Commits for hiram

v504_preview to v504_preview2 (2026-09-07 to 2026-09-14) v504

73625c7a1d0620a7e6e9de61a2b4fd2fd1fa7685 Wed Sep 9 16:08:15 2026 -0700

• adjust trfBig to use 500 kb windows for calculation and corresponding script from claude to reassembly broken annotations at this smaller window size refs #38321
  • src/hg/trfBig/trfBig.c - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/mergeTrf.py - lines changed 270, context: html, text, full: html, text

3de452af33eb095927dc7305001f950b81f05693 Wed Sep 9 16:13:30 2026 -0700

• adjust trfBig to use 500 kb windows for calculation and corresponding script from claude to reassembly broken annotations at this smaller window size refs #38321
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 3, context: html, text, full: html, text

f271ed112e3a9facaebc08ec6d05e463790988e0 Wed Sep 9 16:34:19 2026 -0700

• now using the merged trf output from the 500 kb operation refs #38321
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 17, context: html, text, full: html, text

3cb4d150856825931e385cff4d4d19173ec5a723 Wed Sep 9 16:39:37 2026 -0700

• adding a couple per user request refs #29545
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

1fc16d4ddd373fa0c4f3ae555feac1c053b5d012 Wed Sep 9 16:55:28 2026 -0700

• re-enable otto creation of new asmAlias table refs #38082
  • src/hg/utils/otto/genArk/asmAlias/runUpdate.sh - lines changed 9, context: html, text, full: html, text

20da4c889251225224be1661d4f3f7f9d4d0d8fa Thu Sep 10 11:24:58 2026 -0700

• eliminate obsolete information
  • src/hg/utils/otto/genArk/README - lines changed 18, context: html, text, full: html, text

af19b68a0dc2b8e4057fe762f1805b060e38ed77 Thu Sep 10 21:51:33 2026 -0700

• updating RepeatMasker and RepeatModeler to next version refs #38337
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/automation/doRepeatModeler.pl - lines changed 1, context: html, text, full: html, text

d40445e1154b5384876ca6b69bd069518762ea6d Thu Sep 10 21:52:57 2026 -0700

• working with new simpleRepeat output refs #38321
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 5, context: html, text, full: html, text

6359c2dd09c8520e2a03b14d916f1f23deac63ed Fri Sep 11 09:55:28 2026 -0700

• correct reference to the mergeTrf script refs #38321
  • src/hg/utils/automation/doSimpleRepeat.pl - lines changed 3, context: html, text, full: html, text

441ec7ab39569a301912b2b08981747d98fdb752 Fri Sep 11 15:11:40 2026 -0700

• the exactNameSearch() was the wrong way to go, back that out and do this correctly from claude code review refs #38290
  • src/hg/hubApi/findGenome.c - lines changed 44, context: html, text, full: html, text

d522ecef8f0426e8323009094dee2fa04798ffc1 Fri Sep 11 15:12:36 2026 -0700

• add a regression test that was uncovered with v504 preview 1 build refs #38290
  • src/hg/hubApi/tests/findGenome.sh - lines changed 7, context: html, text, full: html, text

8f030ca5d3d1ff1983acb8bcb0ea1de7fe56e3a5 Fri Sep 11 16:06:50 2026 -0700

• correctly lead users to download or generate GC data from bigWigs or 2bits refs #38290
  • src/hg/utils/automation/asmHubGc5Percent.pl - lines changed 78, context: html, text, full: html, text

0b88e0fa63875f67aaf77a4fefc4038ee6caee58 Fri Sep 11 16:09:16 2026 -0700

• meat puppet here, claude didn't like the name mismatch, oh well, whatever, it isn't important what the name is here refs #38224
  • src/hg/makeDb/trackDb/contrib/RCPediaVGP_v1/retrocopies.html - lines changed 67, context: html, text, full: html, text

3cdeeced0d0a25cf6de114092f6ad62a35d63a97 Fri Sep 11 16:09:35 2026 -0700

• meat puppet here, claude didn't like the name mismatch, oh well, whatever, it isn't important what the name is here refs #38224
  • src/hg/makeDb/trackDb/contrib/RCPediaVGP_v1/RCPediaVGP_v1.html - lines changed 67, context: html, text, full: html, text

cbf5cf161c1be2f6bfdcee0a29f334564ac9435e Fri Sep 11 16:11:38 2026 -0700

• silence claude noise refs #38290
  • src/hg/utils/automation/asmHubGc5Percent.pl - lines changed 1, context: html, text, full: html, text

646f392ab8ff4d3ca9740c199ecb59317eccae78 Fri Sep 11 16:13:11 2026 -0700

• silence claude noise refs #38290
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 2, context: html, text, full: html, text

ca3e7270f30b554962e47a8ee1cec08a00de5862 Fri Sep 11 16:24:26 2026 -0700

• silence claude noise refs #38290
  • src/hg/makeDb/trackDb/contrib/RCPediaVGP_v1/README.txt - lines changed 61, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/contrib/RCPediaVGP_v1/mkSymLinks.sh - lines changed 47, context: html, text, full: html, text