Commits for braney

v408_base to v409_preview (2020-12-07 to 2021-01-04) v409

ff51fb89b5ea359ce375fe2219d76b2f4c45a996 Mon Dec 7 10:16:57 2020 -0800

• be smarter about when to go into codon numbering mode on genePreds #26628
  • src/hg/hgTracks/cds.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 1, context: html, text, full: html, text

093995328667118cf901ec6bb93e36c4464c93c4 Mon Dec 7 10:37:41 2020 -0800

• move a routine into a different file so it has access to the global definitions of fonts
  • src/hg/hgTracks/config.c - lines changed 22, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 23, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 2, context: html, text, full: html, text

4efa2a1c3d370f0c36bfae6a4e96cb6c36fb83ff Mon Dec 7 11:46:58 2020 -0800

• scale fonts used on the y axis labels in lollipop graphs
  • src/hg/hgTracks/lollyTrack.c - lines changed 93, context: html, text, full: html, text

004d56eff1d9b74e312104b30ea872201e92cf97 Thu Dec 10 15:50:57 2020 -0800

• add the ability for bigPsl tracks to show query sequences like genePred if they have the sequence and CDS. #24672
  • src/hg/hgc/hgc.c - lines changed 132, context: html, text, full: html, text

d79c89ce226eed40e2d000d423f9d23b28e26391 Thu Dec 10 15:53:00 2020 -0800

• add bigDataUrl for LRG track
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text

71ca786dd00a42ee4f187619b3d6746cb54a82eb Mon Dec 14 15:33:56 2020 -0800

• fiddling with the mouseovers #26330
  • src/hg/hgTracks/imageV2.c - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/clinvarSubLolly.txt - lines changed 4, context: html, text, full: html, text

a879c24ca720e1de4c34d4a1e3407f4baa0259d6 Mon Dec 14 15:35:45 2020 -0800

• some tweaks to sequence output from bigPsl if they have sequence and maybe cds
  • src/hg/hgc/hgc.c - lines changed 15, context: html, text, full: html, text

0e7d9cb854ff492af1565a061fe0070a3f0f693e Thu Dec 17 17:33:44 2020 -0800

• add a flush tables after loading trackDb and hgFindSpec tables to prevent an error with myisamchk saying that they are still open
  • src/hg/makeDb/hgFindSpec/hgFindSpec.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 1, context: html, text, full: html, text

77041cdec2060274397a745305d0b575aa7ac731 Sat Dec 19 10:00:28 2020 -0800

• re-connect the postscript output to the font setting, which had disappeared a while back. #26681
  • src/inc/psGfx.h - lines changed 1, context: html, text, full: html, text
  • src/lib/psGfx.c - lines changed 3, context: html, text, full: html, text
  • src/lib/pscmGfx.c - lines changed 6, context: html, text, full: html, text

cff0a237099d06f16896ec781a85cccb1a663849 Mon Dec 21 14:21:59 2020 -0800

• make sure that trackDb cache on hubs keeps track of files that are included in the trackDb.txt file
  • src/hg/hubApi/apiUtils.c - lines changed 1, context: html, text, full: html, text
  • src/hg/inc/trackDb.h - lines changed 8, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/hubConnect.c - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/trackDbCache.c - lines changed 54, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 1, context: html, text, full: html, text

780985dafe4ff8687576e91b84596d94a0a4ad2d Mon Dec 21 14:47:21 2020 -0800

• oops, missed a place
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 1, context: html, text, full: html, text

e1ba1d9a147724de16cb65a1d5006ecd6c4cfdc8 Wed Dec 23 14:57:42 2020 -0800

• a silly hack to get mafGene to work on alignments that have assembly names with a dot in them
  • src/hg/lib/mafGene.c - lines changed 14, context: html, text, full: html, text

f673475f54b9ac05139b41a477048d7ca5f38599 Mon Jan 4 10:01:25 2021 -0800

• v409 preview1
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text