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/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra
index 26d25db..6ef84a9 100644
--- src/hg/makeDb/trackDb/refSeqComposite.ra
+++ src/hg/makeDb/trackDb/refSeqComposite.ra
@@ -83,31 +83,30 @@
         priority 6
         type bigBed 9 +
         skipEmptyFields on
         shortLabel RefSeq Diffs
         longLabel Differences between NCBI RefSeq Transcripts and the Reference Genome
         bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb
         itemRgb on
 
         track refGene override
         parent refSeqComposite off
         shortLabel UCSC RefSeq
         longLabel UCSC annotations of RefSeq RNAs (NM_* and NR_*)
         color 12,12,120
         type genePred refPep refMrna
         idXref hgFixed.refLink mrnaAcc name
-        dataVersion 
         priority 7
         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