All File Changes

v468_base to v469_preview (2024-07-15 to 2024-07-22) v469

• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3a03d84833b102b228aee6961ecefa1b3ab4218e Sun Jul 21 01:11:17 2024 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    3a03d84833b102b228aee6961ecefa1b3ab4218e Sun Jul 21 01:11:17 2024 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cgilib/cartEdit4.c
  • lines changed 16, context: html, text, full: html, text
    459e2288153379fa730eb1b648145bfb7bbc8dc2 Tue Jul 16 17:52:06 2024 -0700
    add rewrite rule for OMiM tracks to consolidate them in super track
• src/hg/cgilib/cartRewrite.c
  • lines changed 2, context: html, text, full: html, text
    459e2288153379fa730eb1b648145bfb7bbc8dc2 Tue Jul 16 17:52:06 2024 -0700
    add rewrite rule for OMiM tracks to consolidate them in super track
• src/hg/cgilib/makefile
  • lines changed 1, context: html, text, full: html, text
    459e2288153379fa730eb1b648145bfb7bbc8dc2 Tue Jul 16 17:52:06 2024 -0700
    add rewrite rule for OMiM tracks to consolidate them in super track
• src/hg/hgBlat/hgBlat.c
  • lines changed 5, context: html, text, full: html, text
    d2482e22232f8a2296fcc6706b2630f5499f7a83 Wed Jul 17 13:45:02 2024 -0700
    change chroms to chromAuthority names in hgBlat and hgPcr
• src/hg/hgPcr/hgPcr.c
  • lines changed 9, context: html, text, full: html, text
    d2482e22232f8a2296fcc6706b2630f5499f7a83 Wed Jul 17 13:45:02 2024 -0700
    change chroms to chromAuthority names in hgBlat and hgPcr
• src/hg/hgTracks/decorator.c
  • lines changed 1, context: html, text, full: html, text
    7197002e0c71569ef55b52a3892c1c766a83695e Wed Jun 26 15:52:30 2024 -0700
    Fixing minor function name typo, no ticket
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    e19d7059297b1a3d436540d3774ab1a4af71eacb Tue Jul 16 15:59:52 2024 -0700
    honor defaultIsClosed flag and sort groups by name without regard to case
  • lines changed 13, context: html, text, full: html, text
    c36f910c093e47caa21035a3cc16bba46fb30371 Wed Jul 17 12:32:22 2024 -0700
    add a little widget to let user see aliases. Right now they're in a mouse-over
  • lines changed 11, context: html, text, full: html, text
    74009a95f1c1871f910292b98005957b328d3699 Thu Jul 18 00:24:31 2024 -0700
    fixing measureTiming in hgtracks for cart load time, refs #33932
  • lines changed 4, context: html, text, full: html, text
    cfeba2ec254a47dc9ceb7a228ce85af5b77a3212 Thu Jul 18 00:25:17 2024 -0700
    adding contact email to hub mouseover, email from Mark
  • lines changed 3, context: html, text, full: html, text
    a53bf1793b4936c6f39a315b432e5f87ac57aff3 Sat Jul 20 21:08:08 2024 -0700
    take out aliases widget until someone is going to put it in the right place
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    7197002e0c71569ef55b52a3892c1c766a83695e Wed Jun 26 15:52:30 2024 -0700
    Fixing minor function name typo, no ticket
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    7197002e0c71569ef55b52a3892c1c766a83695e Wed Jun 26 15:52:30 2024 -0700
    Fixing minor function name typo, no ticket
  • lines changed 4, context: html, text, full: html, text
    13fcc22034ccaa154c07db85ce50e6ad2e843245 Wed Jul 17 15:42:49 2024 -0700
    cap each track height at 31,000
  • lines changed 1, context: html, text, full: html, text
    34f1ae45061da2d77da0b7fa4a8a7eaae0a9ee44 Fri Jul 19 03:28:30 2024 -0700
    increasing buffer size, refs #34136
• src/hg/hgc/hgc.c
  • lines changed 7, context: html, text, full: html, text
    d2482e22232f8a2296fcc6706b2630f5499f7a83 Wed Jul 17 13:45:02 2024 -0700
    change chroms to chromAuthority names in hgBlat and hgPcr
• src/hg/htdocs/cite.html
  • lines changed 49, context: html, text, full: html, text
    41c63e4b0795abf47b9fcbaf7554da7f50741ad5 Fri Jul 19 16:29:55 2024 -0700
    Sprucing up the cite.html page with general improvements and organization, refs #31996
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 3, context: html, text, full: html, text
    505da6cd60ae9dc005b085a2e713ccbf4e7e808a Thu Jul 18 09:31:36 2024 -0700
    Adding a dbSNP search example to the query page. Refs #34128
  • lines changed 1, context: html, text, full: html, text
    772e9b6cbf1a55065db077535c2b9a8cb2dc42bf Fri Jul 19 16:44:51 2024 -0700
    Clarifying search text, the rsID results in multiple hits and the rsID is a location and not a variant, refs #34128
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 5, context: html, text, full: html, text
    6f6c019b987b3951b1cae04da2bc971a93cc68ad Mon Jul 15 16:07:53 2024 -0700
    Fixing the month in the news post. Adding a link on the indexNews page, refs #32302
  • lines changed 7, context: html, text, full: html, text
    37a8930e3a492001f14a73f8a676cc50fbfcd16d Tue Jul 16 17:21:18 2024 -0700
    Adding Gerardo's suggestions from the code review, refs #34117
  • lines changed 4, context: html, text, full: html, text
    85618608a8e4df568d51c3e96a8c134ee93a2ebe Wed Jul 17 14:24:27 2024 -0700
    Updating the newsarch with 2023, added a column, no redmine.
