22f0c874d90f86f1bfa4014ee29f9c0ee0bff517
markd
  Tue Jun 25 23:17:29 2019 -0700
load transMap V5

diff --git src/hg/makeDb/trackDb/trackDb.transMap.ra src/hg/makeDb/trackDb/trackDb.transMap.ra
index c607238..90d5d63 100644
--- src/hg/makeDb/trackDb/trackDb.transMap.ra
+++ src/hg/makeDb/trackDb/trackDb.transMap.ra
@@ -1,232 +1,253 @@
 track transMap
 superTrack on
 shortLabel TransMap
 longLabel TransMap Alignments
 group genes
 
-    track transMapAlnUcscGenes
-    superTrack transMap pack
-    shortLabel TransMap UCSC
-    longLabel TransMap UCSC Gene Mappings
-    trackHandler transMap
+track transMapV4
+superTrack on
+shortLabel TransMap V4
+longLabel TransMap Alignments Version 4
+html transMap
+group genes
+
+    track transMapEnsemblV4
+    superTrack transMapV4 pack
+    shortLabel TransMap Ensembl
+    longLabel TransMap Ensembl and GENCODE Mappings Version 4
+    html transMapEnsembl
+    transMapSrcSet ensembl
     group genes
-    type psl
-    priority 12.002
+    type bigPsl
+    priority 10.001
     color 0,100,0
+    canPack on
     visibility pack
-    transMapInfo transMapInfoUcscGenes
-    transMapSrc hgFixed.transMapSrcUcscGenes
-    transMapGene hgFixed.transMapGeneUcscGenes
     baseColorDefault diffCodons
-    baseColorUseCds table hgFixed.transMapGeneUcscGenes
-    baseColorUseSequence extFile hgFixed.transMapSeqUcscGenes hgFixed.transMapExtFileUcscGenes
+    baseColorUseCds given
+    baseColorUseSequence lfExtra
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     showCdsAllScales .
     showCdsMaxZoom 10000.0
+    labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId,geneType,transcriptType
+    defaultLabelFields orgAbbrev,geneName
+    labelSeparator " "
+    bigDataUrl /gbdb/$D/transMap/V4/$D.ensembl.transMapV4.bigPsl
+    searchIndex name,srcTransId,geneName,geneId
 
-searchTable transMapAlnUcscGenes
-searchType psl
-searchMethod prefix
-searchPriority 2.31
+searchTable transMapEnsemblV4
+searchType bigPsl
 
-    track transMapAlnRefSeq
-    superTrack transMap pack
+    track transMapRefSeqV4
+    superTrack transMapV4 pack
     shortLabel TransMap RefGene
-    longLabel TransMap RefSeq Gene Mappings
-    trackHandler transMap
+    longLabel TransMap RefSeq Gene Mappings Version 4
+    html transMapRefSeq
+    transMapSrcSet refseq
     group genes
-    type psl
-    priority 12.003
+    type bigPsl
+    priority 10.003
     color 0,100,0
+    canPack on
     visibility pack
-    transMapInfo transMapInfoRefSeq
-    transMapSrc hgFixed.transMapSrcRefSeq
-    transMapGene hgFixed.transMapGeneRefSeq
     baseColorDefault diffCodons
-    baseColorUseCds table hgFixed.transMapGeneRefSeq
-    baseColorUseSequence extFile hgFixed.transMapSeqRefSeq hgFixed.transMapExtFileRefSeq
+    baseColorUseCds given
+    baseColorUseSequence lfExtra
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     showCdsAllScales .
     showCdsMaxZoom 10000.0
+    labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId
+    defaultLabelFields orgAbbrev,geneName
+    labelSeparator " "
+    bigDataUrl /gbdb/$D/transMap/V4/$D.refseq.transMapV4.bigPsl
+    searchIndex name,srcTransId,geneName,geneId
 
-searchTable transMapAlnRefSeq
-searchType psl
-searchMethod prefix
-searchPriority 2.31
+searchTable transMapRefSeqV4
+searchType bigPsl
 
