1432ae4e828ddb697a130a2e8fb54dc4a4ee8623
hiram
  Thu Oct 17 15:34:40 2019 -0700
adding chainNet definitions for susScr11 refs #21579

diff --git src/hg/makeDb/trackDb/trackDb.chainNet.ra src/hg/makeDb/trackDb/trackDb.chainNet.ra
index 4bab191..44db79d 100644
--- src/hg/makeDb/trackDb/trackDb.chainNet.ra
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra
@@ -2743,30 +2743,81 @@
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date) Chained Alignments
     type chain mm5
     html chainNet
 
     track netMm5
     release alpha
     parent chainNetMm5
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date) Alignment Net
     type netAlign mm5 chainMm5
     html chainNet
 
+track chainNetRegenRn1
+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 209
+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 regenRn1
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+    track chainNetRegenRn1Viewchain
+    shortLabel Chain
+    view chain
+    visibility pack
+    parent chainNetRegenRn1
+    spectrum on
+
+        track chainRegenRn1
+        parent chainNetRegenRn1Viewchain
+        subGroups view=chain
+        shortLabel $o_Organism Chain
+        longLabel $o_Organism ($o_date) Chained Alignments
+        type chain regenRn1
+        html chainNet
+
+    track chainNetRegenRn1Viewnet
+    shortLabel Net
+    view net
+    visibility full
+    parent chainNetRegenRn1
+
+        track netRegenRn1
+        parent chainNetRegenRn1Viewnet
+        subGroups view=net
+        shortLabel $o_Organism Net
+        longLabel $o_Organism ($o_date) Alignment Net
+        type netAlign regenRn1 chainRegenRn1
+        html chainNet
+
 track chainNetRegenRn0
 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 209
 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
@@ -3616,30 +3667,83 @@
 
     track chainNetVicPac1Viewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetVicPac1
 
         track netVicPac1
         parent chainNetVicPac1Viewnet
         subGroups view=net
         shortLabel $o_Organism Net
         longLabel $o_Organism ($o_date) Alignment Net
         type netAlign vicPac1 chainVicPac1
         html chainNet
 
+##############################################################################
+# susScr11 - Pig - Sus scrofa - taxId: 9823
+##############################################################################
+track chainNetSusScr11
+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 465.3
+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
+chainMinScore 3000
+chainLinearGap medium
+matrixHeader A, C, G, T
+otherDb susScr11
+html chainNet
+
+    track chainNetSusScr11Viewchain
+    shortLabel Chain
+    view chain
+    visibility pack
+    parent chainNetSusScr11
+    spectrum on
+
+        track chainSusScr11
+        parent chainNetSusScr11Viewchain
+        subGroups view=chain
+        shortLabel $o_Organism Chain
+        longLabel $o_Organism ($o_date) Chained Alignments
+        type chain susScr11
+        html chainNet
+
+    track chainNetSusScr11Viewnet
+    shortLabel Net
+    view net
+    visibility full
+    parent chainNetSusScr11
+
+        track netSusScr11
+        parent chainNetSusScr11Viewnet
+        subGroups view=net
+        shortLabel $o_Organism Net
+        longLabel $o_Organism ($o_date) Alignment net
+        type netAlign susScr11 chainSusScr11
+        html chainNet
+
 track chainNetSusScr3
 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 475.3
 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