966c6acca66b653cfbccc2575db57f250c37dd15
brianlee
  Thu Nov 21 12:29:02 2019 -0800
Adding baseColorDefault genomicCodons to NCBI gene tracks refs #24553

diff --git src/hg/makeDb/trackDb/refSeqComposite.ra src/hg/makeDb/trackDb/refSeqComposite.ra
index 52343d7..51bda0a 100644
--- src/hg/makeDb/trackDb/refSeqComposite.ra
+++ src/hg/makeDb/trackDb/refSeqComposite.ra
@@ -9,48 +9,51 @@
 noInherit on
 #subGroup1 view Views aNcbiRefSeq=NCBI_RefSeq zUcscRefSeq=UCSC_RefSeq
 allButtonPair on
 dataVersion /gbdb/$D/ncbiRefSeq/ncbiRefSeqVersion.txt
 priority 2
 dbPrefixUrls hg="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" dm="http://flybase.org/reports/$$" ce="http://www.wormbase.org/db/gene/gene?name=$$" rn="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" sacCer="https://www.yeastgenome.org/locus/$$" danRer="https://zfin.org/$$" mm="http://www.informatics.jax.org/marker/$$" xenTro="https://www.xenbase.org/gene/showgene.do?method=display&geneId=$$"
 dbPrefixLabels hg="HGNC" dm="FlyBase" ce="WormBase" rn="RGD" sacCer="SGD" danRer="ZFIN" mm="MGI" xenTro="XenBase"
 
         track ncbiRefSeq
         parent refSeqComposite off
         color 12,12,120
         shortLabel RefSeq All
         longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*)
         idXref ncbiRefSeqLink mrnaAcc name
         baseColorUseCds given
+        baseColorDefault genomicCodons
         priority 1
 
         track ncbiRefSeqCurated
         color 12,12,120
         parent refSeqComposite on
         shortLabel RefSeq Curated
         longLabel NCBI RefSeq genes, curated subset (NM_*, NR_*, NP_* or YP_*)
         idXref ncbiRefSeqLink mrnaAcc name
         baseColorUseCds given
+        baseColorDefault genomicCodons
         priority 2
 
         track ncbiRefSeqPredicted
         color 12,12,120
         parent refSeqComposite off
         shortLabel RefSeq Predicted
         longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*)
         idXref ncbiRefSeqLink mrnaAcc name
         baseColorUseCds given
+        baseColorDefault genomicCodons
         priority 3
 
         track ncbiRefSeqOther
         color 32,32,32
         parent refSeqComposite off
         shortLabel RefSeq Other
         longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*)
         priority 4
         searchIndex name
         searchTrix /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.ix
         bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqOther.bb
         type bigBed 12 +
         labelFields gene
         skipEmptyFields on
         urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/612091" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$"
@@ -83,48 +86,52 @@
         shortLabel RefSeq Diffs
         longLabel Differences between NCBI RefSeq Transcripts and the Reference Genome
         bigDataUrl /gbdb/$D/ncbiRefSeq/ncbiRefSeqGenomicDiff.bb
         itemRgb on
 
         track ncbiRefSeqHgmd
         parent refSeqComposite off
         priority 7
         type genePred
         shortLabel RefSeq HGMD
         longLabel Only NCBI RefSeq manually annotated transcripts with at least one HGMD clinical variant
         trackHandler ncbiRefSeq
         idXref ncbiRefSeqLink mrnaAcc name
         color 20,20,160
         baseColorUseCds given
+        baseColorDefault genomicCodons
 
         track ncbiRefSeqMane
         parent refSeqComposite off
         priority 8
         type genePred
         shortLabel RefSeq MANE
         longLabel RefSeq selected representative transcript for each gene, MANE 0.5
         trackHandler ncbiRefSeq
+        baseColorUseCds given
+        baseColorDefault genomicCodons
 
         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 9
+        baseColorDefault genomicCodons
 
 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