-    track transMapAlnMRna
-    superTrack transMap pack
-    shortLabel TransMap mRNA
-    longLabel TransMap GenBank mRNA Mappings
-    trackHandler transMap
+    track transMapRnaV4
+    superTrack transMapV4 pack
+    shortLabel TransMap RNA
+    longLabel TransMap GenBank RNA Mappings Version 4
+    html transMapRna
+    transMapSrcSet rna
     group genes
-    type psl
-    priority 12.004
+    type bigPsl
+    priority 10.004
     color 0,100,0
+    canPack on
     visibility pack
-    transMapInfo transMapInfoMRna
-    transMapSrc hgFixed.transMapSrcMRna
-    transMapGene hgFixed.transMapGeneMRna
     baseColorDefault diffCodons
-    baseColorUseCds table hgFixed.transMapGeneMRna
-    baseColorUseSequence extFile hgFixed.transMapSeqMRna hgFixed.transMapExtFileMRna
+    baseColorUseCds given
+    baseColorUseSequence lfExtra
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     showCdsAllScales .
     showCdsMaxZoom 10000.0
+    labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName
+    defaultLabelFields orgAbbrev,srcTransId
+    labelSeparator " "
+    bigDataUrl /gbdb/$D/transMap/V4/$D.rna.transMapV4.bigPsl
+    searchIndex name,srcTransId,geneName
 
-searchTable transMapAlnMRna
-searchType psl
-searchMethod prefix
-searchPriority 2.31
+searchTable transMapRnaV4
+searchType bigPsl
 
-    track transMapAlnSplicedEst
-    superTrack transMap hide
+    track transMapEstV4
+    superTrack transMapV4 hide
     shortLabel TransMap ESTs
-    longLabel TransMap Spliced EST Mappings
-    trackHandler transMap
+    longLabel TransMap EST Mappings Version 4
+    html transMapEst
+    transMapSrcSet est
     group genes
-    type psl
-    priority 12.005
+    type bigPsl
+    priority 10.005
     color 0,100,0
+    canPack on
     visibility hide
-    transMapInfo transMapInfoSplicedEst
-    transMapSrc hgFixed.transMapSrcSplicedEst
     baseColorDefault none
-    baseColorUseSequence extFile hgFixed.transMapSeqSplicedEst hgFixed.transMapExtFileSplicedEst
+    baseColorUseSequence lfExtra
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
+    labelFields commonName,orgAbbrev,srcDb,srcTransId,name
+    defaultLabelFields orgAbbrev,srcTransId
+    labelSeparator " "
+    bigDataUrl /gbdb/$D/transMap/V4/$D.est.transMapV4.bigPsl
+    searchIndex name,srcTransId
 
-searchTable transMapAlnSplicedEst
-searchType psl
-searchMethod prefix
-searchPriority 2.31
+searchTable transMapEstV4
+searchType bigPsl
 
-track transMapV4
+track transMapV5
 superTrack on
-shortLabel TransMap 
-longLabel TransMap Alignments Version 4
+shortLabel TransMap V5
+longLabel TransMap Alignments Version 5
+html transMap
 group genes
 
-    track transMapEnsemblV4
-    superTrack transMapV4 pack
+    track transMapEnsemblV5
+    superTrack transMapV5 pack
     shortLabel TransMap Ensembl
-    longLabel TransMap Ensembl Mappings Version 4
+    longLabel TransMap Ensembl and GENCODE Mappings Version 5
+    html transMapEnsembl
     transMapSrcSet ensembl
     group genes
     type bigPsl
     priority 10.001
     color 0,100,0
     canPack on
     visibility pack
     baseColorDefault diffCodons
     baseColorUseCds given
     baseColorUseSequence lfExtra
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     showCdsAllScales .
     showCdsMaxZoom 10000.0
     labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId,geneType,transcriptType
     defaultLabelFields orgAbbrev,geneName
     labelSeparator " "
-    bigDataUrl /gbdb/$D/transMap/V4/$D.ensembl.transMapV4.bigPsl
+    bigDataUrl /gbdb/$D/transMap/V5/$D.ensembl.transMapV5.bigPsl
     searchIndex name,srcTransId,geneName,geneId
 
