06f137f0b7d49def1d0690602cc10a6ad91eb083
hiram
  Mon May 24 13:32:31 2021 -0700
adding canFam6 chainNet definitions refs #27546

diff --git src/hg/makeDb/trackDb/human/chainNetPlacental.ra src/hg/makeDb/trackDb/human/chainNetPlacental.ra
index 83605f8..631bc57 100644
--- src/hg/makeDb/trackDb/human/chainNetPlacental.ra
+++ src/hg/makeDb/trackDb/human/chainNetPlacental.ra
@@ -1,21 +1,21 @@
 track placentalChainNet
 compositeTrack on
 shortLabel Placental Chain/Net
 longLabel Non-primate Placental Mammal Genomes, Chain and Net Alignments
 subGroup1 view Views chain=Chains net=Nets
-subGroup2 species Species s000=Guinea_pig s001=Guinea_pig s002=Chinchilla s003=Chinese_hamster s004a=Chinese_hamster_CHOv1 s004b=Chinese_hamster_CHOv2 s004c=RegenCHO1 s005a=Kangaroo_rat s005b=Beaver s006=Malayan_flying_lemur s007=Naked_mole-rat s008=Naked_mole-rat s0081=Damara_mole-rat s009=Lesser_Egyptian_jerboa s010=Golden_hamster s011=Prairie_vole s012a=Mouse s012b=Mouse38B s012c=Mouse s013=Mouse s014=Mouse s015=Mouse s016=Mouse s017=Upper_Galilee_mountains_blind_mole_rat s018=Pika s019=Pika s020=Brush-tailed_rat s021=Rabbit s022=Rabbit s023=Prairie_deer_mouse s024a=Rat s024b=RegenRn1 s024c=RegenRn0 s024d=Rat s025=Rat s026=Rat s027=Rat s028=Rat s029=Squirrel s030=Squirrel s031=Tree_shrew s032=Chinese_tree_shrew s033=Panda s034a=Dog s034b=Dog s034c=Dog s035=Dog s036=Dog s037=Dog s037b=Cat s038=Cat s039=Cat s040=Cat s041=Cat s042=Weddell_seal s043=Ferret s043a=Southern_sea_otter s044=Hawaiian_monk_seal s045=Pacific_walrus s046=Amur_tiger s047=Polar_bear s048=Minke_whale s049=Bison s050=Wild_yak s051a=Cow s051b=Cow s052=Cow s053=Cow s054=Cow s055=Cow s056=Cow s057=Cow s058=Cow s059=Cow s060=Water_buffalo s061=Bactrian_camel s062=Domestic_goat s063=Yangtze_river_dolphin s064=Killer_whale s065a=Sheep s065b=Sheep s065c=Sheep s065d=Sheep s067=Tibetan_antelope s068=Sperm_whale s069=Pig s070=Pig s071=Pig s072=Pig s073=Dolphin s074=Dolphin s075=Alpaca s076=Alpaca s077=Straw_colored_fruit_bat s078=Big_brown_bat s079=Indian_false_vampire s080=Brandt's_myotis_(bat) s081=David's_myotis_(bat) s082=Microbat s083=Microbat s084=Black_flying-fox s085=Parnell's_mustached_bat s086=Megabat s087=Greater_horseshoe_bat s088=Egyptian_rousette s089=Star-nosed_mole s090=Hedgehog s091=Hedgehog s092=Chinese_pangolin s093=Shrew s094=Shrew s095=White_rhinoceros s096a=Horse s096b=Horse s096c=Horse s098=Przewalski_horse s099=Sloth s100=Armadillo s101=Armadillo s102=Armadillo s103=Cape_golden_mole s104=Tenrec s105=Tenrec s106=Cape_elephant_shrew s107=Elephant s108=Elephant s109=Elephant s110=Aardvark s111=Rock_hyrax s112=Manatee
