930e2ff4a539d4ce430291acb4af9d7190aabf22
hartera
  Thu Feb 28 10:42:46 2013 -0800
Removed oldScore column as no longer needed and renamed oldIntronCount to alignGapCount.
diff --git src/hg/lib/ucscRetroInfo.sql src/hg/lib/ucscRetroInfo.sql
index d79b27a..0595126 100644
--- src/hg/lib/ucscRetroInfo.sql
+++ src/hg/lib/ucscRetroInfo.sql
@@ -1,65 +1,64 @@
 # ucscRetroInfo.sql was originally generated by the autoSql program, which also 
 # generated ucscRetroInfo.c and ucscRetroInfo.h.  This creates the database representation of
 # an object which can be loaded and saved from RAM in a fairly 
 # automatic way.
 
 #Retrogenes based on cDNA alignments that are expressed or processed pseudogenes.
 CREATE TABLE ucscRetroInfo (
     chrom varchar(255) not null,	# Reference sequence chromosome or scaffold col1
     chromStart int unsigned not null,	# pseudogene alignment start position col2
     chromEnd int unsigned not null,	# pseudogene alignment end position col3
     name varchar(255) not null,	# Name of pseudogene col4
     score int unsigned not null,	# score of pseudogene with gene col5
     strand char(2) not null,	# + or -
     thickStart int unsigned not null,	# Start of where display should be thick (start codon)
     thickEnd int unsigned not null,	# End of where display should be thick (stop codon)
     reserved int unsigned not null,	# Always zero for now
     blockCount int not null,	# Number of blocks
     blockSizes longblob not null,	# Comma separated list of block sizes
     chromStarts longblob not null,	# Start positions relative to chromStart
     retroExonCount int not null,	# number of exons in retroGene col13
     axtScore int not null,	# blastz score, parent mrna aligned to pseudogene col14
     type varchar(255) not null,	# type of evidence col15
     gChrom varchar(255) not null,	# Chromosome name col16
     gStart int not null,	# gene alignment start position col17
     gEnd int not null,	# gene alignment end position col18
     gStrand char(2) not null,	# strand of gene col19
     parentSpliceCount int unsigned not null,	# # of splice sites in parent gene col20
     geneOverlap int unsigned not null,	# bases overlapping col21
     polyA int unsigned not null,	# count of As in polyA col22
     polyAstart int not null,	# start of polyA, relative to end of pseudogene col23
     exonCover int not null,	# number of exons in Gene covered col24
     intronCount int unsigned not null,	# number of introns in pseudogene col25
     bestAliCount int unsigned not null,	# number of good mrnas aligning col26
     matches int unsigned not null,	# matches + repMatches col27
     qSize int unsigned not null,	# aligning bases in pseudogene col28
     qEnd int unsigned not null,	# end of cdna alignment col29
     tReps int unsigned not null,	# repeats in gene col30
     coverage int unsigned not null,	# % of bases that align to gene col31
     label int not null,	# 1=pseudogene,-1 not pseudogene -2 expressed retroGene col32
     milliBad int unsigned not null,	# milliBad score, pseudogene aligned to genome col33
-    oldScore int unsigned not null,	# another heuristic col34
-    oldIntronCount int not null,	# old simple intron count col35
-    processedIntrons int not null,	# count of introns removed via retrotransposition col36
-    conservedSpliceSites int not null,	# conserved splice site count col37
-    maxOverlap int not null,	# largest overlap with another mrna col38
-    refSeq varchar(255) not null,	# Name of closest regSeq to gene col39
-    rStart int not null,	# refSeq alignment start position col40
-    rEnd int not null,	# refSeq alignment end position col41
-    mgc varchar(255) not null,	# Name of closest mgc to gene col42
-    mStart int not null,	# mgc alignment start position col43
-    mEnd int not null,	# mgc alignment end position col44
-    kgName varchar(255) not null,	# Name of closest knownGene to gene col45
-    kStart int not null,	# kg alignment start position col46
-    kEnd int not null,	# kg alignment end position col47
-    overName varchar(255) not null,	# name of overlapping mrna col48
-    overStart int not null,	# overlapping mrna start position col49
-    overExonCover int not null,	# count of overlapping mrna exons col50
-    overStrand char(2) not null,	# strand of overlapping mrna col51
-    posConf float not null,	# pvalue for positive col52
-    polyAlen int unsigned not null,	# length of polyA col53
+    alignGapCount int not null,	# old simple intron count col34
+    processedIntrons int not null,	# count of introns removed via retrotransposition col35
+    conservedSpliceSites int not null,	# conserved splice site count col36
+    maxOverlap int not null,	# largest overlap with another mrna col37
+    refSeq varchar(255) not null,	# Name of closest regSeq to gene col38
+    rStart int not null,	# refSeq alignment start position col39
+    rEnd int not null,	# refSeq alignment end position col40
+    mgc varchar(255) not null,	# Name of closest mgc to gene col41
+    mStart int not null,	# mgc alignment start position col42
+    mEnd int not null,	# mgc alignment end position col43
+    kgName varchar(255) not null,	# Name of closest knownGene to gene col44
+    kStart int not null,	# kg alignment start position col45
+    kEnd int not null,	# kg alignment end position col46
+    overName varchar(255) not null,	# name of overlapping mrna col47
+    overStart int not null,	# overlapping mrna start position col48
+    overExonCover int not null,	# count of overlapping mrna exons col49
+    overStrand char(2) not null,	# strand of overlapping mrna col50
+    posConf float not null,	# pvalue for positive col51
+    polyAlen int unsigned not null,	# length of polyA col52
               #Indices
     PRIMARY KEY(name),
     index(kgName(10)),
     index(refSeq(10))
 );
