cad24d48147c54fec5574b6841027b1d51a9fdf3
hiram
  Thu Jan 7 17:49:28 2021 -0800
adding chainNet plus mafNet alignments for assembly hub chainNet tracks refs #26584

diff --git src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
index cb899f2..e916765 100644
--- src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
+++ src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
@@ -1,168 +1,170 @@
-################################################################
-# GCF_003668045.3_CriGri-PICRH-1.0 - Chinese hamster - Cricetulus griseus - mammals
-################################################################
-track chainNetGCF_003668045.3
+##############################################################################
+# GCA_901343595v1_MONAX5 - woodchuck - Marmota monax - mammal
+##############################################################################
+track chainNetGCA_901343595v1
 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 200.3
 color 0,0,0
 altColor 255,255,0
 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 GCF_003668045.3
+otherDb GCA_901343595v1
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
-    track chainNetGCF_003668045.3Viewchain
+    track chainNetGCA_901343595v1Viewchain
     shortLabel Chain
     view chain
     visibility pack
-    parent chainNetGCF_003668045.3
+    parent chainNetGCA_901343595v1
     spectrum on
 
-        track chainGCF_003668045.3_CriGri-PICRH-1.0i
-        parent chainNetGCF_003668045.3Viewchain
+        track chainGCA_901343595v1_MONAX5
+        parent chainNetGCA_901343595v1Viewchain
         subGroups view=chain
         shortLabel $o_Organism Chain
         longLabel $o_Organism ($o_date) Chained Alignments
-        type bigChain GCF_003668045.3
-        bigDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_003668045.3.bb
-        linkDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_003668045.3Link.bb
+        type chain GCA_901343595v1
         html chainNet
 
-    track chainNetGCF_003668045.3Viewnet
+    track chainNetGCA_901343595v1Viewnet
     shortLabel Net
     view net
     visibility dense
-    parent chainNetGCF_003668045.3
+    parent chainNetGCA_901343595v1
 
-        track netGCF_003668045.3_CriGri-PICRH-1.0i
-        parent chainNetGCF_003668045.3Viewnet
+        track netGCA_901343595v1_MONAX5
+        parent chainNetGCA_901343595v1Viewnet
         subGroups view=net
         shortLabel $o_Organism Net
         longLabel $o_Organism ($o_date) Alignment Net
-        type netAlign GCF_003668045.3 chainGCF_003668045.3_CriGri-PICRH-1.0i
+        type netAlign GCA_901343595v1 chainGCA_901343595v1_MONAX5
         html chainNet
 
-################################################################
-################################################################
-# GCA_901343595v1_MONAX5 - woodchuck - Marmota monax - mammal
-################################################################
-track chainNetGCA_901343595v1
+##############################################################################
+# GCF_003668045.3 - Chinese hamster - Cricetulus griseus - taxId: 10029 - mammal
+##############################################################################
+track chainNetGCF_003668045.3
 compositeTrack on
-shortLabel $o_Organism Chain/Net
-longLabel $o_Organism ($o_date), Chain and Net Alignments
+shortLabel Chinese hamster Chain/Net
+longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
-priority 200.3
+priority 100.1
 color 0,0,0
-altColor 255,255,0
+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 GCA_901343595v1
-chainMinScore 3000
 chainLinearGap medium
-spectrum on
+chainMinScore 3000
+matrixHeader A, C, G, T
+otherDb GCF_003668045.3
 html chainNet
 
-    track chainNetGCA_901343595v1Viewchain
+    track chainNetGCF_003668045.3Viewchain
     shortLabel Chain
     view chain
     visibility pack
-    parent chainNetGCA_901343595v1
+    parent chainNetGCF_003668045.3
     spectrum on
 
-        track chainGCA_901343595v1_MONAX5
-        parent chainNetGCA_901343595v1Viewchain
+        track chainGCF_003668045.3
+        parent chainNetGCF_003668045.3Viewchain
         subGroups view=chain
-        shortLabel $o_Organism Chain
-        longLabel $o_Organism ($o_date) Chained Alignments
-        type chain GCA_901343595v1
+        shortLabel Chinese hamster Chain
+        longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0) Chained Alignments
+        type bigChain GCF_003668045.3
+        bigDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_003668045.3.bb
+        linkDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_003668045.3Link.bb
         html chainNet
 
