7b52d31632f9b473eba9939d2d30ce703e401553
hiram
  Fri Oct 29 15:58:44 2021 -0700
lastz chainNet on GCF_002742125.1 Ramboullet sheep refs #28409

diff --git src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
index cf0a235..3b96459 100644
--- src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
+++ src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
@@ -193,51 +193,88 @@
 html chainNet
 
     track chainNetGCF_002742125.1Viewchain
     shortLabel Chain
     view chain
     visibility pack
     parent chainNetGCF_002742125.1
     spectrum on
 
         track chainGCF_002742125.1
         parent chainNetGCF_002742125.1Viewchain
         subGroups view=chain
         shortLabel Rambouillet sheep Chain
         longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Chained Alignments
         type bigChain GCF_002742125.1
-        bigDataUrl /gbdb/$D/bbi/chainNet/chainGCF_002742125.1.bb
-        linkDataUrl /gbdb/$D/bbi/chainNet/chainGCF_002742125.1Link.bb
-        html chainNet
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_002742125.1.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_002742125.1Link.bb
+
+        track chainSynGCF_002742125.1
+        parent chainNetGCF_002742125.1Viewchain
+        subGroups view=chain
+        shortLabel Rambouillet sheep Chain
+        longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Syntenic Chained Alignments
+        type bigChain GCF_002742125.1
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_002742125.1.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_002742125.1Link.bb
+
+        track chainRBestGCF_002742125.1
+        parent chainNetGCF_002742125.1Viewchain
+        subGroups view=chain
+        shortLabel Rambouillet sheep Chain
+        longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Reciprocal Best Chained Alignments
+        type bigChain GCF_002742125.1
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_002742125.1.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_002742125.1Link.bb
 
     track mafNetGCF_002742125.1Viewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetGCF_002742125.1
 
         track netGCF_002742125.1
         parent mafNetGCF_002742125.1Viewnet
         subGroups view=net
         shortLabel Rambouillet sheep mafNet
         longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) mafNet Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.net.summary.bb
         speciesOrder GCF_002742125.1
         html chainNet
 
+        track synNetGCF_002742125.1
+        parent mafNetGCF_002742125.1Viewnet
+        subGroups view=net
+        shortLabel Rambouillet sheep mafNet
+        longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Syntenic Net Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.synNet.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.synNet.summary.bb
+        speciesOrder GCF_002742125.1
+
+        track rbestNetGCF_002742125.1
+        parent mafNetGCF_002742125.1Viewnet
+        subGroups view=net
+        shortLabel Rambouillet sheep mafNet
+        longLabel Rambouillet sheep (Nov. 2017 GCF_002742125.1_Oar_rambouillet_v1.0) Reciprocal Best Net Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.rbestNet.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCF_002742125.1.rbestNet.summary.bb
+        speciesOrder GCF_002742125.1
+
 ##############################################################################
 # GCA_018400075.1 - Zebrafish T5D - Danio rerio - taxId: 7955 - fish
 ##############################################################################
 track chainNetGCA_018400075.1
 compositeTrack on
 shortLabel Zebrafish T5D Chain/Net
 longLabel Zebrafish T5D (May 2021 GCA_018400075.1_ASM1840007v1), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
 priority 100.1
 color 0,0,0
 altColor 100,50,0
@@ -404,49 +441,49 @@
 
     track chainNetGCF_000349665.1iewchain
     shortLabel Chain
     view chain
     visibility pack
     parent chainNetGCF_000349665.1
     spectrum on
 
         track chainGCF_000349665.1
         parent chainNetGCF_000349665.1iewchain
         subGroups view=chain
         shortLabel Golden hamster Chain
         longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Chained Alignments
         type bigChain GCF_000349665.1
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_000349665.1.bb
-        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_000349665.1.Link.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCF_000349665.1Link.bb
 
         track chainSynGCF_000349665.1
         parent chainNetGCF_000349665.1iewchain
         subGroups view=chain
         shortLabel Golden hamster synChain
         longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Syntenic Chained Alignments
         type bigChain GCF_000349665.1
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_000349665.1.bb
-        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_000349665.1.Link.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCF_000349665.1Link.bb
 
         track chainRBestGCF_000349665.1
         parent chainNetGCF_000349665.1iewchain
         subGroups view=chain
         shortLabel Golden hamster rbChain
         longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Reciprocal Best Chained Alignments
         type bigChain GCF_000349665.1
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_000349665.1.bb
-        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_000349665.1.Link.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCF_000349665.1Link.bb
 
     track mafNetGCF_000349665.1iewnet
     shortLabel Net
     view net
     visibility full
     parent chainNetGCF_000349665.1
 
         track netGCF_000349665.1
         parent mafNetGCF_000349665.1iewnet
         subGroups view=net
         shortLabel Golden hamster net
         longLabel Golden hamster (Mar. 2013 (MesAur1.0/GCF_000349665.1) Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCF_000349665.1.net.summary.bb