7c77ad4dabbb32ac8790b0b1751001a0f73e960e
hartera
  Fri Apr 19 15:55:19 2013 -0700
Modified comment for alignGapCount field.
diff --git src/hg/lib/ucscRetroInfo.sql src/hg/lib/ucscRetroInfo.sql
index 0595126..a5e9ecc 100644
--- src/hg/lib/ucscRetroInfo.sql
+++ src/hg/lib/ucscRetroInfo.sql
@@ -1,64 +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
-    alignGapCount int not null,	# old simple intron count col34
+    alignGapCount int not null,	# 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))
 );