Commits for braney

v427_preview to v427_preview2 (2022-02-07 to 2022-02-14) v427

9575c7ded6204e195d050b3bc18b77e43359423c Mon Feb 7 14:37:55 2022 -0800

• remove links to PDB images which are no longer present. Change URL to structure to conform to current PDB site.
  • src/hg/hgGene/domains.c - lines changed 15, context: html, text, full: html, text

20473f03adfc10172e8cc39b23656e077aece62e Mon Feb 7 14:48:45 2022 -0800

• add GENCODE V39 log files to doc
  • src/hg/makeDb/doc/ucscGenes/hg38.gencodeV39.log - lines changed 3674, context: html, text, full: html, text

98f8d8fe3c4c43d4030a61ccec76e88c4719213a Thu Feb 10 11:51:25 2022 -0800

• upgrade to V39
  • src/hg/hgGene/hgGeneData/Human/hg38/links.ra - lines changed 2, context: html, text, full: html, text

d51631f0fa655b66dfd432cfb3ba95b3b058fa64 Thu Feb 10 12:00:02 2022 -0800

• change sequence logo view back to coming on at codon coloring level instead of base level since I cannot replicate the bug I was seeing.
  • src/hg/hgTracks/wigTrack.c - lines changed 6, context: html, text, full: html, text

bb0ba2f4936af96f32f4cbc01dfab0a8b0b957ea Thu Feb 10 12:41:32 2022 -0800

• more parameterization of knownGene build
  • src/hg/utils/otto/knownGene/copyFilesToAssembly.sh - lines changed 2, context: html, text, full: html, text

339f301a906608e65e98d494054ef975a5b68f44 Thu Feb 10 12:43:04 2022 -0800

• take Lynx out of knownGene build
  • src/hg/utils/otto/knownGene/buildTo.sh - lines changed 6, context: html, text, full: html, text

c014326efaedb835a44760dbe4e2ed4c8e992412 Thu Feb 10 14:13:21 2022 -0800

• add some tests to subColumn
  • src/utils/subColumn/tests/expected/outputMiss.bed - lines changed 209, context: html, text, full: html, text
  • src/utils/subColumn/tests/expected/passMissing.tab - lines changed 268, context: html, text, full: html, text
  • src/utils/subColumn/tests/expected/skipMissing.tab - lines changed 59, context: html, text, full: html, text
  • src/utils/subColumn/tests/input/colored.bed - lines changed 268, context: html, text, full: html, text
  • src/utils/subColumn/tests/input/ensembl.tab - lines changed 194, context: html, text, full: html, text
  • src/utils/subColumn/tests/makefile - lines changed 24, context: html, text, full: html, text

fe2dff20936a2f7d3cd570360b1d6fe0e1b65cc1 Thu Feb 10 14:15:36 2022 -0800

• add an option to subColumn to skip lines that don't match
  • src/utils/subColumn/subColumn.c - lines changed 16, context: html, text, full: html, text

bbad3a22ae7d64cb72f5af7e24963cf3c219fbe4 Sat Feb 12 10:03:39 2022 -0800

• import MANE v1.0
  • src/hg/makeDb/doc/hg38/mane.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mane.alpha.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/mane.alpha.ra - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text

c924092bcdeb2b5e1b8e10f260854fa4ca9ac9c2 Sat Feb 12 13:14:03 2022 -0800

• a little clean-up of the doc
  • src/hg/makeDb/doc/hg38/mane.txt - lines changed 4, context: html, text, full: html, text