src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.27
1.27 2009/12/29 23:27:33 hiram
clean up chain net composites for non-released genomes on hg18
Index: src/hg/makeDb/trackDb/trackDb.chainNet.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.chainNet.ra,v
retrieving revision 1.26
retrieving revision 1.27
diff -b -B -U 4 -r1.26 -r1.27
--- src/hg/makeDb/trackDb/trackDb.chainNet.ra 28 Dec 2009 23:43:28 -0000 1.26
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra 29 Dec 2009 23:27:33 -0000 1.27
@@ -909,8 +909,90 @@
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign braFlo1 chainBraFlo1
+track chainNetLoxAfr2
+release alpha
+compositeTrack on
+shortLabel $o_db Chain/Net
+longLabel $o_Organism ($o_date/$o_db), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 191
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb loxAfr2
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+ track chainLoxAfr2
+ release alpha
+ subTrack chainNetLoxAfr2
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain loxAfr2
+
+ track netLoxAfr2
+ release alpha
+ subTrack chainNetLoxAfr2
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign loxAfr2 chainLoxAfr2
+
+track chainNetLoxAfr1
+release alpha
+compositeTrack on
+shortLabel $o_Organism Chain/Net
+longLabel $o_Organism ($o_date/$o_db), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 191
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb loxAfr1
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+ track chainLoxAfr1
+ release alpha
+ subTrack chainNetLoxAfr1
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain loxAfr1
+
+ track netLoxAfr1
+ release alpha
+ subTrack chainNetLoxAfr1
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign loxAfr1 chainLoxAfr1
+
track chainNetMonDom1
release alpha
compositeTrack on
shortLabel $o_Organism Chain/Net
@@ -1029,8 +1111,88 @@
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign monDom5 chainMonDom5
+track chainNetEriEur1
+release alpha
+compositeTrack on
+shortLabel $o_Organism Chain/Net
+longLabel $o_Organism ($o_date/$o_db), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 191
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb eriEur1
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+ track chainEriEur1
+ subTrack chainNetEriEur1
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain eriEur1
+
+ track netEriEur1
+ subTrack chainNetEriEur1
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign eriEur1 chainEriEur1
+
+track chainNetSorAra1
+release alpha
+compositeTrack on
+shortLabel $o_Organism Chain/Net
+longLabel $o_Organism ($o_date/$o_db), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 209
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb sorAra1
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+ track chainSorAra1
+ release alpha
+ subTrack chainNetSorAra1
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain sorAra1
+
+ track netSorAra1
+ release alpha
+ subTrack chainNetSorAra1
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign sorAra1 chainSorAra1
+
# release alpha until mm9 individual chain/net tracks phased out
track chainNetMm9
release alpha
compositeTrack on
@@ -1365,8 +1527,90 @@
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign cavPor2 chainCavPor2
+track chainNetOryCun2
+release alpha
+compositeTrack on
+shortLabel $o_Organism Chain/Net
+longLabel $o_Organism ($o_date/$o_db), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 209
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb oryCun2
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+ track chainOryCun2
+ release alpha
+ subTrack chainNetOryCun2
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain oryCun2
+
+ track netOryCun2
+ release alpha
+ subTrack chainNetOryCun2
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign oryCun2 chainOryCun2
+
+track chainNetOryCun1
+release alpha
+compositeTrack on
+shortLabel $o_Organism Chain/Net
+longLabel $o_Organism ($o_date/$o_db), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 209
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb oryCun1
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+ track chainOryCun1
+ release alpha
+ subTrack chainNetOryCun1
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain oryCun1
+
+ track netOryCun1
+ release alpha
+ subTrack chainNetOryCun1
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign oryCun1 chainOryCun1
+
track chainNetEquCab2
compositeTrack on
shortLabel $o_Organism Chain/Net
longLabel $o_Organism (Sep. 2007/equCab2), Chain and Net Alignments
@@ -1888,8 +2132,48 @@
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment net
type netAlign panTro1 chainPanTro1
+track chainNetGorGor1
+release alpha
+compositeTrack on
+shortLabel $o_Organism Chain/Net
+longLabel $o_Organism ($o_date/$o_db), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 498
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb gorGor1
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+ track chainGorGor1
+ release alpha
+ subTrack chainNetGorGor1
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain gorGor1
+
+ track netGorGor1
+ release alpha
+ subTrack chainNetGorGor1
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment net
+ type netAlign gorGor1 chainGorGor1
+
track chainNetPonAbe2
release alpha
compositeTrack on
shortLabel $o_Organism Chain/Net
@@ -1928,8 +2212,88 @@
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment net
type netAlign ponAbe2 chainPonAbe2
+track chainNetTupBel1
+release alpha
+compositeTrack on
+shortLabel $o_Organism Chain/Net
+longLabel $o_Organism ($o_date/$o_db), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 498
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb tupBel1
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+ track chainTupBel1
+ release alpha
+ subTrack chainNetTupBel1
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain tupBel1
+
+ track netTupBel1
+ release alpha
+ subTrack chainNetTupBel1
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment net
+ type netAlign tupBel1 chainTupBel1
+
+track chainNetOtoGar1
+release alpha
+compositeTrack on
+shortLabel $o_Organism Chain/Net
+longLabel $o_Organism ($o_date/$o_db), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 498
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb otoGar1
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+ track chainOtoGar1
+ release alpha
+ subTrack chainNetOtoGar1
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain otoGar1
+
+ track netOtoGar1
+ release alpha
+ subTrack chainNetOtoGar1
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment net
+ type netAlign otoGar1 chainOtoGar1
+
track chainNetCalJac1
release alpha
compositeTrack on
shortLabel $o_Organism Chain/Net