  • lines changed 4, context: html, text, full: html, text
    1a59b509cebd53b0e7f2d322fd0fb46586f53840 Fri Jul 19 18:38:05 2024 -0700
    Restructuring some of the menus based on feedback, refs #33509
• src/hg/htdocs/inc/gbFooterHardcoded.html
  • lines changed 8, context: html, text, full: html, text
    1a59b509cebd53b0e7f2d322fd0fb46586f53840 Fri Jul 19 18:38:05 2024 -0700
    Restructuring some of the menus based on feedback, refs #33509
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 14, context: html, text, full: html, text
    1a59b509cebd53b0e7f2d322fd0fb46586f53840 Fri Jul 19 18:38:05 2024 -0700
    Restructuring some of the menus based on feedback, refs #33509
• src/hg/htdocs/inc/gbsFooter.html
  • lines changed 7, context: html, text, full: html, text
    1a59b509cebd53b0e7f2d322fd0fb46586f53840 Fri Jul 19 18:38:05 2024 -0700
    Restructuring some of the menus based on feedback, refs #33509
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 14, context: html, text, full: html, text
    1a59b509cebd53b0e7f2d322fd0fb46586f53840 Fri Jul 19 18:38:05 2024 -0700
    Restructuring some of the menus based on feedback, refs #33509
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    6f6c019b987b3951b1cae04da2bc971a93cc68ad Mon Jul 15 16:07:53 2024 -0700
    Fixing the month in the news post. Adding a link on the indexNews page, refs #32302
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    8e98f2a8e4862455c37c4fc2acb9ac3f3874dc9f Tue Jul 16 04:37:23 2024 -0700
    found a better way to increase font size of all dialog windows, refs #27236
  • lines changed 1, context: html, text, full: html, text
    8898cca24758ce96d619ff5f96144b62b236dc25 Tue Jul 16 04:37:57 2024 -0700
    removing stray comment
• src/hg/htdocs/util.html
  • lines changed 11, context: html, text, full: html, text
    1a59b509cebd53b0e7f2d322fd0fb46586f53840 Fri Jul 19 18:38:05 2024 -0700
    Restructuring some of the menus based on feedback, refs #33509
• src/hg/hubApi/assemblyList.py
  • lines changed 766, context: html, text, full: html, text
    455920818135586578c0382cf43a165aaafdcb8e Fri Jul 19 11:09:42 2024 -0700
    transition the prototype genomePriority.py to this production script to be used by otto cronjob refs #33720
• src/hg/hubApi/genomePriority.py
  • lines changed 1, context: html, text, full: html, text
    f0b12c9e7b7a5311f66cce4a76aeac3837003ecd Mon Jul 15 11:31:47 2024 -0700
    correctly compare database version numbers refs #33720
  • lines changed 33, context: html, text, full: html, text
    2d41a88dd1243e8aa51f32e001a80a529c40ea4a Thu Jul 18 13:41:34 2024 -0700
    adding hubUrl to the table ready for transition to assemblyList.py refs #33720
• src/hg/inc/assemblyList.h
  • lines changed 89, context: html, text, full: html, text
    2390b3f3a5623be111160d4f96fc6ea4c197ca4a Fri Jul 19 11:12:57 2024 -0700
    assemblyList table definition for gateway search and findGenome API functions refs #33720
• src/hg/inc/fakeCurl.h
  • lines changed 46, context: html, text, full: html, text
    032653c06fe43263c625613a538389fc2425976b Tue Jul 16 17:16:51 2024 -0700
    Updated hic straw library adapted for UCSC, with a udc-enabled curl substitute. refs #33225
• src/hg/inc/grp.h
  • lines changed 3, context: html, text, full: html, text
    a3739b776a1dff6f5b07d035faa320d22c975c48 Mon Jul 15 14:08:31 2024 -0700
    make priority optional in groups.txt. Also actually sort by priority if specified
• src/hg/lib/assemblyList.as
  • lines changed 13, context: html, text, full: html, text
    2390b3f3a5623be111160d4f96fc6ea4c197ca4a Fri Jul 19 11:12:57 2024 -0700
