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/chainNetVertebrate.ra src/hg/makeDb/trackDb/human/chainNetVertebrate.ra index 7d89da0..5af17ee 100644 --- src/hg/makeDb/trackDb/human/chainNetVertebrate.ra +++ src/hg/makeDb/trackDb/human/chainNetVertebrate.ra @@ -1,21 +1,21 @@ track vertebrateChainNet compositeTrack on shortLabel Vertebrate Chain/Net longLabel Non-placental Vertebrate Genomes, Chain and Net Alignments subGroup1 view Views chain=Chains net=Nets -subGroup2 species Species s000=Wallaby s001=Wallaby s002=Tasmanian_devil s003=Opossum s004=Platypus s005=Platypus s006=Turkey s007=Turkey s008=Chicken s009=Chicken s010=Chicken s011=Mallard_duck s012=Scarlet_macaw s013=Medium_ground_finch s014=White-throated_sparrow s015=Collared_flycatcher s016=Golden_eagle s017=Peregrine_falcon s018=Saker_falcon s019=Rock_pigeon s020=Parrot s021=Budgerigar s022=Tibetan_ground_jay s023=Zebra_finch s024=Zebra_finch s025=American_alligator s026=Chinese_alligator s027=Lizard s028=Lizard s028b=Garter_snake s029a=Axolotl s029b=X._tropicalis s030=X._tropicalis s031=X._tropicalis s032=X._tropicalis s033=X._tropicalis s034=African_clawed_frog s035=Spiny_softshell_turtle s036=Chinese_softshell_turtle s037=Painted_turtle s038=Painted_turtle s039=Green_seaturtle s040=Coelacanth s041=Spotted_gar s042=Mexican_tetra_(cavefish) s043=Zebrafish s044=Zebrafish s045=Zebrafish s046=Zebrafish s047=Zebrafish s048=Atlantic_cod s049=Stickleback s050=Southern_platyfish s051=Medaka s052=Pundamilia_nyererei s053=Zebra_mbuna s054=Princess_of_Burundi s055=Burton's_mouthbreeder s056=Nile_tilapia s057=Nile_tilapia s058=Nile_tilapia s059=Yellowbelly_pufferfish s060=Fugu s061=Fugu s062=Tetraodon s063=Tetraodon s064a=Lamprey s064b=Lamprey s065=Lamprey s066=Arctic_lamprey +subGroup2 species Species s000=Wallaby s001=Wallaby s002=Tasmanian_devil s003=Opossum s004=Platypus s005=Platypus s006=Turkey s007a=Turkey s007b=Japanese_quail s008a=Chicken s008b=Chicken s009=Chicken s010=Chicken s011=Mallard_duck s012=Scarlet_macaw s013=Medium_ground_finch s014=White-throated_sparrow s015=Collared_flycatcher s016=Golden_eagle s017=Peregrine_falcon s018=Saker_falcon s019=Rock_pigeon s020=Parrot s021=Budgerigar s022=Tibetan_ground_jay s023=Zebra_finch s024=Zebra_finch s025=American_alligator s026=Chinese_alligator s027=Lizard s028=Lizard s028b=Garter_snake s029a=Axolotl s029b=X._tropicalis s030=X._tropicalis s031=X._tropicalis s032=X._tropicalis s033=X._tropicalis s034=African_clawed_frog s035=Spiny_softshell_turtle s036=Chinese_softshell_turtle s037=Painted_turtle s038=Painted_turtle s039=Green_seaturtle s040=Coelacanth s041=Spotted_gar s042=Mexican_tetra_(cavefish) s043=Zebrafish s044=Zebrafish s045=Zebrafish s046=Zebrafish s047=Zebrafish s048=Atlantic_cod s049=Stickleback s050=Southern_platyfish s051=Medaka s052=Pundamilia_nyererei s053=Zebra_mbuna s054=Princess_of_Burundi s055=Burton's_mouthbreeder s056=Nile_tilapia s057=Nile_tilapia s058=Nile_tilapia s059=Yellowbelly_pufferfish s060=Fugu s061=Fugu s062=Tetraodon s063=Tetraodon s064a=Lamprey s064b=Lamprey s065=Lamprey s066=Arctic_lamprey subGroup3 clade Clade c00=mammalia c01=dinosauria c02=lepidosauria c03=amphibia c04=cryptodira c05=coelancanthimorpha c06=neopterygii c07=hyperoartia 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 