Commits for hiram

v469_base to v470_preview (2024-08-05 to 2024-08-12) v470

dc88954b3214a3b414711c9e73dfa654bf0dffd9 Tue Aug 6 12:58:18 2024 -0700

• fixup mouseOver wiggle track when a track in wiggle mode switches to not wiggle mode, do not display the mouseOver. refs #34222
  • src/hg/js/hgTracks.js - lines changed 33, context: html, text, full: html, text

21a18bb99f000d0da8cfbb15cc33138f4127947a Wed Aug 7 10:26:30 2024 -0700

• correct for loop variable declaration no redmine
  • src/hg/js/hgTracks.js - lines changed 1, context: html, text, full: html, text

8796500caefe26d7872e2d6a8ffbed913d70a8f0 Wed Aug 7 11:30:21 2024 -0700

• an update for VGP to add 67 assemblies refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 67, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 26, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 16, context: html, text, full: html, text

584b7af6bcac17cc116ca2c4801e60a149d49c2c Wed Aug 7 15:23:41 2024 -0700

• BIGNUM needs to be a bit larger for chain/net processing on sequences over 1 Gb refs #34248
  • src/hg/mouseStuff/axtBest/axtBest.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/axtBestNear/axtBestNear.c - lines changed 3, context: html, text, full: html, text
  • src/hg/mouseStuff/axtFilter/axtFilter.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/chainFilter/chainFilter.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/chainNet/chainNet.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/chainToAxt/chainToAxt.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToAxt/lavToAxt.c - lines changed 3, context: html, text, full: html, text
  • src/hg/mouseStuff/lavToPsl/lavToPsl.c - lines changed 3, context: html, text, full: html, text
  • src/hg/mouseStuff/netFilter/netFilter.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/netToAxt/netToAxt.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/netToBed/netToBed.c - lines changed 2, context: html, text, full: html, text
  • src/lib/chain.c - lines changed 2, context: html, text, full: html, text

344c5e2d07b4517677ea9a70fbededda133fc34f Wed Aug 7 16:01:44 2024 -0700

• VGP update with 48 added primary assemblies and 25 alternates refs #29545
  • src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 48, context: html, text, full: html, text
  • src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt - lines changed 70, context: html, text, full: html, text

9cea4ceb4ee3f5c28c3315f63f0c696e82f6a8d4 Thu Aug 8 12:57:18 2024 -0700

• adding the assemblyList table creation to the cron job refs #32596
  • src/hg/utils/otto/genArk/addAssemblyList.sh - lines changed 35, context: html, text, full: html, text
  • src/hg/utils/otto/genArk/updateHgcentral.sh - lines changed 14, context: html, text, full: html, text

e83574e4d897147878ee3f50d7c37e49e30effa8 Fri Aug 9 09:16:55 2024 -0700

• eliminate the /gbdb/GC* symlinks for bigBed files no redmine
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 6, context: html, text, full: html, text

e12feaeaef7d5378709131fd36f53b7b87e48d72 Fri Aug 9 16:44:52 2024 -0700

• adding 11-way multiz and cactus alignments no redmine
  • src/hg/makeDb/trackDb/human/hg38/primates11way.html - lines changed 277, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/primates11way.ra - lines changed 90, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text

624d014a418548f0a73d8400eee3cae42e81bdaf Fri Aug 9 16:46:10 2024 -0700

• adding 11-way multiz and cactus alignments no redmine
  • src/hg/makeDb/trackDb/human/hs1/primates11way.html - lines changed 277, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/primates11way.ra - lines changed 89, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 2, context: html, text, full: html, text