    assemblyList table definition for gateway search and findGenome API functions refs #33720
• src/hg/lib/assemblyList.c
  • lines changed 332, context: html, text, full: html, text
    2390b3f3a5623be111160d4f96fc6ea4c197ca4a Fri Jul 19 11:12:57 2024 -0700
    assemblyList table definition for gateway search and findGenome API functions refs #33720
• src/hg/lib/assemblyList.sql
  • lines changed 20, context: html, text, full: html, text
    2390b3f3a5623be111160d4f96fc6ea4c197ca4a Fri Jul 19 11:12:57 2024 -0700
    assemblyList table definition for gateway search and findGenome API functions refs #33720
• src/hg/lib/fakeCurl.c
  • lines changed 168, context: html, text, full: html, text
    032653c06fe43263c625613a538389fc2425976b Tue Jul 16 17:16:51 2024 -0700
    Updated hic straw library adapted for UCSC, with a udc-enabled curl substitute. refs #33225
• src/hg/lib/featureBits.c
  • lines changed 3, context: html, text, full: html, text
    9c5826b0163085be9b62f68597f6a8f710568101 Thu Jul 18 09:25:45 2024 -0700
    short cut for bigWigs not being positional. This was causing a problem on track hubs.
• src/hg/lib/grp.c
  • lines changed 12, context: html, text, full: html, text
    a3739b776a1dff6f5b07d035faa320d22c975c48 Mon Jul 15 14:08:31 2024 -0700
    make priority optional in groups.txt. Also actually sort by priority if specified
  • lines changed 1, context: html, text, full: html, text
    e19d7059297b1a3d436540d3774ab1a4af71eacb Tue Jul 16 15:59:52 2024 -0700
    honor defaultIsClosed flag and sort groups by name without regard to case
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    032653c06fe43263c625613a538389fc2425976b Tue Jul 16 17:16:51 2024 -0700
    Updated hic straw library adapted for UCSC, with a udc-enabled curl substitute. refs #33225
• src/hg/lib/straw/new_cStraw.cpp
  • lines changed 192, context: html, text, full: html, text
    032653c06fe43263c625613a538389fc2425976b Tue Jul 16 17:16:51 2024 -0700
    Updated hic straw library adapted for UCSC, with a udc-enabled curl substitute. refs #33225
• src/hg/lib/straw/new_straw.cpp
  • lines changed 69, context: html, text, full: html, text
    032653c06fe43263c625613a538389fc2425976b Tue Jul 16 17:16:51 2024 -0700
    Updated hic straw library adapted for UCSC, with a udc-enabled curl substitute. refs #33225
• src/hg/lib/straw/new_straw.h
  • lines changed 15, context: html, text, full: html, text
    032653c06fe43263c625613a538389fc2425976b Tue Jul 16 17:16:51 2024 -0700
    Updated hic straw library adapted for UCSC, with a udc-enabled curl substitute. refs #33225
• src/hg/lib/trackHub.c
  • lines changed 9, context: html, text, full: html, text
    a3739b776a1dff6f5b07d035faa320d22c975c48 Mon Jul 15 14:08:31 2024 -0700
    make priority optional in groups.txt. Also actually sort by priority if specified
• src/hg/makeDb/doc/asmHubs/commonNames.pl
  • lines changed 1, context: html, text, full: html, text
    9d98499c2484b4bb31788c4e20d9c145c2a6ae92 Thu Jul 18 14:10:32 2024 -0700
    eliminate the useless "Organism name:" from the common name string refs #33720
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 18, context: html, text, full: html, text
    582bbd0a6f94ec0d8d4778f2ee90bdd4189e3c3e Tue Jul 16 16:50:27 2024 -0700
    update adding some fungi and invertebrate assemblies refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    582bbd0a6f94ec0d8d4778f2ee90bdd4189e3c3e Tue Jul 16 16:50:27 2024 -0700
    update adding some fungi and invertebrate assemblies refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    582bbd0a6f94ec0d8d4778f2ee90bdd4189e3c3e Tue Jul 16 16:50:27 2024 -0700
