Commits for lrnassar

v456_preview to v456_preview2 (2023-10-16 to 2023-10-23) v456

a6333e7e8be2fbc9c8e3ba3753fa6a25fa8e9c2e Mon Oct 16 12:01:36 2023 -0700

• Adding bigGenePred to the mouseOver support since it works fine, refs #32459
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

14b1f8804bcd230f2252b79b002b23348c354113 Tue Oct 17 15:28:29 2023 -0700

• Reverting some stages phyloP changes #29898 and adding the logoMaf setting back after a fix to the performance issue was put in place, refs #32267
  • src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm39/trackDb.35way.ra - lines changed 1, context: html, text, full: html, text

76d933ccf24bd1a2a360f9b6a437c2e8445c7583 Wed Oct 18 11:01:51 2023 -0700

• Fixing up a small encoding bug in the GenCC otto job and clarification of the printed message. Refs #31795
  • src/hg/utils/otto/genCC/doGenCC.py - lines changed 2, context: html, text, full: html, text

cf24bf1f4d870e1b6d2d9067c04ff480cfb469b2 Fri Oct 20 12:54:49 2023 -0700

• Adding an updated cosmic makedoc after a user wrote in with multiple errors found, refs #32430
  • src/hg/makeDb/doc/hg38/cosmicV98.txt - lines changed 159, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/hg38.txt - lines changed 2, context: html, text, full: html, text

e6d21fe68e1179e21bbb8b944b35518ff5241160 Fri Oct 20 13:47:28 2023 -0700

• Fixing up liftOver page where we mention for T2T minimap and the UCSC liftOver pipeline, except we never released the UCSC alignments. Refs #32422
  • src/hg/makeDb/trackDb/human/hs1/html/hgLiftOver.html - lines changed 77, context: html, text, full: html, text

b39119efb42cec014dfe6cba948bc7717b0176c4 Fri Oct 20 14:10:18 2023 -0700

• Changing the abuse message to point to private ML instead of public, refs #22423
  • src/hg/das/das.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hubApi/hubApi.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/botDelay.c - lines changed 1, context: html, text, full: html, text