vertebrateChainNet priority 9 @@ -73,44 +73,60 @@ shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain ornAna1 otherDb ornAna1 track chainMelGal5 subTrack vertebrateChainNetViewchain off subGroups view=chain species=s006 clade=c01 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain melGal5 otherDb melGal5 track chainMelGal1 subTrack vertebrateChainNetViewchain off - subGroups view=chain species=s007 clade=c01 + subGroups view=chain species=s007a clade=c01 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain melGal1 otherDb melGal1 + track chainCotJap2 + subTrack vertebrateChainNetViewchain off + subGroups view=chain species=s007b clade=c01 + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain cotJap2 + otherDb cotJap2 + track chainGalGal6 subTrack vertebrateChainNetViewchain off - subGroups view=chain species=s008 clade=c01 + subGroups view=chain species=s008a clade=c01 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain galGal6 otherDb galGal6 + track chainGalGal5 + subTrack vertebrateChainNetViewchain off + subGroups view=chain species=s008b clade=c01 + shortLabel $o_Organism Chain + longLabel $o_Organism ($o_date) Chained Alignments + type chain galGal5 + otherDb galGal5 + track chainGalGal4 subTrack vertebrateChainNetViewchain off subGroups view=chain species=s009 clade=c01 shortLabel $o_db Chain longLabel $o_Organism ($o_date) Chained Alignments type chain galGal4 otherDb galGal4 track chainGalGal3 subTrack vertebrateChainNetViewchain off subGroups view=chain species=s010 clade=c01 shortLabel $o_Organism Chain longLabel $o_Organism ($o_date) Chained Alignments type chain galGal3 otherDb galGal3 @@ -639,44 +655,60 @@ shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign ornAna1 chainOrnAna1 otherDb ornAna1 track netMelGal5 subTrack vertebrateChainNetViewnet off subGroups view=net species=s006 clade=c01 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign melGal5 chainMelGal5 otherDb melGal5 track netMelGal1 subTrack vertebrateChainNetViewnet off - subGroups view=net species=s007 clade=c01 + subGroups view=net species=s007a clade=c01 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign melGal1 chainMelGal1 otherDb melGal1 + track netCotJap2 + subTrack vertebrateChainNetViewnet off + subGroups view=net species=s007b clade=c01 + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign cotJap2 chainCotJap2 + otherDb cotJap2 + track netGalGal6 subTrack vertebrateChainNetViewnet on - subGroups view=net species=s008 clade=c01 + subGroups view=net species=s008a clade=c01 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign galGal6 chainGalGal6 otherDb galGal6 + track netGalGal5 + subTrack vertebrateChainNetViewnet on + subGroups view=net species=s008b clade=c01 + shortLabel $o_Organism Net + longLabel $o_Organism ($o_date) Alignment Net + type netAlign galGal5 chainGalGal5 + otherDb galGal5 + track netGalGal4 subTrack vertebrateChainNetViewnet off subGroups view=net species=s009 clade=c01 shortLabel $o_db Net longLabel $o_Organism ($o_date) Alignment Net type netAlign galGal4 chainGalGal4 otherDb galGal4 track netGalGal3 subTrack vertebrateChainNetViewnet off subGroups view=net species=s010 clade=c01 shortLabel $o_Organism Net longLabel $o_Organism ($o_date) Alignment Net type netAlign galGal3 chainGalGal3 otherDb galGal3