c9f040b7cd79e62f2082a62fb0ae6ccbc90b02c6
hiram
  Tue Mar 29 12:49:56 2022 -0700
adding chainNet definition to CHM13 T2T GCA_009914755.4 assembly hub refs #28907

diff --git src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
index 3b96459..19aeb26 100644
--- src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
+++ src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
@@ -1,16 +1,111 @@
 ##############################################################################
+# GCA_009914755.4_CHM13_T2T_v2.0 - human - Homo sapiens - taxId: 9606 - primate
+##############################################################################
+track chainNetGCA_009914755.4
+compositeTrack on
+shortLabel CHM13 T2T Chain/Net
+longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0), 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
+type bed 3
+sortOrder view=+
+matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
+chainMinScore 5000
+chainLinearGap medium
+matrixHeader A, C, G, T
+otherDb GCA_009914755.4
+html chainNet
+
+    track chainNetGCA_009914755.4Viewchain
+    shortLabel Chain
+    view chain
+    visibility pack
+    parent chainNetGCA_009914755.4
+    spectrum on
+
+        track chainGCA_009914755.4
+        parent chainNetGCA_009914755.4Viewchain
+        subGroups view=chain
+        shortLabel CHM13 T2T Chain
+        longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Chained Alignments
+        type bigChain GCA_009914755.4
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_009914755.4.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_009914755.4Link.bb
+
+        track chainSynGCA_009914755.4
+        parent chainNetGCA_009914755.4Viewchain
+        subGroups view=chain
+        shortLabel CHM13 T2T Chain
+        longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Syntenic Chained Alignments
+        type bigChain GCA_009914755.4
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_009914755.4.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_009914755.4Link.bb
+
+        track chainRBestGCA_009914755.4
+        parent chainNetGCA_009914755.4Viewchain
+        subGroups view=chain
+        shortLabel CHM13 T2T Chain
+        longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Reciprocal Best Chained Alignments
+        type bigChain GCA_009914755.4
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_009914755.4.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_009914755.4Link.bb
+
+    track mafNetGCA_009914755.4Viewnet
+    shortLabel Net
+    view net
+    visibility full
+    parent chainNetGCA_009914755.4
+
+        track netGCA_009914755.4
+        parent mafNetGCA_009914755.4Viewnet
+        subGroups view=net
+        shortLabel CHM13 T2T mafNet
+        longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) mafNet Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.net.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.net.summary.bb
+        speciesOrder GCA_009914755.4
+        html chainNet
+
+        track synNetGCA_009914755.4
+        parent mafNetGCA_009914755.4Viewnet
+        subGroups view=net
+        shortLabel CHM13 T2T mafNet
+        longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Syntenic Net Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.synNet.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.synNet.summary.bb
+        speciesOrder GCA_009914755.4
+
+        track rbestNetGCA_009914755.4
+        parent mafNetGCA_009914755.4Viewnet
+        subGroups view=net
+        shortLabel CHM13 T2T mafNet
+        longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Reciprocal Best Net Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.rbestNet.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.rbestNet.summary.bb
+        speciesOrder GCA_009914755.4
+
+##############################################################################
 # 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