bbca1ee6f90a46e7a139434849dbf32bd206b522
chmalee
  Thu Sep 21 12:27:34 2023 -0700
First cut of adding a historical refseq transcripts track, and getting hgvs searching to work with them, refs #26016

diff --git src/hg/makeDb/trackDb/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra
index 17fce5a..75d3aa1 100644
--- src/hg/makeDb/trackDb/refSeqComposite.ra
+++ src/hg/makeDb/trackDb/refSeqComposite.ra
@@ -100,30 +100,41 @@
         baseColorUseCds given
         baseColorDefault genomicCodons
 
         track ncbiRefSeqHgmd
         parent refSeqComposite off
         priority 9
         type genePred
         shortLabel RefSeq HGMD
         longLabel NCBI RefSeq HGMD subset: transcripts with clinical variants in HGMD
         trackHandler ncbiRefSeq
         idXref ncbiRefSeqLink mrnaAcc name
         color 20,20,160
         baseColorUseCds given
         baseColorDefault genomicCodons
 
+        track ncbiRefSeqHistorical
+        parent refSeqComposite off
+        priority 10000
+        type bigBed 12 .
+        skipEmptyFields on
+        shortLabel RefSeq Historical
+        longLabel NCBI RefSeq Historical Transcript Versions
+        bigDataUrl /gbdb/$D/ncbiRefSeq/refSeqHistorical.bb
+        searchIndex name
+        release alpha
+
 searchName ncbiRefSeqCuratedName2
 searchTable ncbiRefSeqCurated
 searchMethod prefix
 query select chrom, txStart,txEnd, name from %s where name2 like '%s%%'
 searchPriority 1.07200
 
 searchName ncbiRefSeqPredictedName2
 searchTable ncbiRefSeqPredicted
 searchMethod prefix
 query select chrom, txStart,txEnd, name from %s where name2 like '%s%%'
 searchPriority 1.07201
 
 searchName ncbiRefSeqCuratedProtAcc
 searchTable ncbiRefSeqCurated
 searchType genePred
@@ -181,15 +192,19 @@
 semiShortCircuit 1
 termRegex X[MR]_[0-9]{6}[0-9]*\.[0-9]+
 searchPriority 2.07204
 
 searchName ncbiRefSeqPredictedNoVersion
 searchTable ncbiRefSeqPredicted
 query select chrom,txStart,txEnd,name from %s where name like '%s.%%'
 semiShortCircuit 1
 termRegex X[MR]_[0-9]{6}[0-9]*
 dontCheck X[MR]_[0-9]{6}[0-9]*\.[0-9]+
 searchPriority 2.07204
 
 searchTable ncbiRefSeqOther
 searchPriority 2.07207
 searchType bigBed
+
+searchTable ncbiRefSeqHistorical
+searchPriority 20
+searchType bigBed