2ffc9d13a7475fbf6eb60a6b50d463ee11e7ff41
kate
  Wed Oct 25 18:06:54 2017 -0700
Implement V2 GTEx eQTL clusters as described in RM as 'permissive with ID'.  This adds Ensembl gene ID to schemas.  Also adding summary columns to cluster track (maxEffect, maxPvalue, effectType) to provide alternative to parsing comma-sep fields for table filtering. refs #15646

diff --git src/hg/lib/gtexEqtl.sql src/hg/lib/gtexEqtl.sql
index 05200d6..c7b3a5b 100644
--- src/hg/lib/gtexEqtl.sql
+++ src/hg/lib/gtexEqtl.sql
@@ -1,29 +1,31 @@
 # gtexEqtl.sql was originally generated by the autoSql program, which also 
 # generated gtexEqtl.c and gtexEqtl.h.  This creates the database representation of
 # an object which can be loaded and saved from RAM in a fairly 
 # automatic way.
 
 #BED 9+ of expression Quantitative Trait Loci (eQTL). These are variants affecting gene expression
 CREATE TABLE gtexEqtl (
-    bin smallint not null,             # Bin number for browser speedup
+    bin int unsigned not null,	# Bin number for browser speedup
     chrom varchar(255) not null,	# Reference sequence chromosome or scaffold
     chromStart int unsigned not null,	# Start position in chromosome
     chromEnd int unsigned not null,	# End position in chromosome
-    name varchar(255) not null,	        # Variant/gene
+    name varchar(255) not null,	# Variant/gene pair
     score int unsigned not null,	# Score from 0-1000 (highest probabiliity in cluster * 1000)
     strand char(1) not null,	# .
     thickStart int unsigned not null,	# Start position
     thickEnd int unsigned not null,	# End position
     reserved int unsigned not null,	# R,G,B color: red +effect, blue -effect. Bright for high, pale for lower (cutoff effectSize 2.0 RPKM).
     variant varchar(255) not null,	# Variant (rsID or GTEx identifier if none)
-    gene varchar(255) not null,	# Target gene
+    geneId varchar(255) not null,	# Target gene identifier
+    gene varchar(255) not null,	# Target gene symbol
     distance int not null,	# Distance from TSS
     effectSize float not null,	# Effect size (FPKM)
     pValue float not null,	# Nominal p-value
-    causalProb float not null,	# Probability variant is in 95 percent credible set
+    causalProb float not null,	# Probability variant is in high confidence causal set
               #Indices
     INDEX (chrom,bin),
-    PRIMARY KEY (name),
+    INDEX (geneId),
     INDEX (gene),
-    INDEX (variant)
+    INDEX (variant),
+    PRIMARY KEY (geneId,variant)
 );