c036ff920227730eb81df27d750ce6af006d92a5 hiram Wed Oct 7 16:32:54 2020 -0700 cleaning up stray chainNet tracks outside composites refs #22271 diff --git src/hg/makeDb/trackDb/human/chainNetPrimate.ra src/hg/makeDb/trackDb/human/chainNetPrimate.ra index 6159111..4eebf84 100644 --- src/hg/makeDb/trackDb/human/chainNetPrimate.ra +++ src/hg/makeDb/trackDb/human/chainNetPrimate.ra @@ -1,52 +1,60 @@ track primateChainNet compositeTrack on shortLabel Primate Chain/Net longLabel Primate Genomes, Chain and Net Alignments subGroup1 view Views chain=Chains net=Nets -subGroup2 species Species s000=Human s001=Human s002=J._Craig_Venter s0025=Chimp s003=Chimp s004=Chimp s005=Chimp s006=Chimp s007a=Bonobo s007b=Bonobo s008=Bonobo s009a=Gorilla s009b=Gorilla s010=Gorilla s011=Gorilla s012=Gorilla s013a=Orangutan s013b=Orangutan s014=Gibbon s015=Gibbon s016=Proboscis_monkey s017=Black_snub-nosed_monkey s018=Golden_snub-nosed_monkey s019=Angolan_colobus s020=Crab-eating_macaque s021=Rhesus s022=Rhesus s023=Rhesus s024=Baboon s025=Baboon s026=Baboon s027=Pig-tailed_macaque s028=Sooty_mangabey s029=Green_monkey s030=Green_monkey s031=Drill s032=Squirrel_monkey s033=Ma's_night_monkey s034a=Marmoset s034b=Marmoset s035=Marmoset s036=White-faced_sapajou s037=Tarsier s038=Tarsier s039=Sclater's_lemur s040=Black_lemur s041=Coquerel's_sifaka s042=Mouse_lemur s043=Mouse_lemur s044=Mouse_lemur s045=Bushbaby s046=Bushbaby +subGroup2 species Species s000a=Human s000b=Hg38P2 s001=Human s002=J._Craig_Venter s0025=Chimp s003=Chimp s004=Chimp s005=Chimp s006=Chimp s007a=Bonobo s007b=Bonobo s008=Bonobo s009a=Gorilla s009b=Gorilla s010=Gorilla s011=Gorilla s012=Gorilla s013a=Orangutan s013b=Orangutan s014=Gibbon s015=Gibbon s016=Proboscis_monkey s017=Black_snub-nosed_monkey s018=Golden_snub-nosed_monkey s019=Angolan_colobus s020=Crab-eating_macaque s021=Rhesus s022=Rhesus s023a=Rhesus s023b=Rhesus s024=Baboon s025=Baboon s026=Baboon s027=Pig-tailed_macaque s028=Sooty_mangabey s029=Green_monkey s030=Green_monkey s031=Drill s032=Squirrel_monkey s033=Ma's_night_monkey s034a=Marmoset s034b=Marmoset s035=Marmoset s036=White-faced_sapajou s037=Tarsier s038=Tarsier s039=Sclater's_lemur s040=Black_lemur s041=Coquerel's_sifaka s042=Mouse_lemur s043=Mouse_lemur s044=Mouse_lemur s045=Bushbaby s046=Bushbaby subGroup3 clade Clade c00=hominidae c01=cercopithecinae c02=haplorrhini c03=strepsirrhini dragAndDrop subTracks visibility hide group compGeno noInherit on color 0,0,0 altColor 255,255,0 type bed 3 chainLinearGap loose chainMinScore 5000 dimensions dimensionX=clade dimensionY=species sortOrder species=+ view=+ clade=+ configurable on html primateChainNet priority 7 track primateChainNetViewchain shortLabel Chains view chain visibility pack subTrack primateChainNet spectrum on track chainHg38 subTrack primateChainNetViewchain off - subGroups view=chain species=s000 clade=c00 + subGroups view=chain species=s000a clade=c00 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain hg38 otherDb hg38 + track chainHg38Patch2 + subTrack primateChainNetViewchain off + subGroups view=chain species=s000b clade=c00 + shortLabel $o_db Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain hg38Patch2 + otherDb hg38Patch2 + track chainHg18 subTrack primateChainNetViewchain off subGroups view=chain species=s001 clade=c00 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain hg18 otherDb hg18 track chainVenter1 subTrack primateChainNetViewchain off subGroups view=chain species=s002 clade=c00 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain venter1 otherDb venter1 @@ -223,33 +231,41 @@ subTrack primateChainNetViewchain off subGroups view=chain species=s021 clade=c01 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain rheMac10 otherDb rheMac10 track chainRheMac8 subTrack primateChainNetViewchain off subGroups view=chain species=s022 clade=c01 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain rheMac8 otherDb rheMac8 + track chainRheMac3 + subTrack primateChainNetViewchain off + subGroups view=chain species=s023a clade=c01 + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain rheMac3 + otherDb rheMac3 + track chainRheMac2 subTrack primateChainNetViewchain off - subGroups view=chain species=s023 clade=c01 + subGroups view=chain species=s023b clade=c01 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain rheMac2 otherDb rheMac2 track chainPapAnu4 subTrack primateChainNetViewchain off subGroups view=chain species=s024 clade=c01 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain papAnu4 otherDb papAnu4 track chainPapAnu3 subTrack primateChainNetViewchain off @@ -439,36 +455,44 @@ subTrack primateChainNetViewchain off subGroups view=chain species=s046 clade=c03 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain otoGar1 otherDb otoGar1 track primateChainNetViewnet shortLabel Nets view net visibility dense subTrack primateChainNet track netHg38 subTrack primateChainNetViewnet off - subGroups view=net species=s000 clade=c00 + subGroups view=net species=s000a clade=c00 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign hg38 chainHg38 otherDb hg38 + track netHg38Patch2 + subTrack primateChainNetViewnet off + subGroups view=net species=s000b clade=c00 + shortLabel $o_db Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign hg38Patch2 chainHg38Patch2 + otherDb hg38Patch2 + track netHg18 subTrack primateChainNetViewnet off subGroups view=net species=s001 clade=c00 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign hg18 chainHg18 otherDb hg18 track netVenter1 subTrack primateChainNetViewnet off subGroups view=net species=s002 clade=c00 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign venter1 chainVenter1 otherDb venter1 @@ -645,33 +669,41 @@ subTrack primateChainNetViewnet off subGroups view=net species=s021 clade=c01 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign rheMac10 chainRheMac10 otherDb rheMac10 track netRheMac8 subTrack primateChainNetViewnet on subGroups view=net species=s022 clade=c01 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign rheMac8 chainRheMac8 otherDb rheMac8 + track netRheMac3 + subTrack primateChainNetViewnet on + subGroups view=net species=s023a clade=c01 + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign rheMac3 chainRheMac3 + otherDb rheMac3 + track netRheMac2 subTrack primateChainNetViewnet off - subGroups view=net species=s023 clade=c01 + subGroups view=net species=s023b clade=c01 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign rheMac2 chainRheMac2 otherDb rheMac2 track netPapAnu4 subTrack primateChainNetViewnet off subGroups view=net species=s024 clade=c01 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign papAnu4 chainPapAnu4 otherDb papAnu4 track netPapAnu3 subTrack primateChainNetViewnet off