-    track chainNetGCA_901343595v1Viewnet
+    track mafNetGCF_003668045.3Viewnet
     shortLabel Net
     view net
-    visibility dense
-    parent chainNetGCA_901343595v1
+    visibility full
+    parent chainNetGCF_003668045.3
 
-        track netGCA_901343595v1_MONAX5
-        parent chainNetGCA_901343595v1Viewnet
+        track netGCF_003668045.3
+        parent mafNetGCF_003668045.3Viewnet
         subGroups view=net
-        shortLabel $o_Organism Net
-        longLabel $o_Organism ($o_date) Alignment Net
-        type netAlign GCA_901343595v1 chainGCA_901343595v1_MONAX5
+        shortLabel Chinese hamster mafNet
+        longLabel Chinese hamster (Jun. 2020 GCF_003668045.3_CriGri-PICRH-1.0) mafNet Alignment
+        type bigMaf
+        bigDataUrl /gbdb/mm39/bbi/chainNet/mm39.GCF_003668045.3.net.bb
+        summary /gbdb/mm39/bbi/chainNet/mm39.GCF_003668045.3.net.summary.bb
+        speciesOrder GCF_003668045.3
         html chainNet
 
-################################################################
-# GCF_009829145.1_bChiLan1.pri - lance-tailed manakin - Chiroxiphia lanceolata - birds
-################################################################
+##############################################################################
+# GCF_009829145.1 - lance-tailed manakin - Chiroxiphia lanceolata - taxId: 296741 - birds
+##############################################################################
 track chainNetGCF_009829145.1
 compositeTrack on
-shortLabel $o_Organism Chain/Net
-longLabel $o_Organism ($o_date), Chain and Net Alignments
+shortLabel lance-tailed manakin Chain/Net
+longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
-priority 200.3
+priority 100.1
 color 0,0,0
-altColor 255,255,0
+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 GCF_009829145.1
 chainMinScore 3000
 chainLinearGap medium
-spectrum on
+matrixHeader A, C, G, T
+otherDb GCF_009829145.1
 html chainNet
 
     track chainNetGCF_009829145.1Viewchain
     shortLabel Chain
     view chain
     visibility pack
     parent chainNetGCF_009829145.1
     spectrum on
 
-        track chainGCF_009829145.1_bChiLan1.pri
+        track chainGCF_009829145.1
         parent chainNetGCF_009829145.1Viewchain
         subGroups view=chain
-        shortLabel $o_Organism Chain
-        longLabel $o_Organism ($o_date) Chained Alignments
+        shortLabel lance-tailed manakin Chain
+        longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri) Chained Alignments
         type bigChain GCF_009829145.1
         bigDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_009829145.1.bb
         linkDataUrl /gbdb/mm39/bbi/chainNet/chainGCF_009829145.1Link.bb
         html chainNet
 
-    track chainNetGCF_009829145.1Viewnet
+    track mafNetGCF_009829145.1Viewnet
     shortLabel Net
     view net
-    visibility dense
+    visibility full
     parent chainNetGCF_009829145.1
 
-        track netGCF_009829145.1_bChiLan1.pri
-        parent chainNetGCF_009829145.1Viewnet
+        track netGCF_009829145.1
+        parent mafNetGCF_009829145.1Viewnet
         subGroups view=net
-        shortLabel $o_Organism Net
-        longLabel $o_Organism ($o_date) Alignment Net
-        type netAlign GCF_009829145.1 chainGCF_009829145.1_bChiLan1.pri
+        shortLabel lance-tailed manakin mafNet
+        longLabel lance-tailed manakin (Jan. 2020 GCF_009829145.1_bChiLan1.pri) mafNet Alignment
+        type bigMaf
+        bigDataUrl /gbdb/mm39/bbi/chainNet/mm39.GCF_009829145.1.net.bb
+        summary /gbdb/mm39/bbi/chainNet/mm39.GCF_009829145.1.net.summary.bb
+        speciesOrder GCF_009829145.1
         html chainNet
 
-################################################################