Commits for hiram

v495_base to v496_preview (2026-03-09 to 2026-03-16) v496

a65ee2b4427852eca3993f8203b0b3ea8ce1cedc Mon Mar 9 14:27:14 2026 -0700

• Claude code fixing Claude code
  • src/hg/hubApi/apiUtils.c - lines changed 3, context: html, text, full: html, text

cab953dd5332d8e2a52af9d6b01c9245fd13d29a Tue Mar 10 21:16:23 2026 -0700

• VGP update in progress
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 86, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 24, context: html, text, full: html, text

3024edbfb4af164c8ef34eded35ec41015437c5c Wed Mar 11 14:56:35 2026 -0700

• allow GenArk hubs to exist as "curated" hubs with a dbDb entry such as rn8 and a nibPath to the GenArk /gbdb/ directory refs #32985
  • src/hg/lib/hubConnect.c - lines changed 74, context: html, text, full: html, text

1ef3fd9ec2124b1e8a88370d6ac9629aebed02a8 Fri Mar 13 12:30:21 2026 -0700

• should have a compile target no redmine
  • src/oneShot/randDNA/makefile - lines changed 3, context: html, text, full: html, text

1883f988de556896f2f60633ca0e3e87bbc8ae18 Fri Mar 13 12:54:20 2026 -0700

• adding tests for the newly improved faSize command
  • src/utils/faSize/tests/expected/allThree.txt - lines changed 6, context: html, text, full: html, text
  • src/utils/faSize/tests/expected/s1.s2.txt - lines changed 6, context: html, text, full: html, text
  • src/utils/faSize/tests/expected/s1.txt - lines changed 2, context: html, text, full: html, text
  • src/utils/faSize/tests/expected/s1Ands2.txt - lines changed 6, context: html, text, full: html, text
  • src/utils/faSize/tests/expected/s2.txt - lines changed 2, context: html, text, full: html, text
  • src/utils/faSize/tests/input/s1.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faSize/tests/input/s1.fa.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faSize/tests/input/s1.s2.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faSize/tests/input/s1.s2.fa.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faSize/tests/input/s2.2bit - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faSize/tests/input/s2.fa.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/utils/faSize/tests/makefile - lines changed 52, context: html, text, full: html, text

e89a47bff299bdd888d5b7f0a470b20aed221e01 Fri Mar 13 12:57:40 2026 -0700

• improved faSize inputs to allow 2bit files and added tests - code by claude
  • src/utils/faSize/faSize.c - lines changed 21, context: html, text, full: html, text
  • src/utils/faSize/makefile - lines changed 3, context: html, text, full: html, text

976f6c37c274d5ec80b98883b5f2018496763174 Fri Mar 13 13:13:33 2026 -0700

• add the detailed tab and veryDetailed test options no redmine
  • src/utils/faSize/tests/expected/s1.s2.detailed.txt - lines changed 2, context: html, text, full: html, text
  • src/utils/faSize/tests/expected/s1.s2.tab.txt - lines changed 22, context: html, text, full: html, text
  • src/utils/faSize/tests/expected/s1.s2.veryDetailed.txt - lines changed 2, context: html, text, full: html, text
  • src/utils/faSize/tests/makefile - lines changed 26, context: html, text, full: html, text

4409063550e6c4cc87cfd37f92f7b8db2699f885 Fri Mar 13 17:13:14 2026 -0700

• with the aid of claude add a genome argument to the ucscGenomes endpoint and manage assembly alias a bit more than previously for ucscGenomes and genarkGenomes refs #35972
  • src/hg/hubApi/hubApi.c - lines changed 23, context: html, text, full: html, text
  • src/hg/hubApi/list.c - lines changed 18, context: html, text, full: html, text
  • src/hg/hubApi/tests/expected/err31.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/list27b.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/list27c.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/notSup01.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/makefile - lines changed 13, context: html, text, full: html, text