b260fe1f52db8c7e5362d4f9db3770409c24e197
hiram
  Thu Apr 14 18:57:29 2022 -0700
add the liftOver chainNet tracks refs #29272

diff --git src/hg/makeDb/trackDb/human/chainNetHuman.ra src/hg/makeDb/trackDb/human/chainNetHuman.ra
index cfa76b9..96a3375 100644
--- src/hg/makeDb/trackDb/human/chainNetHuman.ra
+++ src/hg/makeDb/trackDb/human/chainNetHuman.ra
@@ -47,30 +47,41 @@
         linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_009914755.4Link.bb
         otherDb GCA_009914755.4
         priority 2
 
         track chainRBestGCA_009914755.4
         parent humanChainNetViewchain
         subGroups view=chain species=s000 clade=c00
         shortLabel CHM13 T2T RBest 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
         otherDb GCA_009914755.4
         priority 3
 
+        track chainLiftOverGCA_009914755.4
+        parent humanChainNetViewchain
+        subGroups view=chain species=s000 clade=c00
+        shortLabel CHM13 T2T LiftOver Chain
+        longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Lift Over Chained Alignments
+        type bigChain GCA_009914755.4
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_009914755.4.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_009914755.4Link.bb
+        otherDb GCA_009914755.4
+        priority 4
+
         track chainGCA_021951015.1
         parent humanChainNetViewchain
         subGroups view=chain species=s001 clade=c00
         shortLabel HG002 mat Chain
         longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Chained Alignments
         type bigChain GCA_021951015.1
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_021951015.1.bb
         linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_021951015.1Link.bb
         otherDb GCA_021951015.1
         priority 5
 
         track chainSynGCA_021951015.1
         parent humanChainNetViewchain
         subGroups view=chain species=s001 clade=c00
         shortLabel HG002 mat Syn Chain
@@ -80,30 +91,41 @@
         linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_021951015.1Link.bb
         otherDb GCA_021951015.1
         priority 6
 
         track chainRBestGCA_021951015.1
         parent humanChainNetViewchain
         subGroups view=chain species=s001 clade=c00
         shortLabel HG002 mat RBest Chain
         longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Reciprocal Best Chained Alignments
         type bigChain GCA_021951015.1
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_021951015.1.bb
         linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_021951015.1Link.bb
         otherDb GCA_021951015.1
         priority 7
 
+        track chainLiftOverGCA_021951015.1
+        parent humanChainNetViewchain
+        subGroups view=chain species=s001 clade=c00
+        shortLabel HG002 mat Lift Over Chain
+        longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Lift Over Chained Alignments
+        type bigChain GCA_021951015.1
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_021951015.1.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_021951015.1Link.bb
+        otherDb GCA_021951015.1
+        priority 8
+
         track chainGCA_021950905.1
         parent humanChainNetViewchain
         subGroups view=chain species=s002 clade=c00
         shortLabel HG002 pat Chain
         longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Chained Alignments
         type bigChain GCA_021950905.1
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_021950905.1.bb
         linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainGCA_021950905.1Link.bb
         otherDb GCA_021950905.1
         priority 9
 
         track chainSynGCA_021950905.1
         parent humanChainNetViewchain
         subGroups view=chain species=s002 clade=c00
         shortLabel HG002 pat Syn Chain
@@ -113,30 +135,41 @@
         linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_021950905.1Link.bb
         otherDb GCA_021950905.1
         priority 10
 
         track chainRBestGCA_021950905.1
         parent humanChainNetViewchain
         subGroups view=chain species=s002 clade=c00
         shortLabel HG002 pat RBest Chain
         longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Reciprocal Best Chained Alignments
         type bigChain GCA_021950905.1
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_021950905.1.bb
         linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainRBestGCA_021950905.1Link.bb
         otherDb GCA_021950905.1
         priority 11
 
