0db3d4c0bab5801bcae7920c3fa5749651ecbe05
hiram
  Tue Jul 22 15:38:33 2014 -0700
setup indexes for these new rmsk tables refs #9741
diff --git src/hg/lib/rmskAlign.sql src/hg/lib/rmskAlign.sql
index c5193ba..b3f41ee 100644
--- src/hg/lib/rmskAlign.sql
+++ src/hg/lib/rmskAlign.sql
@@ -1,27 +1,27 @@
 # rmskAlign.sql was originally generated by the autoSql program, which also 
 # generated rmskAlign.c and rmskAlign.h.  This creates the database representation of
 # an object which can be loaded and saved from RAM in a fairly 
 # automatic way.
 
 #RepeatMasker .align record
 CREATE TABLE rmskAlign (
     swScore int unsigned not null,	# Smith Waterman alignment score
     milliDiv int unsigned not null,	# Base mismatches in parts per thousand
     milliDel int unsigned not null,	# Bases deleted in parts per thousand
     milliIns int unsigned not null,	# Bases inserted in parts per thousand
     genoName varchar(255) not null,	# Genomic sequence name
     genoStart int unsigned not null,	# Start in genomic sequence
     genoEnd int unsigned not null,	# End in genomic sequence
     genoLeft int not null,	# -#bases after match in genomic sequence
     strand char(1) not null,	# Relative orientation + or -
     repName varchar(255) not null,	# Name of repeat
     repClass varchar(255) not null,	# Class of repeat
     repFamily varchar(255) not null,	# Family of repeat
     repStart int not null,	# Start in repeat sequence
     repEnd int unsigned not null,	# End in repeat sequence
     repLeft int not null,	# -#bases after match in repeat sequence
     id int unsigned not null,	# The ID of the hit. Used to link related fragments
     alignment longblob not null,	# The alignment data stored as a single string
               #Indices
-    PRIMARY KEY(swScore)
+    INDEX chromId (genoName,id)
 );