+subGroup2 species Species s000=Guinea_pig s001=Guinea_pig s002=Chinchilla s003=Chinese_hamster s004a=Chinese_hamster_CHOv1 s004b=Chinese_hamster_CHOv2 s004c=RegenCHO1 s005a=Kangaroo_rat s005b=Beaver s006=Malayan_flying_lemur s007=Naked_mole-rat s008=Naked_mole-rat s0081=Damara_mole-rat s009=Lesser_Egyptian_jerboa s010=Golden_hamster s011=Prairie_vole s012a=Mouse s012b=Mouse38B s012c=Mouse s013=Mouse s014=Mouse s015=Mouse s016=Mouse s017=Upper_Galilee_mountains_blind_mole_rat s018=Pika s019=Pika s020=Brush-tailed_rat s021=Rabbit s022=Rabbit s023=Prairie_deer_mouse s024a=Rat s024b=RegenRn1 s024c=RegenRn0 s024d=Rat s025=Rat s026=Rat s027=Rat s028=Rat s029=Squirrel s030=Squirrel s031=Tree_shrew s032=Chinese_tree_shrew s033=Panda s034a=Dog s034b=Dog s034c=Dog s034d=Dog s035=Dog s036=Dog s037=Dog s037b=Cat s038=Cat s039=Cat s040=Cat s041=Cat s042=Weddell_seal s043=Ferret s043a=Southern_sea_otter s044=Hawaiian_monk_seal s045=Pacific_walrus s046=Amur_tiger s047=Polar_bear s048=Minke_whale s049=Bison s050=Wild_yak s051a=Cow s051b=Cow s052=Cow s053=Cow s054=Cow s055=Cow s056=Cow s057=Cow s058=Cow s059=Cow s060=Water_buffalo s061=Bactrian_camel s062=Domestic_goat s063=Yangtze_river_dolphin s064=Killer_whale s065a=Sheep s065b=Sheep s065c=Sheep s065d=Sheep s067=Tibetan_antelope s068=Sperm_whale s069=Pig s070=Pig s071=Pig s072=Pig s073=Dolphin s074=Dolphin s075=Alpaca s076=Alpaca s077=Straw_colored_fruit_bat s078=Big_brown_bat s079=Indian_false_vampire s080=Brandt's_myotis_(bat) s081=David's_myotis_(bat) s082=Microbat s083=Microbat s084=Black_flying-fox s085=Parnell's_mustached_bat s086=Megabat s087=Greater_horseshoe_bat s088=Egyptian_rousette s089=Star-nosed_mole s090=Hedgehog s091=Hedgehog s092=Chinese_pangolin s093=Shrew s094=Shrew s095=White_rhinoceros s096a=Horse s096b=Horse s096c=Horse s098=Przewalski_horse s099=Sloth s100=Armadillo s101=Armadillo s102=Armadillo s103=Cape_golden_mole s104=Tenrec s105=Tenrec s106=Cape_elephant_shrew s107=Elephant s108=Elephant s109=Elephant s110=Aardvark s111=Rock_hyrax s112=Manatee
 subGroup3 clade Clade c00=Euarchontoglires c01=Carnivora c02=Cetartiodactyla c03=Chiroptera c04=Laurasiatheria c05=Perissodactyla c06=Xenarthra c07=Afrotheria
 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 placentalChainNet
 priority 8
@@ -367,43 +367,57 @@
         subTrack placentalChainNetViewchain off
         subGroups view=chain species=s032 clade=c00
         shortLabel $o_Organism Chain
         longLabel $o_Organism ($o_date) Chained Alignments
         type chain tupChi1
         otherDb tupChi1
 