+        track chainLiftOverGCA_021950905.1
+        parent humanChainNetViewchain
+        subGroups view=chain species=s002 clade=c00
+        shortLabel HG002 pat Lift Over Chain
+        longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Lift Over Chained Alignments
+        type bigChain GCA_021950905.1
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_021950905.1.bb
+        linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainLiftOverGCA_021950905.1Link.bb
+        otherDb GCA_021950905.1
+        priority 12
+
     track humanMafNetViewnet
     shortLabel Nets
     view net
     visibility dense
     subTrack humanChainNet
 
         track netGCA_009914755.4
         parent humanMafNetViewnet
         subGroups view=net species=s000 clade=c00
         shortLabel CHM13 T2T Net
         longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Net 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
@@ -156,30 +189,42 @@
         otherDb GCA_009914755.4
         priority 2
 
         track rbestNetGCA_009914755.4
         parent humanMafNetViewnet
         subGroups view=net species=s000 clade=c00
         shortLabel CHM13 T2T RBest Net
         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
         otherDb GCA_009914755.4
         priority 3
 
+        track liftOverNetGCA_009914755.4
+        parent humanMafNetViewnet
+        subGroups view=net species=s000 clade=c00
+        shortLabel CHM13 T2T liftOverNet
+        longLabel CHM13 T2T (Jan. 2022 GCA_009914755.4_CHM13_T2T_v2.0) Lift Over Net Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.liftOverNet.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCA_009914755.4.liftOverNet.summary.bb
+        speciesOrder GCA_009914755.4
+        otherDb GCA_009914755.4
+        priority 4
+
         track netGCA_021951015.1
         parent humanMafNetViewnet
         subGroups view=net species=s001 clade=c00
         shortLabel HG002 mat Net
         longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.net.summary.bb
         speciesOrder GCA_021951015.1
         html chainNet
         otherDb GCA_021951015.1
         priority 5
 
         track synNetGCA_021951015.1
         parent humanMafNetViewnet
@@ -193,30 +238,42 @@
         otherDb GCA_021951015.1
         priority 6
 
         track rbestNetGCA_021951015.1
         parent humanMafNetViewnet
         subGroups view=net species=s001 clade=c00
         shortLabel HG002 mat RBest Net
         longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.rbestNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.rbestNet.summary.bb
         speciesOrder GCA_021951015.1
         otherDb GCA_021951015.1
         priority 7
 
+        track liftOverNetGCA_021951015.1
+        parent humanMafNetViewnet
+        subGroups view=net species=s001 clade=c00
+        shortLabel HG002 mat liftOverNet
+        longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Lift Over Net Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.liftOverNet.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.liftOverNet.summary.bb
+        speciesOrder GCA_021951015.1
+        otherDb GCA_021951015.1
+        priority 8
+
         track netGCA_021950905.1
         parent humanMafNetViewnet
         subGroups view=net species=s002 clade=c00
         shortLabel HG002 pat Net
         longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.net.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.net.summary.bb
         speciesOrder GCA_021950905.1
         html chainNet
         otherDb GCA_021950905.1
         priority 9
 
         track synNetGCA_021950905.1
         parent humanMafNetViewnet
@@ -229,15 +286,27 @@
         speciesOrder GCA_021950905.1
         otherDb GCA_021950905.1
         priority 10
 
         track rbestNetGCA_021950905.1
         parent humanMafNetViewnet
         subGroups view=net species=s002 clade=c00
         shortLabel HG002 pat RBest Net
         longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Reciprocal Best Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.rbestNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.rbestNet.summary.bb
         speciesOrder GCA_021950905.1
         otherDb GCA_021950905.1
         priority 11
+
+        track liftOverNetGCA_021950905.1
+        parent humanMafNetViewnet
+        subGroups view=net species=s002 clade=c00
+        shortLabel HG002 pat liftOverNet
+        longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Lift Over Net Alignment
+        type bigMaf
+        bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.liftOverNet.bb
+        summary /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.liftOverNet.summary.bb
+        speciesOrder GCA_021950905.1
+        otherDb GCA_021950905.1
+        priority 12