cfda5d697701c33ce782310b6343ad3469791620
lrnassar
  Wed Jul 17 17:08:36 2024 -0700
Doing some refSeq surgery to fix mm9 issue on #34008. Essentially it was OK to have human include at that level - which allowed for an override at the species level. The reason for these overrides is Terrence asked us to make ncbiRefSeq (refseq all) the default on all organisms other than human and mouse. Having the addition at the hg38/hg19 level would mean duplicating the entire trackDb stanza in ncbiRefseqComposite.ra. For mouse, however, mm9 was having a conflict with the addition at the mouse level. So I moved mm10 and mm39 to have a new file at the mouse level and removed the mouse include. Refs #34008

diff --git src/hg/makeDb/trackDb/mouse/trackDb.ra src/hg/makeDb/trackDb/mouse/trackDb.ra
index 606d0bf..c90e061 100644
--- src/hg/makeDb/trackDb/mouse/trackDb.ra
+++ src/hg/makeDb/trackDb/mouse/trackDb.ra
@@ -851,27 +851,15 @@
 searchTable snp142Mult
 searchMethod exact
 searchType bed
 #semiShortCircuit 1
 termRegex rs[0-9]+
 searchPriority 12.9863
 padding 250
 
 searchTable snp142
 searchMethod exact
 searchType bed
 semiShortCircuit 1
 termRegex rs[0-9]+
 searchPriority 12.9864
 padding 250
-
-track ncbiRefSeqSelect
-parent refSeqComposite off
-priority 8
-type genePred
-shortLabel RefSeq Select
-longLabel NCBI RefSeq Select: One representative transcript per protein-coding gene
-trackHandler ncbiRefSeq
-idXref ncbiRefSeqLink mrnaAcc name
-color 20,20,160
-baseColorUseCds given
-baseColorDefault genomicCodons