c371f31291a175307f0bd092439a802edee30894
hiram
  Wed Mar 30 10:37:22 2022 -0700
adding in chainNet composite for alignments to CHM13 and the two HG002 assemblies refs #28907

diff --git src/hg/makeDb/trackDb/human/chainNetHuman.ra src/hg/makeDb/trackDb/human/chainNetHuman.ra
new file mode 100644
index 0000000..2ea287a
--- /dev/null
+++ src/hg/makeDb/trackDb/human/chainNetHuman.ra
@@ -0,0 +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
+
+    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