a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a
braney
  Wed May 21 17:22:17 2025 -0700
add bedMethyl type for custom and native tracks

diff --git src/hg/lib/bedMethyl.sql src/hg/lib/bedMethyl.sql
new file mode 100644
index 00000000000..7f84c4b3e0d
--- /dev/null
+++ src/hg/lib/bedMethyl.sql
@@ -0,0 +1,26 @@
+# bedMethyl.sql was originally generated by the autoSql program, which also 
+# generated bedMethyl.c and bedMethyl.h.  This creates the database representation of
+# an object which can be loaded and saved from RAM in a fairly 
+# automatic way.
+
+#Browser extensible data for bedmethyl files (bed9+9)
+CREATE TABLE bedMethyl (
+    chrom varchar(255) not null,	# Chromosome (or contig, scaffold, etc.)
+    chromStart int unsigned not null,	# Start position in chromosome
+    chromEnd int unsigned not null,	# End position in chromosome
+    name varchar(255) not null,	# Name of item
+    score int unsigned not null,	# Score from 0-1000
+    strand char(1) not null,	# + or -
+    thickStart int unsigned not null,	# Start of where display should be thick (start codon)
+    thickEnd int unsigned not null,	# End of where display should be thick (stop codon)
+    reserved int unsigned not null,	# Used as itemRgb as of 2004-11-22
+    nValidCov varchar(255) not null,	# Valid Coverage|N_mod + N_otherMod + N_canonical
+    percMod varchar(255) not null,	# Percent Modified
+    nMod varchar(255) not null,	# N_mod|Number of calls with a modified base
+    nCanon varchar(255) not null,	# N_canonical|Number of calls with a canonical base
+    nOther varchar(255) not null,	# N_otherMod|Number of calls with a modified base, other modification
+    nDelete varchar(255) not null,	# N_delete|Number of reads with a deletion at this reference position
+    nFail varchar(255) not null,	# N_fail|Number of calls where the probability of the call was below the threshold. 
+    nDiff varchar(255) not null,	# N_diff|Number of reads with a base other than the canonical base for this modification. 
+    nNoCall varchar(255) not null	# N_nocall|Number of reads aligned to this reference position, with the correct canonical base, but without a base modification call.
+);