7fa908f40df50ecd4d078811aea7c25c5556c63a
hiram
  Fri Apr 1 16:47:11 2022 -0700
documentation for the human chainNets refs #29189

diff --git src/hg/makeDb/trackDb/human/chainNetHuman.ra src/hg/makeDb/trackDb/human/chainNetHuman.ra
index 2ea287a..f60b486 100644
--- src/hg/makeDb/trackDb/human/chainNetHuman.ra
+++ src/hg/makeDb/trackDb/human/chainNetHuman.ra
@@ -1,225 +1,225 @@
 track humanChainNet
 compositeTrack on
 shortLabel Human Chain/Net
 longLabel Human Genomes, Chain and Net Alignments
 subGroup1 view Views chain=Chains net=Nets
 subGroup2 species Species s000=CHM13 s001=HG002_mat s002=HG002_pat
 subGroup3 clade Clade c00=human
 dragAndDrop subTracks
 visibility hide
 group compGeno
 noInherit on
 color 0,0,0
 altColor 255,255,0
 type bed 3
 chainLinearGap loose
 chainMinScore 5000
 dimensions dimensionX=clade dimensionY=species
 sortOrder species=+ view=+ clade=+
 configurable on
-html humanChainNet
+html homoSapiensChainNet
 
     track humanChainNetViewchain
     shortLabel Chains
     view chain
     visibility pack
     subTrack humanChainNet
     spectrum on
 
         track chainGCA_009914755.4
         parent humanChainNetViewchain
         subGroups view=chain species=s000 clade=c00
         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
         otherDb GCA_009914755.4
 
         track chainSynGCA_009914755.4
         parent humanChainNetViewchain
         subGroups view=chain species=s000 clade=c00
         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
         otherDb GCA_009914755.4
 
         track chainRBestGCA_009914755.4
         parent humanChainNetViewchain
         subGroups view=chain species=s000 clade=c00
         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
         otherDb GCA_009914755.4
 
         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
 
         track chainSynGCA_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) Syntenic Chained Alignments
         type bigChain GCA_021951015.1
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_021951015.1.bb
         linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_021951015.1Link.bb
         otherDb GCA_021951015.1
 
         track chainRBestGCA_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) 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
 
         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
 
         track chainSynGCA_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) Syntenic Chained Alignments
         type bigChain GCA_021950905.1
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_021950905.1.bb
         linkDataUrl /gbdb/$D/bbi/chainNet/$D.chainSynGCA_021950905.1Link.bb
         otherDb GCA_021950905.1
 
         track chainRBestGCA_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) 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
 
     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 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
         otherDb GCA_009914755.4
 
         track synNetGCA_009914755.4
         parent humanMafNetViewnet
         subGroups view=net species=s000 clade=c00
         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
         otherDb GCA_009914755.4
 
         track rbestNetGCA_009914755.4
         parent humanMafNetViewnet
         subGroups view=net species=s000 clade=c00
         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
         otherDb GCA_009914755.4
 
         track netGCA_021951015.1
         parent humanMafNetViewnet
         subGroups view=net species=s001 clade=c00
         shortLabel HG002 mat mafNet
         longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) mafNet 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
 
         track synNetGCA_021951015.1
         parent humanMafNetViewnet
         subGroups view=net species=s001 clade=c00
         shortLabel HG002 mat mafNet
         longLabel HG002 mat (Feb. 2022 GCA_021951015.1_HG002.mat.cur.20211005) Syntenic Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.synNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCA_021951015.1.synNet.summary.bb
         speciesOrder GCA_021951015.1
         otherDb GCA_021951015.1
 
         track rbestNetGCA_021951015.1
         parent humanMafNetViewnet
         subGroups view=net species=s001 clade=c00
         shortLabel HG002 mat mafNet
         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
 
         track netGCA_021950905.1
         parent humanMafNetViewnet
         subGroups view=net species=s002 clade=c00
         shortLabel HG002 pat mafNet
         longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) mafNet 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
 
         track synNetGCA_021950905.1
         parent humanMafNetViewnet
         subGroups view=net species=s002 clade=c00
         shortLabel HG002 pat mafNet
         longLabel HG002 pat (Feb. 2022 GCA_021950905.1_HG002.pat.cur.20211005) Syntenic Net Alignment
         type bigMaf
         bigDataUrl /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.synNet.bb
         summary /gbdb/$D/bbi/chainNet/$D.GCA_021950905.1.synNet.summary.bb
         speciesOrder GCA_021950905.1
         otherDb GCA_021950905.1
 
         track rbestNetGCA_021950905.1
         parent humanMafNetViewnet
         subGroups view=net species=s002 clade=c00
         shortLabel HG002 pat mafNet
         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