42ccdd815277a3dc7d78b48fa0ac36d469ab628a
markd
  Mon Feb 28 19:07:04 2022 -0800
added bigRmsk autoSql files from Robert Hubley

diff --git src/hg/lib/bigRmskAlignBed.sql src/hg/lib/bigRmskAlignBed.sql
new file mode 100644
index 0000000..51273e2
--- /dev/null
+++ src/hg/lib/bigRmskAlignBed.sql
@@ -0,0 +1,27 @@
+# bigRmskAlignBed.sql was originally generated by the autoSql program, which also 
+# generated bigRmskAlignBed.c and bigRmskAlignBed.h.  This creates the database representation of
+# an object which can be loaded and saved from RAM in a fairly 
+# automatic way.
+
+#Repetitive Element Alignment Auxilary Data
+CREATE TABLE bigRmskAlignBed (
+    chrom varchar(255) not null,	# Reference sequence chromosome or scaffold
+    chromStart int unsigned not null,	# Start position of alignment on chromosome
+    chromEnd int unsigned not null,	# End position of alignment on chromosome
+    chromRemain int unsigned not null,	# Remaining bp in the chromosome or scaffold
+    score float not null,	# alignment score (sw, bits or evalue)
+    percSubst float not null,	# Base substitution percentage
+    percDel float not null,	# Base deletion percentage
+    percIns float not null,	# Bases insertion percentage
+    strand char(1) not null,	# Strand - either + or -
+    repName varchar(255) not null,	# Name of repeat
+    repType varchar(255) not null,	# Type of repeat
+    repSubtype varchar(255) not null,	# Subtype of repeat
+    repStart int unsigned not null,	# Start in repeat sequence
+    repEnd int unsigned not null,	# End in repeat sequence
+    repRemain int unsigned not null,	# Remaining unaligned bp in the repeat sequence
+    id int unsigned not null,	# The ID of the hit. Used to link related fragments
+    calignData longblob not null,	# The alignment data stored as a single string
+              #Indices
+    PRIMARY KEY(chrom)
+);