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.as src/hg/lib/txAliDiff.as
new file mode 100644
index 0000000..e5e04b9
--- /dev/null
+++ src/hg/lib/txAliDiff.as
@@ -0,0 +1,24 @@
+table txAliDiff
+"Differences between reference genome and transcript sequences"
+    (   
+    string chrom;       "Reference sequence chromosome or scaffold"
+    uint   chromStart;  "Start position in chromosome of ambiguous gap placement region"
+    uint   chromEnd;    "End position in chromosome of ambiguous gap placement region"
+    string name;        "Name of item"
+    uint   score;       "Not used"
+    char[1] strand;     "Transcript orientation on genome: + or -"
+    uint   thickStart;  "Start position of 3'-most location for gaps that can shift position without introducing mismatches"
+    uint   thickEnd;    "End position of 3'-most gap location for gaps that can shift position without introducing mismatches"
+    uint reserved;         "RGB color of this item"
+    string txName;      "Transcript identifier"
+    uint   txStart;     "Start position in transcript (of ambiguous gap placement region where applicable)"
+    uint   txEnd;       "End position in transcript (of ambiguous gap placement region where applicable)"
+    uint gSkipped;    "Number of bases skipped on genome, if any"
+    uint txSkipped;   "Number of bases skipped on transcript, if any"
+    uint shiftL;      "Number of bases that gap can be shifted left on genome with no mismatches"
+    uint shiftR;      "Number of bases that gap can be shifted right on genome with no mismatches" 
+    lstring hgvsG;      "HGVS g. notation of genome change to match transcript"
+    lstring hgvsCN;     "HGVS c./n. notation of part of transcript not matched in genome"
+    lstring hgvsN;      "HGVS c./n. notation of transcript change to match genome"
+    lstring hgvsPosCN;  "HGVS c./n. position range of transcript ambiguous gap placement region"
+    )