All File Changes

v451_preview to v451_preview2 (2023-07-03 to 2023-07-10) v451

• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    6ed2a694cb4ca93a76fa4a8bf057380ad5774af5 Sun Jul 9 01:11:20 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cartReset/cartReset.c
  • lines changed 1, context: html, text, full: html, text
    15dec6458047446acf4f6c982042cbee2a6bb6d5 Thu Jul 6 04:47:10 2023 -0700
    fixing spurious warning message in apache logs, refs #31707
• src/hg/cgilib/pcrResult.c
  • lines changed 30, context: html, text, full: html, text
    d3aaebb71ef2b82ece4340766c0de67541ce7362 Wed Jul 5 16:41:56 2023 -0700
    Fix for multiple hgPcr results feature, actually use the stored primer pair in the psl qName, refs #31608
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 48, context: html, text, full: html, text
    ea7173bd838a0f4795a1222eb5b49c85defbc4cf Mon Jul 3 05:13:11 2023 -0700
    the proper fix for hgGeneGraph unicode problems, taking back some of the earlier changes, refs #31563
  • lines changed 6, context: html, text, full: html, text
    5b1c8caa82d1924be9c2ec82a3b5d27182ed52ab Tue Jul 4 06:03:58 2023 -0700
    sys.stdout.buffer is not actually needed here, trying to avoid using buffer and using the normal buffered stdout instead, refs #31563
  • lines changed 1, context: html, text, full: html, text
    4914f5562d357582e9af010f479c5208ea887454 Tue Jul 4 06:13:51 2023 -0700
    on hgwbeta, we got '_io.BufferedWriter' object has no attribute 'buffer' when accessing stdout.buffer, not on hgwdev, see #31591. No idea why this happens but just in case, using the old-school way to wrap stdout now, as a file-like object, refs #31563
  • lines changed 1, context: html, text, full: html, text
    e84ee6d76d371ced4a8d5d75c69af730358f95a6 Fri Jul 7 02:58:18 2023 -0700
    fixing seed in hgGeneGraph, refs #31712
  • lines changed 5, context: html, text, full: html, text
    d14478c21d156caceb881995f8603433f24a9a99 Fri Jul 7 05:37:47 2023 -0700
    removing stray debug lines that got committed, thanks to Galt for pointing this out, refs #31712
• src/hg/hgPcr/hgPcr.c
  • lines changed 8, context: html, text, full: html, text
    d3aaebb71ef2b82ece4340766c0de67541ce7362 Wed Jul 5 16:41:56 2023 -0700
    Fix for multiple hgPcr results feature, actually use the stored primer pair in the psl qName, refs #31608
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 4, context: html, text, full: html, text
    105a881599567f756a6cddba548f4496edb54144 Wed Jul 5 17:00:30 2023 -0700
    Make hgSuggest use distinct mysql keyword to prevent bugs when tables contain duplicate rows, refs #31705
• src/hg/hgTracks/cds.c
  • lines changed 10, context: html, text, full: html, text
    d3aaebb71ef2b82ece4340766c0de67541ce7362 Wed Jul 5 16:41:56 2023 -0700
    Fix for multiple hgPcr results feature, actually use the stored primer pair in the psl qName, refs #31608
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    fea9f3be2871b26692d7e27574077668b2fe338e Tue Jul 4 06:50:35 2023 -0700
    changing default track control table to 90% of screen width. This has the disadvantage that the window size affects the layout more, but allows us to show more tracks on the screen. todays screens are wider. It sounded like a majority at the group meeting favored the 90% + 8 columns approach. refs #31609
  • lines changed 27, context: html, text, full: html, text
    d3aaebb71ef2b82ece4340766c0de67541ce7362 Wed Jul 5 16:41:56 2023 -0700
    Fix for multiple hgPcr results feature, actually use the stored primer pair in the psl qName, refs #31608
  • lines changed 4, context: html, text, full: html, text
    447513356fcfa684846bdd1b63476e68d9c17ce9 Thu Apr 6 09:04:41 2023 -0700
    Add code to create tooltips under our control. Convert title attributes on hgTracks into these tooltips
• src/hg/hgTracks/imageV2.c
  • lines changed 10, context: html, text, full: html, text
    447513356fcfa684846bdd1b63476e68d9c17ce9 Thu Apr 6 09:04:41 2023 -0700
    Add code to create tooltips under our control. Convert title attributes on hgTracks into these tooltips
• src/hg/hgc/hgc.c
  • lines changed 42, context: html, text, full: html, text
    d3aaebb71ef2b82ece4340766c0de67541ce7362 Wed Jul 5 16:41:56 2023 -0700
    Fix for multiple hgPcr results feature, actually use the stored primer pair in the psl qName, refs #31608
  • lines changed 1, context: html, text, full: html, text
    e1f6707123162e197537d28c3aa914fd0294bb0d Thu Jul 6 07:23:08 2023 -0700
    Initialize primer strings to avoid compile error, refs build email
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    fea9f3be2871b26692d7e27574077668b2fe338e Tue Jul 4 06:50:35 2023 -0700
    changing default track control table to 90% of screen width. This has the disadvantage that the window size affects the layout more, but allows us to show more tracks on the screen. todays screens are wider. It sounded like a majority at the group meeting favored the 90% + 8 columns approach. refs #31609
  • lines changed 17, context: html, text, full: html, text
    447513356fcfa684846bdd1b63476e68d9c17ce9 Thu Apr 6 09:04:41 2023 -0700
    Add code to create tooltips under our control. Convert title attributes on hgTracks into these tooltips
  • lines changed 18, context: html, text, full: html, text
