7ae4a70c26c3414a34b262329b2f7febe831923c
hiram
  Thu Jul 18 10:26:34 2013 -0700
checking in Robert's code refs #9741
diff --git src/hg/lib/rmskAlign.sql src/hg/lib/rmskAlign.sql
new file mode 100644
index 0000000..c5193ba
--- /dev/null
+++ src/hg/lib/rmskAlign.sql
@@ -0,0 +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)
+);