    update adding some fungi and invertebrate assemblies refs #29545
• src/hg/makeDb/trackDb/human/abSplice.ra
  • lines changed 1, context: html, text, full: html, text
    a99ca8e7ccf4b4eedd8de9c343690e85e6e1d26b Tue Jul 16 13:03:29 2024 -0700
    Sqashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/bayesDel.ra
  • lines changed 1, context: html, text, full: html, text
    a99ca8e7ccf4b4eedd8de9c343690e85e6e1d26b Tue Jul 16 13:03:29 2024 -0700
    Sqashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/knownGeneArchive.ra
  • lines changed 4, context: html, text, full: html, text
    8597e80f96a6c632c87c64a803f57c661867b3a3 Thu Jul 18 15:55:42 2024 -0700
    Changing the long and short labels for the knownGene archive tracks, refs #34042
• src/hg/makeDb/trackDb/human/hg19/predictionScoresSuper.ra
  • lines changed 1, context: html, text, full: html, text
    a99ca8e7ccf4b4eedd8de9c343690e85e6e1d26b Tue Jul 16 13:03:29 2024 -0700
    Sqashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg19/reMap.ra
  • lines changed 1, context: html, text, full: html, text
    c0ddfaebb3c2a75261a4400ab688340d51ce425e Wed Jul 17 15:41:57 2024 -0700
    Tweaking maxItems to a value that works reasonably well without turning the track off due to vertical limit. Refs #33767
  • lines changed 2, context: html, text, full: html, text
    b30321dea90350bcc8f184f9d40f3b5f41411433 Wed Jul 17 16:05:37 2024 -0700
    Raising maxItems back to 10k after Braney's new change #34127 that allows for bigger track heights, refs #33767
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    a99ca8e7ccf4b4eedd8de9c343690e85e6e1d26b Tue Jul 16 13:03:29 2024 -0700
    Sqashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/gnomad.alpha.ra
  • lines changed 2, context: html, text, full: html, text
    3a69ab82c95400a63bfb6d2c9542af7fb6f36487 Mon Jul 22 10:03:16 2024 -0700
    Updating mouseOver text display for gnomAD v4.1, refs #33746
• src/hg/makeDb/trackDb/human/hg38/gnomad.constraint.public.ra
  • lines changed 1, context: html, text, full: html, text
    a99ca8e7ccf4b4eedd8de9c343690e85e6e1d26b Tue Jul 16 13:03:29 2024 -0700
    Sqashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    a99ca8e7ccf4b4eedd8de9c343690e85e6e1d26b Tue Jul 16 13:03:29 2024 -0700
    Sqashing old pennantIcons.
• src/hg/makeDb/trackDb/human/hg38/gnomadV4.1.html
  • lines changed 3, context: html, text, full: html, text
    35a39e694464483b0aa51714c2bdf3f9e72bce86 Tue Jul 16 17:45:00 2024 -0700
    Code review edits for the gnomadV4.1.html, refs #34115
• src/hg/makeDb/trackDb/human/hg38/mane.html
  • lines changed 4, context: html, text, full: html, text
    5606e66bdcb63689fd37f9b653088a0551f2e239 Fri Jul 19 16:03:14 2024 -0700
    Adding a link to MANE desc page to let people know we have an archive with the previous versions, refs #27524
• src/hg/makeDb/trackDb/human/hg38/reMap.ra
  • lines changed 1, context: html, text, full: html, text
    c0ddfaebb3c2a75261a4400ab688340d51ce425e Wed Jul 17 15:41:57 2024 -0700
    Tweaking maxItems to a value that works reasonably well without turning the track off due to vertical limit. Refs #33767
  • lines changed 2, context: html, text, full: html, text
    b30321dea90350bcc8f184f9d40f3b5f41411433 Wed Jul 17 16:05:37 2024 -0700
    Raising maxItems back to 10k after Braney's new change #34127 that allows for bigger track heights, refs #33767
• src/hg/makeDb/trackDb/human/jaspar.ra
  • lines changed 2, context: html, text, full: html, text
    a99ca8e7ccf4b4eedd8de9c343690e85e6e1d26b Tue Jul 16 13:03:29 2024 -0700
    Sqashing old pennantIcons.
