41ab5fa75567827d1b4141f9f352b0fc63922cee hiram Tue Apr 5 23:09:19 2022 -0700 priority ordering on the chain and net tracks refs #28907 diff --git src/hg/makeDb/trackDb/human/chainNetHuman.ra src/hg/makeDb/trackDb/human/chainNetHuman.ra index f60b486..cfa76b9 100644 --- src/hg/makeDb/trackDb/human/chainNetHuman.ra +++ src/hg/makeDb/trackDb/human/chainNetHuman.ra @@ -1,225 +1,243 @@ 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 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 + priority 1 track chainSynGCA_009914755.4 parent humanChainNetViewchain subGroups view=chain species=s000 clade=c00 - shortLabel CHM13 T2T Chain + shortLabel CHM13 T2T Syn 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 + priority 2 track chainRBestGCA_009914755.4 parent humanChainNetViewchain subGroups view=chain species=s000 clade=c00 - shortLabel CHM13 T2T Chain + 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 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 Chain + shortLabel HG002 mat Syn 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 + priority 6 track chainRBestGCA_021951015.1 parent humanChainNetViewchain subGroups view=chain species=s001 clade=c00 - shortLabel HG002 mat Chain + 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 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 Chain + shortLabel HG002 pat Syn 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 + priority 10 track chainRBestGCA_021950905.1 parent humanChainNetViewchain subGroups view=chain species=s002 clade=c00 - shortLabel HG002 pat Chain + 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 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 + 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 html chainNet otherDb GCA_009914755.4 + priority 1 track synNetGCA_009914755.4 parent humanMafNetViewnet subGroups view=net species=s000 clade=c00 - shortLabel CHM13 T2T mafNet + shortLabel CHM13 T2T Syn Net 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 + priority 2 track rbestNetGCA_009914755.4 parent humanMafNetViewnet subGroups view=net species=s000 clade=c00 - shortLabel CHM13 T2T mafNet + 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 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 + 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 subGroups view=net species=s001 clade=c00 - shortLabel HG002 mat mafNet + shortLabel HG002 mat Syn Net 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 + priority 6 track rbestNetGCA_021951015.1 parent humanMafNetViewnet subGroups view=net species=s001 clade=c00 - shortLabel HG002 mat mafNet + 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 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 + 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 subGroups view=net species=s002 clade=c00 - shortLabel HG002 pat mafNet + shortLabel HG002 pat Syn Net 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 + priority 10 track rbestNetGCA_021950905.1 parent humanMafNetViewnet subGroups view=net species=s002 clade=c00 - shortLabel HG002 pat mafNet + 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