Commits for hiram

v450_base to v451_preview (2023-06-26 to 2023-07-03) v451

2b2c919006aa13c1a98deeb45fd5112a1b8e5422 Mon Jun 26 17:56:58 2023 -0700

• place alpha tag on 447way no redmine
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

923cb1e06520e8f302baabded147081a64db5666 Tue Jun 27 14:20:10 2023 -0700

• construction procedure for the 447-way alignment refs #31528
  • src/hg/makeDb/doc/hg38/cactus447.txt - lines changed 305, context: html, text, full: html, text

d1c1f4a37a01868c7e3b2b025c8757ce306fe7ef Wed Jun 28 16:12:46 2023 -0700

• adding GCA_011100615.1 crab-eating macaque chain/net no redmine
  • src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra - lines changed 97, context: html, text, full: html, text

739d5df01bb223681bb832826d48c137484034f8 Wed Jun 28 16:32:16 2023 -0700

• beginning to package the HPRC chains as their own track refs #31561
  • src/hg/makeDb/trackDb/human/hg38/chainNetHprc.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/chainNetHprc.ra - lines changed 907, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/chainNetHumanExperiment.ra - lines changed 9061, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcChain.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcCoverage.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 5, context: html, text, full: html, text

4499d20f21a554b50e0e35a208010a31f1aafe42 Thu Jun 29 11:10:27 2023 -0700

• turn on a matrix to control groups of the tracks as one set refs #31561
  • src/hg/makeDb/trackDb/human/hg38/chainNetHprc.ra - lines changed 91, context: html, text, full: html, text

88671a65c8bff92cbcd7eadf4bac3e9dad9df7d0 Thu Jun 29 12:30:57 2023 -0700

• listings of HPRC meta data from their git pages refs #31561
  • src/hg/makeDb/doc/hg38/hprc.metaData.tsv - lines changed 48, context: html, text, full: html, text

0b248354b16bae38d735588644d54244d966dd1a Thu Jun 29 13:13:24 2023 -0700

• adding population and subpopulation descriptions refs #31561
  • src/hg/makeDb/doc/hg38/hprc.metaData.tsv - lines changed 4, context: html, text, full: html, text

bcd1fb8bbdaa113c9da8f9cc87ae48b89c9842e8 Thu Jun 29 14:02:47 2023 -0700

• now with subpopulation groupings although there seems to be no order refs #31561
  • src/hg/makeDb/trackDb/human/hg38/chainNetHprc.ra - lines changed 377, context: html, text, full: html, text

3d7016e97048a97da6d04b9dec3b035aa06205a3 Thu Jun 29 14:40:19 2023 -0700

• attempted ordering of the subpopulations refs #31561
  • src/hg/makeDb/trackDb/human/hg38/chainNetHprc.ra - lines changed 943, context: html, text, full: html, text

932e4f0802f70251dd0fd8d74e862675902080e0 Thu Jun 29 14:50:33 2023 -0700

• trying sortOrder subpop=+ only but it does not sort the matrix refs #31561
  • src/hg/makeDb/trackDb/human/hg38/chainNetHprc.ra - lines changed 1, context: html, text, full: html, text

c520a7d55b8fb32a24b5293c7a516d132d97bd54 Fri Jun 30 11:25:10 2023 -0700

• there is nothing about net in this track, should be no mention of net refs #31561
  • src/hg/makeDb/trackDb/human/hg38/chainsHprc.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/chainsHprc.ra - lines changed 989, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

2045e76bd07314f248db64d6d60b2ab46a1f19f3 Fri Jun 30 11:51:55 2023 -0700

• names changed to chainsHprc refs #31561
  • src/hg/makeDb/trackDb/human/hg38/chainNetHprc.html - lines changed 57, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/chainNetHprc.ra - lines changed 996, context: html, text, full: html, text

7b9b6f6f3a35a1b35d8cd40c06b6267623b957cd Fri Jun 30 14:30:05 2023 -0700

• adding coverage/complement tracks from the HPRC chainLinks refs #31561
  • src/hg/makeDb/doc/hg38/hprcCoverage.txt - lines changed 82, context: html, text, full: html, text

7f94d1a000ee66db823bb7749aee3d995bd0a29f Fri Jun 30 14:31:42 2023 -0700

• adding new coverage track refs #31561
  • src/hg/makeDb/trackDb/human/hg38/hprcCoverage.ra - lines changed 59, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcCoverage97.ra - lines changed 65, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 4, context: html, text, full: html, text

f83b9b55ba06b07733ba018859b9a9e2b8960df5 Fri Jun 30 15:53:03 2023 -0700

• adding T2T-CHM13 and add haplotype group refs #31561
  • src/hg/makeDb/trackDb/human/hg38/chainsHprc.ra - lines changed 190, context: html, text, full: html, text

5a84569301fd828c42f868c5a3de353fc9b39c29 Fri Jun 30 16:00:20 2023 -0700

• now with the full iRow annotated big file and add species name labels refs #31528
  • src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra - lines changed 2, context: html, text, full: html, text

caadfdf9e08221f25f774498ed2706f16ba4724b Fri Jun 30 17:39:50 2023 -0700

• add a complement for this one to compare to the other refs #31561
  • src/hg/makeDb/trackDb/human/hg38/hprcCoverage97.ra - lines changed 13, context: html, text, full: html, text