b91a917e39c8d58d0de5e6325606f098ef0fb60b
angie
  Wed Mar 21 09:22:21 2018 -0700
New util pslMismatchGapToBed searches for sequence mismatches and indels between reference genome and transcripts.
Five output BED+ files are created, with corresponding hg/lib/txAli*.as autoSql files for generating bigBed.
This could be used to create 'Anomalies' subtracks for the NCBI RefSeq track.  refs #21079

diff --git src/hg/lib/txAliMismatch.as src/hg/lib/txAliMismatch.as
new file mode 100644
index 0000000..43fd5a6
--- /dev/null
+++ src/hg/lib/txAliMismatch.as
@@ -0,0 +1,14 @@
+table txAliMismatch
+"Mismatches between reference genome assembly and transcript sequences"
+    (
+    string chrom;      "Reference sequence chromosome or scaffold"
+    uint   chromStart; "Start position in chromosome"
+    uint   chromEnd;   "End position in chromosome"
+    string name;       "Mismatching bases: transcript bases > genomic bases"
+    char[1] strand;    "Transcript orientation on genome: + or -"
+    string txName;     "Transcript identifier"
+    uint   txStart;    "Start position in transcript"
+    uint   txEnd;      "End position in transcript"
+    lstring hgvsG;     "HGVS g. notation of genome change to match transcript"
+    lstring hgvsCN;    "HGVS c./n. notation of transcript change to match genome"
+    )