for Gencode gene
+    level int not null,	# Gencode level
+    class varchar(255) not null,	# Class of gene.  enum('Antisense', 'Antisense_val', 'Artifact', 'Known', 'Novel_CDS', 'Novel_transcript', 'Novel_transcript_val', 'Putative', 'Putative_val', 'TEC', 'Processed_pseudogene', 'Unprocessed_pseudogene', 'Pseudogene_fragment', 'Undefined')
+    ottGeneId varchar(255) not null,	# Otter Gene id for Gencode gene
+    ottTranscriptId varchar(255) not null,	# Otter Transcript id for Gencode gene
               #Indices
     PRIMARY KEY(name)
 );