    06f5aa43bac0a32b2996caa8e1c507b1aa702f86 Mon Jul 10 03:02:20 2023 -0700
    forcing word break in track list, refs #31724
• src/hg/inc/hui.h
  • lines changed 4, context: html, text, full: html, text
    fea9f3be2871b26692d7e27574077668b2fe338e Tue Jul 4 06:50:35 2023 -0700
    changing default track control table to 90% of screen width. This has the disadvantage that the window size affects the layout more, but allows us to show more tracks on the screen. todays screens are wider. It sounded like a majority at the group meeting favored the 90% + 8 columns approach. refs #31609
• src/hg/inc/pcrResult.h
  • lines changed 6, context: html, text, full: html, text
    d3aaebb71ef2b82ece4340766c0de67541ce7362 Wed Jul 5 16:41:56 2023 -0700
    Fix for multiple hgPcr results feature, actually use the stored primer pair in the psl qName, refs #31608
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    f5f4c748361b9244ad682ea3955fa34ae553917c Thu Jul 6 10:15:04 2023 -0700
    slow down ct trash disposal, refs #31504
  • lines changed 25, context: html, text, full: html, text
    447513356fcfa684846bdd1b63476e68d9c17ce9 Thu Apr 6 09:04:41 2023 -0700
    Add code to create tooltips under our control. Convert title attributes on hgTracks into these tooltips
• src/hg/js/utils.js
  • lines changed 279, context: html, text, full: html, text
    447513356fcfa684846bdd1b63476e68d9c17ce9 Thu Apr 6 09:04:41 2023 -0700
    Add code to create tooltips under our control. Convert title attributes on hgTracks into these tooltips
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    fea9f3be2871b26692d7e27574077668b2fe338e Tue Jul 4 06:50:35 2023 -0700
    changing default track control table to 90% of screen width. This has the disadvantage that the window size affects the layout more, but allows us to show more tracks on the screen. todays screens are wider. It sounded like a majority at the group meeting favored the 90% + 8 columns approach. refs #31609
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 10, context: html, text, full: html, text
    9414d4d39f80a1cfb34d4184e5016913d857d134 Tue Jul 4 22:20:11 2023 -0700
    add ssh key checks before running sendDownload no redmine
• src/hg/makeDb/trackDb/human/hg19/refSeqComposite.html
  • lines changed 21, context: html, text, full: html, text
    ab9183fde1b3d79ee51a52c1f6a0b05455767597 Wed Jul 5 06:18:10 2023 -0700
    adding more details to refseq docs page, have come up in various ml tickets, refs #31077
• src/hg/pyLib/hgLib3.py
  • lines changed 20, context: html, text, full: html, text
    ea7173bd838a0f4795a1222eb5b49c85defbc4cf Mon Jul 3 05:13:11 2023 -0700
    the proper fix for hgGeneGraph unicode problems, taking back some of the earlier changes, refs #31563
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 12, context: html, text, full: html, text
    586d901c9bb52863a5518271533f7ff87972843b Tue Jul 4 12:12:00 2023 -0700
    correctly setup the synNet gbdb links no redmine
• src/hg/utils/gff3ToGenePred/tests/expected/errDupIdDiffParentsTest.out
  • lines changed 5, context: html, text, full: html, text
    21441c54b2c684a56954b0a2b9d7f352b6d99432 Wed Jul 5 21:54:37 2023 -0700
    added checking for GFF3 incorrectly duplicated ids mascrading as the horrible discontinuous features GFF3 mess
• src/hg/utils/gff3ToGenePred/tests/expected/makeBadTest.gp
  • lines changed 1, context: html, text, full: html, text
    21441c54b2c684a56954b0a2b9d7f352b6d99432 Wed Jul 5 21:54:37 2023 -0700
    added checking for GFF3 incorrectly duplicated ids mascrading as the horrible discontinuous features GFF3 mess
• src/hg/utils/gff3ToGenePred/tests/expected/makeBadTest.out
  • lines changed 1, context: html, text, full: html, text
    21441c54b2c684a56954b0a2b9d7f352b6d99432 Wed Jul 5 21:54:37 2023 -0700
    added checking for GFF3 incorrectly duplicated ids mascrading as the horrible discontinuous features GFF3 mess
• src/hg/utils/gff3ToGenePred/tests/input/dupIdDiffParents.gff3
  • lines changed 51, context: html, text, full: html, text
    21441c54b2c684a56954b0a2b9d7f352b6d99432 Wed Jul 5 21:54:37 2023 -0700
    added checking for GFF3 incorrectly duplicated ids mascrading as the horrible discontinuous features GFF3 mess
• src/hg/utils/gff3ToGenePred/tests/input/makerBad.gff3
  • lines changed 1, context: html, text, full: html, text
    21441c54b2c684a56954b0a2b9d7f352b6d99432 Wed Jul 5 21:54:37 2023 -0700
    added checking for GFF3 incorrectly duplicated ids mascrading as the horrible discontinuous features GFF3 mess
• src/hg/utils/gff3ToGenePred/tests/makefile
  • lines changed 6, context: html, text, full: html, text
    21441c54b2c684a56954b0a2b9d7f352b6d99432 Wed Jul 5 21:54:37 2023 -0700
    added checking for GFF3 incorrectly duplicated ids mascrading as the horrible discontinuous features GFF3 mess
• src/lib/gff3.c
  • lines changed 20, context: html, text, full: html, text
    21441c54b2c684a56954b0a2b9d7f352b6d99432 Wed Jul 5 21:54:37 2023 -0700
    added checking for GFF3 incorrectly duplicated ids mascrading as the horrible discontinuous features GFF3 mess
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    010f900c9fda8a52f5d523da146a6937989a5fad Mon Jul 10 10:58:27 2023 -0700
    v451 preview2

• lines changed: 709
• files changed: 38