src/hg/makeDb/trackDb/trackDb.chainNet.ra 1.5

Index: src/hg/makeDb/trackDb/trackDb.chainNet.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.chainNet.ra,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 4 -r1.4 -r1.5
--- src/hg/makeDb/trackDb/trackDb.chainNet.ra	11 Dec 2009 20:01:43 -0000	1.4
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra	11 Dec 2009 22:06:08 -0000	1.5
@@ -487,8 +487,50 @@
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign equCab2 chainEquCab2
 
+# release alpha until bosTau3 individual tracks phased out
+track chainNetBosTau3
+compositeTrack on
+shortLabel Cow Chain/Net
+longLabel Cow (Aug. 2006/bosTau3), 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 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 bosTau3
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+release alpha
+
+    track chainBosTau3
+    release alpha
+    subTrack chainNetBosTau3
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain bosTau3
+
+    track netBosTau3
+    release alpha
+    subTrack chainNetBosTau3
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment Net
+    type netAlign bosTau3 chainBosTau3
+
 # release alpha until bosTau2 individual tracks phased out
 track chainNetBosTau2
 compositeTrack on
 shortLabel Cow Chain/Net
@@ -507,9 +549,9 @@
 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 bosTau2
-chainMinScore 2000
+chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 release alpha