51bd7d1443d629518ab0f9beed9b2c223a6342ae
angie
  Mon Jun 18 14:19:44 2018 -0700
gtexGeneBed.sql used PRIMARY KEY(geneId), which excluded nearly all mappings to chr*_alt.  Change it to (chrom,geneId) to allow mapping to multiple sequences. refs #18853

diff --git src/hg/lib/gtexGeneBed.sql src/hg/lib/gtexGeneBed.sql
index ec3f563..65e703b 100644
--- src/hg/lib/gtexGeneBed.sql
+++ src/hg/lib/gtexGeneBed.sql
@@ -4,18 +4,19 @@
 # automatic way.
 
 #BED6+ with additional fields for gene and transcript IDs, and expression experiment scores
 CREATE TABLE gtexGeneBed (
     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,	# Gene symbol
     score int unsigned not null,	# Score from 0-1000
     strand char(1) not null,	# + or - for strand
     geneId varchar(255) not null,	# Ensembl gene ID, referenced in GTEx data tables
     geneType varchar(255) not null,	# GENCODE gene biotype
     expCount int unsigned not null,	# Number of experiment values
     expScores longblob not null,	# Comma separated list of experiment scores
               #Indices
-    PRIMARY KEY(geneId),
+    PRIMARY KEY(chrom,geneId),
+    INDEX(geneId),
     INDEX(chrom(20), chromStart)
 );