• src/hg/makeDb/trackDb/human/omim.alpha.ra
  • lines changed 83, context: html, text, full: html, text
    a26e6bfa1bc310a809138e7c39bdcf5ea29a79ef Tue Jul 16 17:13:07 2024 -0700
    Nesting OMIM into a single superTrack, refs #25682
  • lines changed 1, context: html, text, full: html, text
    459e2288153379fa730eb1b648145bfb7bbc8dc2 Tue Jul 16 17:52:06 2024 -0700
    add rewrite rule for OMiM tracks to consolidate them in super track
• src/hg/makeDb/trackDb/human/omim.ra
  • lines changed 73, context: html, text, full: html, text
    a26e6bfa1bc310a809138e7c39bdcf5ea29a79ef Tue Jul 16 17:13:07 2024 -0700
    Nesting OMIM into a single superTrack, refs #25682
• src/hg/makeDb/trackDb/human/omimContainer.html
  • lines changed 24, context: html, text, full: html, text
    a26e6bfa1bc310a809138e7c39bdcf5ea29a79ef Tue Jul 16 17:13:07 2024 -0700
    Nesting OMIM into a single superTrack, refs #25682
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 77, context: html, text, full: html, text
    a26e6bfa1bc310a809138e7c39bdcf5ea29a79ef Tue Jul 16 17:13:07 2024 -0700
    Nesting OMIM into a single superTrack, refs #25682
  • lines changed 2, context: html, text, full: html, text
    d43a914eeea67fcf8ea14745e1932859a263c111 Tue Jul 16 19:55:45 2024 -0700
    remove include refSeqComposite.ra from higher level definitions refs #34008
  • lines changed 30, context: html, text, full: html, text
    55cdc0578ebe3463380c79c1913c8386e80856f9 Tue Jul 16 19:58:50 2024 -0700
    remove include refSeqComposite.ra from higher level definitions refs #34008
  • lines changed 30, context: html, text, full: html, text
    7732bcfe0414219fc9642b42118aa2632dd59ab8 Wed Jul 17 16:54:16 2024 -0700
    Revert "remove include refSeqComposite.ra from higher level definitions refs #34008" This reverts commit 55cdc0578ebe3463380c79c1913c8386e80856f9.
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    cfda5d697701c33ce782310b6343ad3469791620 Wed Jul 17 17:08:36 2024 -0700
    Doing some refSeq surgery to fix mm9 issue on #34008. Essentially it was OK to have human include at that level - which allowed for an override at the species level. The reason for these overrides is Terrence asked us to make ncbiRefSeq (refseq all) the default on all organisms other than human and mouse. Having the addition at the hg38/hg19 level would mean duplicating the entire trackDb stanza in ncbiRefseqComposite.ra. For mouse, however, mm9 was having a conflict with the addition at the mouse level. So I moved mm10 and mm39 to have a new file at the mouse level and removed the mouse include. Refs #34008
• src/hg/makeDb/trackDb/jaspar.ra
  • lines changed 2, context: html, text, full: html, text
    a99ca8e7ccf4b4eedd8de9c343690e85e6e1d26b Tue Jul 16 13:03:29 2024 -0700
    Sqashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/jaspar.ra
  • lines changed 2, context: html, text, full: html, text
    a99ca8e7ccf4b4eedd8de9c343690e85e6e1d26b Tue Jul 16 13:03:29 2024 -0700
    Sqashing old pennantIcons.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    cfda5d697701c33ce782310b6343ad3469791620 Wed Jul 17 17:08:36 2024 -0700
    Doing some refSeq surgery to fix mm9 issue on #34008. Essentially it was OK to have human include at that level - which allowed for an override at the species level. The reason for these overrides is Terrence asked us to make ncbiRefSeq (refseq all) the default on all organisms other than human and mouse. Having the addition at the hg38/hg19 level would mean duplicating the entire trackDb stanza in ncbiRefseqComposite.ra. For mouse, however, mm9 was having a conflict with the addition at the mouse level. So I moved mm10 and mm39 to have a new file at the mouse level and removed the mouse include. Refs #34008
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    cfda5d697701c33ce782310b6343ad3469791620 Wed Jul 17 17:08:36 2024 -0700
    Doing some refSeq surgery to fix mm9 issue on #34008. Essentially it was OK to have human include at that level - which allowed for an override at the species level. The reason for these overrides is Terrence asked us to make ncbiRefSeq (refseq all) the default on all organisms other than human and mouse. Having the addition at the hg38/hg19 level would mean duplicating the entire trackDb stanza in ncbiRefseqComposite.ra. For mouse, however, mm9 was having a conflict with the addition at the mouse level. So I moved mm10 and mm39 to have a new file at the mouse level and removed the mouse include. Refs #34008
