f7a1de048f1e4a82213dfbce22ceddd33b095c0e
hiram
  Fri Sep 11 13:31:09 2020 -0700
adding definitions for calJac4 chainNet refs #24074

diff --git src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
index 5bc28e7..91a39a7 100644
--- src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
+++ src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
@@ -2120,16 +2120,173 @@
 
     track chainNetProCoq1Viewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetProCoq1
 
         track netProCoq1
         parent chainNetProCoq1Viewnet
         subGroups view=net
         shortLabel $o_Organism Net
         longLabel $o_Organism ($o_date) Alignment net
         type netAlign proCoq1 chainProCoq1
         html chainNet
 
-##############################################################################
+################################################################
+# calJac4 - marmoset - Callithrix jacchus - primate - taxId 9483
+################################################################
+track chainNetCalJac4
+compositeTrack on
+shortLabel $o_Organism Chain/Net
+longLabel $o_Organism ($o_date), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+group compGeno
+noInherit on
+priority 260.3
+color 0,0,0
+altColor 100,50,0
+type bed 3
+sortOrder view=+
+matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
+matrixHeader A, C, G, T
+otherDb calJac4
+chainMinScore 5000
+chainLinearGap medium
+html chainNet
+
+    track chainNetCalJac4Viewchain
+    shortLabel Chain
+    view chain
+    visibility pack
+    parent chainNetCalJac4
+    spectrum on
+
+        track chainCalJac4
+        parent chainNetCalJac4Viewchain
+        subGroups view=chain
+        shortLabel $o_Organism Chain
+        longLabel $o_Organism ($o_date) Chained Alignments
+        type chain calJac4
+        html chainNet
+
+    track chainNetCalJac4Viewnet
+    shortLabel Net
+    view net
+    visibility full
+    parent chainNetCalJac4
+
+        track netCalJac4
+        parent chainNetCalJac4Viewnet
+        subGroups view=net
+        shortLabel $o_Organism Net
+        longLabel $o_Organism ($o_date) Alignment net
+        type netAlign calJac4 chainCalJac4
+        html chainNet
+
+################################################################
+# calJac3 - marmoset - Callithrix jacchus - primate - taxId 9483
+################################################################
+track chainNetCalJac3
+compositeTrack on
+shortLabel $o_Organism Chain/Net
+longLabel $o_Organism ($o_date), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+group compGeno
+noInherit on
+priority 260.3
+color 0,0,0
+altColor 100,50,0
+type bed 3
+sortOrder view=+
+matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
+matrixHeader A, C, G, T
+otherDb calJac3
+chainMinScore 5000
+chainLinearGap medium
+html chainNet
+
+    track chainNetCalJac3Viewchain
+    shortLabel Chain
+    view chain
+    visibility pack
+    parent chainNetCalJac3
+    spectrum on
+
+        track chainCalJac3
+        parent chainNetCalJac3Viewchain
+        subGroups view=chain
+        shortLabel $o_Organism Chain
+        longLabel $o_Organism ($o_date) Chained Alignments
+        type chain calJac3
+        html chainNet
+
+    track chainNetCalJac3Viewnet
+    shortLabel Net
+    view net
+    visibility full
+    parent chainNetCalJac3
+
+        track netCalJac3
+        parent chainNetCalJac3Viewnet
+        subGroups view=net
+        shortLabel $o_Organism Net
+        longLabel $o_Organism ($o_date) Alignment net
+        type netAlign calJac3 chainCalJac3
+        html chainNet
+
+################################################################
+# calJac1 - marmoset - Callithrix jacchus - primate - taxId 9483
+################################################################
+track chainNetCalJac1
+compositeTrack on
+shortLabel $o_db Chain/Net
+longLabel $o_Organism ($o_date), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+group compGeno
+noInherit on
+priority 498
+color 0,0,0
+altColor 100,50,0
+type bed 3
+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 calJac1
+chainMinScore 3000
+chainLinearGap medium
+html chainNet
+
+    track chainNetCalJac1Viewchain
+    shortLabel Chain
+    view chain
+    visibility pack
+    parent chainNetCalJac1
+    spectrum on
+
+        track chainCalJac1
+        parent chainNetCalJac1Viewchain
+        subGroups view=chain
+        shortLabel $o_db Chain
+        longLabel $o_Organism ($o_date) Chained Alignments
+        type chain calJac1
+        html chainNet
+
+    track chainNetCalJac1Viewnet
+    shortLabel Net
+    view net
+    visibility full
+    parent chainNetCalJac1
+
+        track netCalJac1
+        parent chainNetCalJac1Viewnet
+        subGroups view=net
+        shortLabel $o_db Net
+        longLabel $o_Organism ($o_date) Alignment net
+        type netAlign calJac1 chainCalJac1
+        html chainNet