-searchTable transMapEnsemblV4
+searchTable transMapEnsemblV5
 searchType bigPsl
 
-    track transMapRefSeqV4
-    superTrack transMapV4 pack
+    track transMapRefSeqV5
+    superTrack transMapV5 pack
     shortLabel TransMap RefGene
-    longLabel TransMap RefSeq Gene Mappings Version 4
+    longLabel TransMap RefSeq Gene Mappings Version 5
+    html transMapRefSeq
     transMapSrcSet refseq
     group genes
     type bigPsl
     priority 10.003
     color 0,100,0
     canPack on
     visibility pack
     baseColorDefault diffCodons
     baseColorUseCds given
     baseColorUseSequence lfExtra
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     showCdsAllScales .
     showCdsMaxZoom 10000.0
     labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName,geneId
     defaultLabelFields orgAbbrev,geneName
     labelSeparator " "
-    bigDataUrl /gbdb/$D/transMap/V4/$D.refseq.transMapV4.bigPsl
+    bigDataUrl /gbdb/$D/transMap/V5/$D.refseq.transMapV5.bigPsl
     searchIndex name,srcTransId,geneName,geneId
 
-searchTable transMapRefSeqV4
+searchTable transMapRefSeqV5
 searchType bigPsl
 
-    track transMapRnaV4
-    superTrack transMapV4 pack
+    track transMapRnaV5
+    superTrack transMapV5 pack
     shortLabel TransMap RNA
-    longLabel TransMap GenBank RNA Mappings Version 4
+    longLabel TransMap GenBank RNA Mappings Version 5
+    html transMapRna
     transMapSrcSet rna
     group genes
     type bigPsl
     priority 10.004
     color 0,100,0
     canPack on
     visibility pack
     baseColorDefault diffCodons
     baseColorUseCds given
     baseColorUseSequence lfExtra
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     showCdsAllScales .
     showCdsMaxZoom 10000.0
     labelFields commonName,orgAbbrev,srcDb,srcTransId,name,geneName
     defaultLabelFields orgAbbrev,srcTransId
     labelSeparator " "
-    bigDataUrl /gbdb/$D/transMap/V4/$D.rna.transMapV4.bigPsl
+    bigDataUrl /gbdb/$D/transMap/V5/$D.rna.transMapV5.bigPsl
     searchIndex name,srcTransId,geneName
 
-searchTable transMapRnaV4
+searchTable transMapRnaV5
 searchType bigPsl
 
-    track transMapEstV4
-    superTrack transMapV4 hide
+    track transMapEstV5
+    superTrack transMapV5 hide
     shortLabel TransMap ESTs
-    longLabel TransMap EST Mappings Version 4
+    longLabel TransMap EST Mappings Version 5
+    html transMapEst
     transMapSrcSet est
     group genes
     type bigPsl
     priority 10.005
     color 0,100,0
     canPack on
     visibility hide
     baseColorDefault none
     baseColorUseSequence lfExtra
     indelDoubleInsert on
     indelQueryInsert on
     showDiffBasesAllScales .
     showDiffBasesMaxZoom 10000.0
     labelFields commonName,orgAbbrev,srcDb,srcTransId,name
     defaultLabelFields orgAbbrev,srcTransId
     labelSeparator " "
-    bigDataUrl /gbdb/$D/transMap/V4/$D.est.transMapV4.bigPsl
+    bigDataUrl /gbdb/$D/transMap/V5/$D.est.transMapV5.bigPsl
     searchIndex name,srcTransId
 
-searchTable transMapEstV4
+searchTable transMapEstV5
 searchType bigPsl