• src/hg/makeDb/trackDb/mouse/refSeqComposite.mm10.mm39.ra
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    cfda5d697701c33ce782310b6343ad3469791620 Wed Jul 17 17:08:36 2024 -0700
    Doing some refSeq surgery to fix mm9 issue on #34008. Essentially it was OK to have human include at that level - which allowed for an override at the species level. The reason for these overrides is Terrence asked us to make ncbiRefSeq (refseq all) the default on all organisms other than human and mouse. Having the addition at the hg38/hg19 level would mean duplicating the entire trackDb stanza in ncbiRefseqComposite.ra. For mouse, however, mm9 was having a conflict with the addition at the mouse level. So I moved mm10 and mm39 to have a new file at the mouse level and removed the mouse include. Refs #34008
• src/hg/makeDb/trackDb/mouse/trackDb.ra
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    d43a914eeea67fcf8ea14745e1932859a263c111 Tue Jul 16 19:55:45 2024 -0700
    remove include refSeqComposite.ra from higher level definitions refs #34008
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    55cdc0578ebe3463380c79c1913c8386e80856f9 Tue Jul 16 19:58:50 2024 -0700
    remove include refSeqComposite.ra from higher level definitions refs #34008
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    7732bcfe0414219fc9642b42118aa2632dd59ab8 Wed Jul 17 16:54:16 2024 -0700
    Revert "remove include refSeqComposite.ra from higher level definitions refs #34008" This reverts commit 55cdc0578ebe3463380c79c1913c8386e80856f9.
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    cfda5d697701c33ce782310b6343ad3469791620 Wed Jul 17 17:08:36 2024 -0700
    Doing some refSeq surgery to fix mm9 issue on #34008. Essentially it was OK to have human include at that level - which allowed for an override at the species level. The reason for these overrides is Terrence asked us to make ncbiRefSeq (refseq all) the default on all organisms other than human and mouse. Having the addition at the hg38/hg19 level would mean duplicating the entire trackDb stanza in ncbiRefseqComposite.ra. For mouse, however, mm9 was having a conflict with the addition at the mouse level. So I moved mm10 and mm39 to have a new file at the mouse level and removed the mouse include. Refs #34008
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    cfda5d697701c33ce782310b6343ad3469791620 Wed Jul 17 17:08:36 2024 -0700
    Doing some refSeq surgery to fix mm9 issue on #34008. Essentially it was OK to have human include at that level - which allowed for an override at the species level. The reason for these overrides is Terrence asked us to make ncbiRefSeq (refseq all) the default on all organisms other than human and mouse. Having the addition at the hg38/hg19 level would mean duplicating the entire trackDb stanza in ncbiRefseqComposite.ra. For mouse, however, mm9 was having a conflict with the addition at the mouse level. So I moved mm10 and mm39 to have a new file at the mouse level and removed the mouse include. Refs #34008
• src/hg/utils/otto/panelApp/genes.py
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    79e637df047541eed873a8e0d801b86c72187c18 Tue Jul 16 06:08:37 2024 -0700
    trying to silence the panel app otto job problems
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
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    b48da38d4aa8dcb9dc75cc1a37b528a5b42b3265 Thu Jul 18 03:41:35 2024 -0700
    adding user suggested dash fix, refs #34121
• src/utils/qa/checkHTTPS
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    f5049df8ae200c8c0056bc88dfc41696d03f95f0 Mon Jul 15 13:22:55 2024 -0700
    Removing the gi domain since it isn't under our control as asked by Erich.
• src/utils/qa/checkSessionsFromRR.py
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    15df1e86bb25502cfbb83f776a9063133a672036 Mon Jul 22 09:43:47 2024 -0700
    Deleting an unnecessary step that removes files, refs #32593
• src/utils/qa/weeklybld/buildEnv.csh
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    085a978a047462d7292c0f5158efc7765ad418f3 Mon Jul 22 10:34:00 2024 -0700
    v469 preview1, refs #34044

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• files changed: 94