src/hg/makeDb/trackDb/trackDb.ra 1.517
1.517 2009/07/06 17:50:32 hiram
Composite chain/net tracks for equCab2 release, chicken, platypus, opossum, human, mouse, dog
Index: src/hg/makeDb/trackDb/trackDb.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.ra,v
retrieving revision 1.516
retrieving revision 1.517
diff -b -B -U 4 -r1.516 -r1.517
--- src/hg/makeDb/trackDb/trackDb.ra 2 Jul 2009 22:46:55 -0000 1.516
+++ src/hg/makeDb/trackDb/trackDb.ra 6 Jul 2009 17:50:32 -0000 1.517
@@ -2391,8 +2391,48 @@
spectrum on
type netAlign galGal2 chainGalGal2
otherDb galGal2
+# release alpha until individual galGal3 tracks are obsolete
+track chickenChainNet
+compositeTrack on
+shortLabel Chicken Chain/Net
+longLabel Chicken (May. 2006/galGal3), Chain and Net alignment tracks
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 181
+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 galGal3
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+ track chainGalGal3
+ subTrack chickenChainNet
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain galGal3
+
+ track netGalGal3
+ subTrack chickenChainNet
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign galGal3 chainGalGal3
+
# release alpha: $o_db in shortLabel
track chainGalGal3
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
@@ -2504,8 +2544,48 @@
type netAlign taeGut1 chainTaeGut1
otherDb taeGut1
release beta
+# release alpha until ornAna1 individual chain/net tracks phased out
+track platypusChainNet
+compositeTrack on
+shortLabel Platypus Chain/Net
+longLabel Platypus (Mar. 2007/ornAna1), Chain and Net alignment tracks
+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 ornAna1
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+ track chainOrnAna1
+ subTrack platypusChainNet
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain ornAna1
+
+ track netOrnAna1
+ subTrack platypusChainNet
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign ornAna1 chainOrnAna1
+
track chainOrnAna1
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
group compGeno
@@ -2552,8 +2632,48 @@
spectrum on
type netAlign macEug1 chainMacEug1
otherDb macEug1
+# release alpha until monDom5 individual chain/net tracks phased out
+track opossumChainNet
+compositeTrack on
+shortLabel Opossum Chain/Net
+longLabel Opossum (Oct. 2006/monDom5), Chain and Net alignment tracks
+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 monDom5
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+ track chainMonDom5
+ subTrack opossumChainNet
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain monDom5
+
+ track netMonDom5
+ subTrack opossumChainNet
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign monDom5 chainMonDom5
+
track chainMonDom5
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
group compGeno
@@ -2780,8 +2900,48 @@
spectrum on
type netAlign mm6 chainMm6
otherDb mm6
+# release alpha until mm9 individual chain/net tracks phased out
+track mouseChainNet
+compositeTrack on
+shortLabel Mouse Chain/Net
+longLabel Mouse (Jul. 2007/mm9), Chain and Net alignment tracks
+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 mm9
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+ track chainMm9
+ subTrack mouseChainNet
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain mm9
+
+ track netMm9
+ subTrack mouseChainNet
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign mm9 chainMm9
+
track chainMm9
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
group compGeno
@@ -3022,8 +3182,9 @@
spectrum on
type netAlign bosTau1 chainBosTau1
otherDb bosTau1
+# release alpha until equCab1 phased out
track horseChainNet
compositeTrack on
shortLabel Horse Chain/Net
longLabel Horse (Sep. 2007/equCab2), Chain and Net alignment tracks
@@ -3045,23 +3206,64 @@
chainMinScore 3000
chainLinearGap medium
spectrum on
html chainNet
+release alpha
track chainEquCab2
- subTrack horseChainNet off
+ subTrack horseChainNet
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain equCab2
track netEquCab2
- subTrack horseChainNet off
+ subTrack horseChainNet
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
type netAlign equCab2 chainEquCab2
+# release alpha until canFam2 individual tracks phased out
+track dogChainNet
+compositeTrack on
+shortLabel Dog Chain/Net
+longLabel Dog (May 2005/canFam2), Chain and Net alignment tracks
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 240
+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 canFam2
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+ track chainCanFam2
+ subTrack dogChainNet
+ subGroups view=chain
+ shortLabel $o_Organism Chain
+ longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+ type chain canFam2
+
+ track netCanFam2
+ subTrack dogChainNet
+ subGroups view=net
+ shortLabel $o_Organism Net
+ longLabel $o_Organism ($o_date/$o_db) Alignment Net
+ type netAlign canFam2 chainCanFam2
+
track chainCanFam2
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
group compGeno
@@ -3506,8 +3708,9 @@
spectrum on
type netAlign calJac1 chainCalJac1
otherDb calJac1
+# release beta until equCab2 phased in
track chainEquCab1
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
group compGeno
@@ -3519,9 +3722,11 @@
matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
matrixHeader A, C, G, T
type chain equCab1
otherDb equCab1
+release beta
+# release beta until equCab2 phased in
track netEquCab1
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment Net
group compGeno
@@ -3529,8 +3734,9 @@
visibility hide
spectrum on
type netAlign equCab1 chainEquCab1
otherDb equCab1
+release beta
track chainCi2
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
@@ -4458,18 +4664,19 @@
otherDb hg19
chainMinScore 3000
chainLinearGap medium
html chainNet
+release alpha
track chainHg19
- subTrack humanChainNet off
+ subTrack humanChainNet
subGroups view=chain
shortLabel $o_Organism Chain
longLabel $o_Organism ($o_date/$o_db) Chained Alignments
type chain hg19
track netHg19
- subTrack humanChainNet off
+ subTrack humanChainNet
subGroups view=net
shortLabel $o_Organism Net
longLabel $o_Organism ($o_date/$o_db) Alignment net
type netAlign hg19 chainHg19