Commits for hiram

v474_preview2 to v474_base (2024-11-11 to 2024-11-18) v474

08b62dca54a26736674194ac8f6977ec456f9ddc Tue Nov 12 01:08:45 2024 -0800

• correctly recognize blastDb output files when giant genome refs #34370
  • src/hg/utils/automation/doRepeatModeler.pl - lines changed 1, context: html, text, full: html, text

b58b72be7f4b8847f55197b7f9b2ffe8d5423a34 Tue Nov 12 08:27:53 2024 -0800

• better choice of TMPDIR refs #34370
  • src/hg/utils/automation/doRepeatModeler.pl - lines changed 12, context: html, text, full: html, text

52c1b41e042ce9aa98363debb0bd38723f4c6d55 Tue Nov 12 15:00:48 2024 -0800

• prepare 12-way on danRer10 for release refs #22542
  • src/hg/makeDb/trackDb/zebrafish/danRer10/cons12way.html - lines changed 472, context: html, text, full: html, text

02d708a13d9d1d3548f46ac727201844e5a21c70 Thu Nov 14 02:30:01 2024 -0800

• adding 11 canine assemblies per user request refs #34818
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 11, context: html, text, full: html, text

4c99b03bdf9c3c36b7b579aa3f1e71be540541cd Sat Nov 16 10:58:20 2024 -0800

• remove a stray single quote and correct case on view and request words refs #32596
  • src/hg/js/assemblySearch.js - lines changed 4, context: html, text, full: html, text

1bbc059fb7c243f1fed1d7001666187ea80e7fcf Sat Nov 16 11:00:05 2024 -0800

• correctly safely escape all inputs refs #32596
  • src/hg/gar/asr.cgi.pl - lines changed 34, context: html, text, full: html, text

40dd8ea044842ea6d662bb3676debb3ac0a417ee Sat Nov 16 15:42:30 2024 -0800

• better safely limit length of all incoming strings refs #32596
  • src/hg/gar/asr.cgi.pl - lines changed 5, context: html, text, full: html, text

e4c2e7d703179df583c9749af4f03f5eefe36d49 Sat Nov 16 16:23:30 2024 -0800

• can safely limit all incoming strings to a safe length before passing on refs #32596
  • src/hg/js/assemblySearch.js - lines changed 7, context: html, text, full: html, text

6330bea2eae8c72820e5445770022a0b669e4374 Sun Nov 17 12:17:10 2024 -0800

• adding 5 per Anton request refs #34337
  • src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv - lines changed 6, context: html, text, full: html, text

28a636911e6c047443019dc9db604e2fc68714b6 Sun Nov 17 13:00:07 2024 -0800

• BRC now has some virus sequences that only have 9 tracks refs #34337
  • src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 1, context: html, text, full: html, text

c36d362926f9c85f65e4099f3577a4203af8ef47 Mon Nov 18 03:02:23 2024 -0800

• some name corrections from Richard Durbin refs #34370
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 8, context: html, text, full: html, text

9e40647f805589d9198ff5334d315d5bd79d6b78 Mon Nov 18 03:05:04 2024 -0800

• VGP update refs #34370
  • src/hg/makeDb/doc/vgpAsmHub/vgp.alternate.orderList.tsv - lines changed 4, context: html, text, full: html, text

a9069713e8e31a34cee0921aba821e3a52c38a06 Mon Nov 18 03:23:41 2024 -0800

• name corrections from Richard Durbin refs #34370
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 4, context: html, text, full: html, text