9ed6f979a8ec95ac934e5e8fef028d188b76a035
chmalee
  Mon Aug 6 14:38:57 2018 -0700
pslMismatchGapToBed now outputs a single bed9+ instead of 5 different bed files, refs #21079

diff --git src/hg/lib/txAliDiff.sql src/hg/lib/txAliDiff.sql
new file mode 100644
index 0000000..964628d
--- /dev/null
+++ src/hg/lib/txAliDiff.sql
@@ -0,0 +1,30 @@
+# txAliDiff.sql was originally generated by the autoSql program, which also 
+# generated txAliDiff.c and txAliDiff.h.  This creates the database representation of
+# an object which can be loaded and saved from RAM in a fairly 
+# automatic way.
+
+#Differences between reference genome and transcript sequences
+CREATE TABLE txAliDiff (
+    chrom varchar(255) not null,	# Reference sequence chromosome or scaffold
+    chromStart int unsigned not null,	# Start position in chromosome of ambiguous gap placement region
+    chromEnd int unsigned not null,	# End position in chromosome of ambiguous gap placement region
+    name varchar(255) not null,	# Name of item
+    score int unsigned not null,	# Not used
+    strand char(1) not null,	# Transcript orientation on genome: + or -
+    thickStart int unsigned not null,	# Start position of 3'-most location for gaps that can shift position without introducing mismatches
+    thickEnd int unsigned not null,	# End position of 3'-most gap location for gaps that can shift position without introducing mismatches
+    reserved int unsigned not null,	# RGB color of this item
+    txName varchar(255) not null,	# Transcript identifier
+    txStart int unsigned not null,	# Start position in transcript (of ambiguous gap placement region where applicable)
+    txEnd int unsigned not null,	# End position in transcript (of ambiguous gap placement region where applicable)
+    gSkipped int unsigned not null,	# Number of bases skipped on genome, if any
+    txSkipped int unsigned not null,	# Number of bases skipped on transcript, if any
+    shiftL int unsigned not null,	# Number of bases that gap can be shifted left on genome with no mismatches
+    shiftR int unsigned not null,	# Number of bases that gap can be shifted right on genome with no mismatches
+    hgvsG longblob not null,	# HGVS g. notation of genome change to match transcript
+    hgvsCN longblob not null,	# HGVS c./n. notation of part of transcript not matched in genome
+    hgvsN longblob not null,	# HGVS c./n. notation of transcript change to match genome
+    hgvsPosCN longblob not null,	# HGVS c./n. position range of transcript ambiguous gap placement region
+              #Indices
+    PRIMARY KEY(chrom)
+);