Commits for hiram

v455_base to v456_preview (2023-10-09 to 2023-10-16) v456

3cbcd195f375a1368615ca50be236375507e010f Mon Oct 9 15:01:49 2023 -0700

• added correct construction of the maf summary table refs #31561
  • src/hg/makeDb/doc/hg38/hprc90way.txt - lines changed 40, context: html, text, full: html, text

2f2e49b55d15cd34a675325aec6e08ee0e36a233 Mon Oct 9 15:11:47 2023 -0700

• starting proper description page for this track refs #31561
  • src/hg/makeDb/trackDb/human/hg38/hprc90way.html - lines changed 36, context: html, text, full: html, text

5ed8b946589b8a171e8c3849fd0e1640859c64bf Mon Oct 9 15:20:01 2023 -0700

• starting proper description page for this track refs #31561
  • src/hg/makeDb/trackDb/human/hg38/trackDb.hprc90way.ra - lines changed 1, context: html, text, full: html, text

307976d1f4c1ecbc73a55dea1f6348c19c1336b8 Mon Oct 9 20:08:42 2023 -0700

• adding GCA_026545065.1_CHOZN_v2.4 Chinese hamster (CHO-K1 CHOZN v2.4 2022) per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

c377565e4de6eefa3ed568504aab0c9934282d01 Tue Oct 10 08:21:09 2023 -0700

• adding 2 bacteria Streptomyces ambofaciens per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 2, context: html, text, full: html, text

f79cd21c0f6ffea6776fc04b53a61b10b59dd947 Tue Oct 10 14:30:11 2023 -0700

• adding documentation for HPRC tracks refs #31561
  • src/hg/makeDb/trackDb/human/hg38/hprc90way.html - lines changed 23, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcVCF.html - lines changed 70, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcVCF.ra - lines changed 54, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcVCFTest.html - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcVCFTest.ra - lines changed 72, context: html, text, full: html, text

0dda631e8d39f48e611efe3538d5ae87f2713b28 Tue Oct 10 14:44:41 2023 -0700

• duplicate tag removed refs #31561
  • src/hg/makeDb/trackDb/human/hg38/hprcVCF.ra - lines changed 1, context: html, text, full: html, text

d2b3b8afbf6b9864777b688eb53629c97322ef04 Tue Oct 10 14:51:41 2023 -0700

• move all the HPRC VCF experiements to their own container refs #31561
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

e9db1da60585f8d0f7abda5494a5741348d6a3b5 Wed Oct 11 10:02:04 2023 -0700

• a renaming of the ReChains refs #31561
  • src/hg/makeDb/trackDb/human/hg38/chainsHprc.ra - lines changed 90, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcChains.html - lines changed 70, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcChains.ra - lines changed 820, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

bab374b08238b22ae463c600ca193b469af1544f Wed Oct 11 10:55:12 2023 -0700

• move HPRC test tracks to experimental track group and rename netsReHprc to hprcNets refs #31561
  • src/hg/makeDb/trackDb/human/hg38/chainNetHumanExperiment.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/chainsHprc.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcChain.ra - lines changed 1, 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/hprcNets.html - lines changed 69, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcNets.ra - lines changed 820, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcVCFTest.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/netsReHprc.ra - lines changed 820, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

65a0fd8af813529a001a714b3c550b0063c9de6e Thu Oct 12 13:18:46 2023 -0700

• re-chain the reChains and re-net the reNets refs #31561
  • src/hg/makeDb/doc/hg38/hprcReChain.txt - lines changed 207, context: html, text, full: html, text

72ef049d74b7d9bce6d78508f5b8de6ea8587541 Thu Oct 12 22:37:19 2023 -0700

• adding GCA_030013775.1_ASM3001377v1 Florida manatee (CSIC 2023) per user request an updated version of GCA_000243295.1_TriManLat1.0 refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

b72524bd512ddebff3f125a1a1df7f701c4ed49f Fri Oct 13 08:57:48 2023 -0700

• adding GCA_021461655.1_ASM2146165v1 flatworm S.japonicum (SjaV3_Hu 2022) per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text