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
@@ -1,197 +1,204 @@
 track refSeqComposite
 compositeTrack on
 shortLabel NCBI RefSeq
 longLabel RefSeq gene predictions from NCBI
 group genes
 visibility pack
 type genePred
 dragAndDrop subTracks
 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/$$"
 
         track ncbiRefSeqPsl
         priority 5
         parent refSeqComposite off
         shortLabel RefSeq Alignments
         longLabel RefSeq Alignments of RNAs
         type psl
         indelDoubleInsert on
         indelQueryInsert on
         showDiffBasesAllScales .
         showDiffBasesMaxZoom 10000.0
         showCdsMaxZoom 10000.0
         showCdsAllScales .
         baseColorDefault diffCodons
         pslSequence no
         baseColorUseSequence extFile seqNcbiRefSeq extNcbiRefSeq
         baseColorUseCds table ncbiRefSeqCds
         idXref ncbiRefSeqLink mrnaAcc name
         color 0,0,0
         pepTable ncbiRefSeqPepTable
 
         track ncbiRefSeqGenomicDiff
         parent refSeqComposite off
         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 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
 searchType genePred
 searchMethod prefix
 xrefTable ncbiRefSeqLink
 xrefQuery select id,protAcc from %s where protAcc like '%s%%'
 termRegex [NY]P_[0-9]+(\.[0-9]+)?
 dontCheck XP_[0-9]+(\.[0-9]+)?
 searchPriority 2.07201
 
 searchName ncbiRefSeqPredictedProtAcc
 searchTable ncbiRefSeqPredicted
 searchType genePred
 searchMethod prefix
 xrefTable ncbiRefSeqLink
 xrefQuery select id,protAcc from %s where protAcc like '%s%%'
 termRegex XP_[0-9]+(\.[0-9]+)?
 dontCheck [NY]P_[0-9]+(\.[0-9]+)?
 searchPriority 2.07203
 
 searchName ncbiRefSeqCuratedProduct
 searchTable ncbiRefSeqCurated
 searchType genePred
 searchMethod fuzzy
 xrefTable ncbiRefSeqLink
 xrefQuery select id,product from %s where product like '%%%s%%'
 searchPriority 2.07201
 
 searchName ncbiRefSeqPredictedProduct
 searchTable ncbiRefSeqPredicted
 searchType genePred
 searchMethod fuzzy
 xrefTable ncbiRefSeqLink
 xrefQuery select id,product from %s where product like '%%%s%%'
 searchPriority 2.07203
 
 searchTable ncbiRefSeqCurated
 searchMethod exact
 searchType genePred
 semiShortCircuit 1
 termRegex [NY][MRP]_[0-9]{6}[0-9]*\.[0-9]+
 searchPriority 2.07202
 
 searchName ncbiRefSeqCuratedNoVersion
 searchTable ncbiRefSeqCurated
 query select chrom,txStart,txEnd,name from %s where name like '%s.%%'
 semiShortCircuit 1
 termRegex [NY][MRP]_[0-9]{6}[0-9]*
 dontCheck [NY][MRP]_[0-9]{6}[0-9]*\.[0-9]+
 searchPriority 2.07202
 
 searchTable ncbiRefSeqPredicted
 searchMethod exact
 searchType genePred
 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