         track chainAilMel1
         subTrack placentalChainNetViewchain off
         subGroups view=chain species=s033 clade=c01
         shortLabel $o_Organism Chain
         longLabel $o_Organism ($o_date) Chained Alignments
         type chain ailMel1
         otherDb ailMel1
 
-include trackDb.canFam5.ra alpha
+        track chainCanFam6
+        subTrack placentalChainNetViewchain off
+        subGroups view=chain species=s034a clade=c01
+        shortLabel $o_Organism Chain
+        longLabel $o_Organism ($o_date) Chained Alignments
+        type chain canFam6
+        otherDb canFam6
 
-        track chainCanFam4
+        track chainCanFam5
         subTrack placentalChainNetViewchain off
         subGroups view=chain species=s034b clade=c01
         shortLabel $o_Organism Chain
         longLabel $o_Organism ($o_date) Chained Alignments
+        type chain canFam5
+        otherDb canFam5
+
+        track chainCanFam4
+        subTrack placentalChainNetViewchain off
+        subGroups view=chain species=s034c clade=c01
+        shortLabel $o_Organism Chain
+        longLabel $o_Organism ($o_date) Chained Alignments
         type chain canFam4
         otherDb canFam4
 
         track chainCanFam3
         subTrack placentalChainNetViewchain off
-        subGroups view=chain species=s034c clade=c01
+        subGroups view=chain species=s034d clade=c01
         shortLabel $o_Organism Chain
         longLabel $o_Organism ($o_date) Chained Alignments
         type chain canFam3
         otherDb canFam3
 
         track chainCanFam2
         subTrack placentalChainNetViewchain off
         subGroups view=chain species=s035 clade=c01
         shortLabel $o_Organism Chain
         longLabel $o_Organism ($o_date) Chained Alignments
         type chain canFam2
         otherDb canFam2
 
         track chainCanFam1
         subTrack placentalChainNetViewchain off
@@ -1417,41 +1431,57 @@
         subTrack placentalChainNetViewnet off
         subGroups view=net species=s032 clade=c00
         shortLabel $o_Organism Net
         longLabel $o_Organism ($o_date) Alignment Net
         type netAlign tupChi1 chainTupChi1
         otherDb tupChi1
 
         track netAilMel1
         subTrack placentalChainNetViewnet off
         subGroups view=net species=s033 clade=c01
         shortLabel $o_Organism Net
         longLabel $o_Organism ($o_date) Alignment Net
         type netAlign ailMel1 chainAilMel1
         otherDb ailMel1
 
-        track netCanFam4
+        track netCanFam6
+        subTrack placentalChainNetViewnet on
+        subGroups view=net species=s034a clade=c01
+        shortLabel $o_Organism Net
+        longLabel $o_Organism ($o_date) Alignment Net
+        type netAlign canFam6 chainCanFam6
+        otherDb canFam6
+
+        track netCanFam5
         subTrack placentalChainNetViewnet on
         subGroups view=net species=s034b clade=c01
         shortLabel $o_Organism Net
         longLabel $o_Organism ($o_date) Alignment Net
+        type netAlign canFam5 chainCanFam5
+        otherDb canFam5
+
+        track netCanFam4
+        subTrack placentalChainNetViewnet on
+        subGroups view=net species=s034c clade=c01
+        shortLabel $o_Organism Net
+        longLabel $o_Organism ($o_date) Alignment Net
         type netAlign canFam4 chainCanFam4
         otherDb canFam4
 
         track netCanFam3
         subTrack placentalChainNetViewnet on
-        subGroups view=net species=s034c clade=c01
+        subGroups view=net species=s034d clade=c01
         shortLabel $o_Organism Net
         longLabel $o_Organism ($o_date) Alignment Net
         type netAlign canFam3 chainCanFam3
         otherDb canFam3
 
         track netCanFam2
         subTrack placentalChainNetViewnet off
         subGroups view=net species=s035 clade=c01
         shortLabel $o_db Net
         longLabel $o_Organism ($o_date) Alignment Net
         type netAlign canFam2 chainCanFam2
         otherDb canFam2
 
         track netCanFam1
         subTrack placentalChainNetViewnet off