Commits for hiram

v487_preview to v487_preview2 (2025-08-18 to 2025-08-25) v487

776952d3d5912ea1400d9213f3d0dfef4b10f4f4 Mon Aug 18 16:02:54 2025 -0700

• initial version to identify and load up new entries into liftOverChain from the hasChainNets.txt file refs #35575
  • src/hg/makeDb/doc/asmHubs/updateLiftOverChain.pl - lines changed 182, context: html, text, full: html, text

2c28295e6b1f47a483282b3790208679ba39a5fe Mon Aug 18 17:51:33 2025 -0700

• checking for reciprocal both directions refs #35575
  • src/hg/makeDb/doc/asmHubs/updateLiftOverChain.pl - lines changed 34, context: html, text, full: html, text

6c3cb2166ce2f4deb20accc8509d477d2227affb Mon Aug 18 17:52:01 2025 -0700

• checking for reciprocal both directions refs #35575
  • src/hg/makeDb/doc/asmHubs/checkAllChainNets.sh - lines changed 10, context: html, text, full: html, text

e5fa11d018d7c121165dbfc3b9d8bf4168e696ff Mon Aug 18 21:09:01 2025 -0700

• adding one 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/fungiAsmHub/fungi.orderList.tsv - lines changed 1, context: html, text, full: html, text

ef7aeddfb0a020c7474b839dfda9fed8a67c6a51 Mon Aug 18 21:24:12 2025 -0700

• fixup clade for GCA_017918235.1 LU_Pher_1.0 refs #29545
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text

ca11012b924166d7e0ba584565b69daea10aae79 Tue Aug 19 20:59:23 2025 -0700

• when making a "minimal" set the tsv file does not have the clade name, thus default track count is the minimum 6 refs #34337
  • src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 1, context: html, text, full: html, text

0e15aa95fcdc3dae70dc14bfb45c9769efe50567 Tue Aug 19 21:03:25 2025 -0700

• BRC update adding 35 refs #34337
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 35, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 66, context: html, text, full: html, text

5e5b7eee198e681368cc2b5df6c2ec6460b5c1c2 Tue Aug 19 21:44:48 2025 -0700

• catching up to BRC project list refs #34337
  • src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv - lines changed 599, context: html, text, full: html, text

c300fe6d73053e74556dcdff06ee7abbfda8268a Wed Aug 20 09:13:29 2025 -0700

• alternate alias name list up to date refs #34337
  • src/hg/utils/automation/aliasTextToBed.pl - lines changed 6, context: html, text, full: html, text

cac44b88c8e627bbc36fc9a63c76934855c60f4b Wed Aug 20 21:15:36 2025 -0700

• adding an older version for BRC refs #34337
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 2, context: html, text, full: html, text

3453ccca0f25bd6d1a9648bf0f178fac1de6d794 Thu Aug 21 21:31:04 2025 -0700

• bringing in the rest of RefSeq assemblies refs #29545
  • src/hg/makeDb/doc/archaeaAsmHub/archaea.orderList.tsv - lines changed 1865, context: html, text, full: html, text
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 111, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 14236, context: html, text, full: html, text

44b668e31e1ef8a67ec110786826a62006b8731c Thu Aug 21 21:32:02 2025 -0700

• script to run up a minimal set of steps when new assemblies are added to a group refs #29545
  • src/hg/makeDb/doc/asmHubs/minimalBuild.sh - lines changed 48, context: html, text, full: html, text

e0fa0d154d7c8a3068bdfcd0668ca09b2f57a464 Fri Aug 22 18:33:24 2025 -0700

• initial prototype for a liftOver end point - need to get some of the hgConvert code into a library - refs #35976
  • src/hg/hubApi/dataApi.h - lines changed 9, context: html, text, full: html, text
  • src/hg/hubApi/hubApi.c - lines changed 6, context: html, text, full: html, text
  • src/hg/hubApi/liftOver.c - lines changed 257, context: html, text, full: html, text
  • src/hg/hubApi/makefile - lines changed 1, context: html, text, full: html, text

f3e2edde514273b66db0b8ca5bf77a8a8d404492 Sun Aug 24 12:45:35 2025 -0700

• remove assembly that has disappeared refs #29545
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 2, context: html, text, full: html, text