All File Changes

v457_preview2 to v457_base (2023-11-13 to 2023-11-20) v457

• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 26, context: html, text, full: html, text
    d409d8e8e6c09a6a668752d9d811c95da0873dc5 Mon Nov 13 23:07:24 2023 -0800
    adding info bubbles to hgLiftOver, refs #32011
• src/hg/hgTracks/bedTrack.c
  • lines changed 1, context: html, text, full: html, text
    834f46edc09af6e2b82bad2021629615a678221b Wed Nov 15 11:45:33 2023 -0800
    bigBed items that match hgFind.matches automatically pass filters (this time pay attention to bbi->definedFieldCount to make sure there is a name field.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 7, context: html, text, full: html, text
    834f46edc09af6e2b82bad2021629615a678221b Wed Nov 15 11:45:33 2023 -0800
    bigBed items that match hgFind.matches automatically pass filters (this time pay attention to bbi->definedFieldCount to make sure there is a name field.
• src/hg/hgTracks/decorator.c
  • lines changed 3, context: html, text, full: html, text
    834f46edc09af6e2b82bad2021629615a678221b Wed Nov 15 11:45:33 2023 -0800
    bigBed items that match hgFind.matches automatically pass filters (this time pay attention to bbi->definedFieldCount to make sure there is a name field.
• src/hg/hgTracks/decorator.h
  • lines changed 1, context: html, text, full: html, text
    834f46edc09af6e2b82bad2021629615a678221b Wed Nov 15 11:45:33 2023 -0800
    bigBed items that match hgFind.matches automatically pass filters (this time pay attention to bbi->definedFieldCount to make sure there is a name field.
• src/hg/hgTracks/encode.c
  • lines changed 1, context: html, text, full: html, text
    834f46edc09af6e2b82bad2021629615a678221b Wed Nov 15 11:45:33 2023 -0800
    bigBed items that match hgFind.matches automatically pass filters (this time pay attention to bbi->definedFieldCount to make sure there is a name field.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    834f46edc09af6e2b82bad2021629615a678221b Wed Nov 15 11:45:33 2023 -0800
    bigBed items that match hgFind.matches automatically pass filters (this time pay attention to bbi->definedFieldCount to make sure there is a name field.
• src/hg/hgTracks/lollyTrack.c
  • lines changed 1, context: html, text, full: html, text
    834f46edc09af6e2b82bad2021629615a678221b Wed Nov 15 11:45:33 2023 -0800
    bigBed items that match hgFind.matches automatically pass filters (this time pay attention to bbi->definedFieldCount to make sure there is a name field.
• src/hg/hgTracks/variation.c
  • lines changed 2, context: html, text, full: html, text
    834f46edc09af6e2b82bad2021629615a678221b Wed Nov 15 11:45:33 2023 -0800
    bigBed items that match hgFind.matches automatically pass filters (this time pay attention to bbi->definedFieldCount to make sure there is a name field.
• src/hg/hgTracks/variation.h
  • lines changed 1, context: html, text, full: html, text
    834f46edc09af6e2b82bad2021629615a678221b Wed Nov 15 11:45:33 2023 -0800
    bigBed items that match hgFind.matches automatically pass filters (this time pay attention to bbi->definedFieldCount to make sure there is a name field.
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    0daf709174cdb2a358839e26b1db7821da21e2cd Mon Nov 20 12:13:16 2023 -0800
    Make snp hgc pages use mitochrondrial codon table, refs #32576
• src/hg/htdocs/admin/404.html
  • lines changed 1, context: html, text, full: html, text
    5085d704657809ca3d591f7c1bf19fce66fde44c Fri Nov 17 09:36:25 2023 -0800
    On 404 page, instruct users that write in that we also need the url that doesn't exist, refs #32637
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    a78a9f5e02063bcb252a9e3fe47f6699990ba15d Tue Nov 14 12:47:08 2023 -0800
    Code review edits, adding the relative path to an image and adding a missing period, refs #32467
• src/hg/htdocs/index.html
  • lines changed 15, context: html, text, full: html, text
    c96728649b4bef3f437124019d2a85ff1f15ca30 Mon Nov 20 09:48:08 2023 -0800
    Adding a message to only come up for mirrors, to be clear that you are on a mirror site and should contact the mirror operator. Also a small addition about the new meetings page. Refs #23092 #31573
• src/hg/htdocs/indexMeetings.html
  • lines changed 14, context: html, text, full: html, text
    061a12bb88aae8aa1ca68cdfc8492b1321817eb0 Mon Nov 20 09:48:58 2023 -0800
    Adding a new page which will list out meetings and workshops that we will attend and are open to the public. Refs #31573
• src/hg/htdocs/style/HGStyle.css
  • lines changed 1, context: html, text, full: html, text
    31cdf60a664d06d7b82db008e451c4a524861a56 Mon Nov 20 09:06:52 2023 -0800
    Left-justify mouseover tooltips, refs #31365
• src/hg/inc/bigBedFilter.h
  • lines changed 1, context: html, text, full: html, text
    834f46edc09af6e2b82bad2021629615a678221b Wed Nov 15 11:45:33 2023 -0800
    bigBed items that match hgFind.matches automatically pass filters (this time pay attention to bbi->definedFieldCount to make sure there is a name field.
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    a743fa87e218b7d9219a0878db8ec8357a349e8f Mon Nov 20 12:57:14 2023 -0800
    New version number v457
• src/hg/js/hgSearch.js
  • lines changed 61, context: html, text, full: html, text
    4a5e33685ee92a55d85200b621eb992d4c48cbfe Tue Nov 14 11:46:11 2023 -0800
    Make the Show/Hide results text on hgSearch a link that triggers the showing or hiding of results. Also fix up incorrect comparisons to undefined and use the same linter settings as the rest of the javascript files, refs #31501
  • lines changed 7, context: html, text, full: html, text
    49ab86f5c5c65a60ff9ad81b8cca11d415c3c436 Fri Nov 17 08:10:14 2023 -0800
    Make +/- buttons change when expanding/collapsing search results, refs #31501
• src/hg/js/utils.js
  • lines changed 6, context: html, text, full: html, text
    4f1440aa9222d404b7b8a15a3cafbbbf8c9b1a28 Fri Nov 17 20:18:03 2023 -0800
    adding file forgotten in previous tooltip commit, thanks to Chris, refs #32011
• src/hg/lib/genePred.c
  • lines changed 2, context: html, text, full: html, text
    d7592ea7cb7e4d6126a201cd89d62b87fdcd2981 Wed Nov 15 22:02:20 2023 -0800
    generate error message rather than abort when bigGenePred is incorrect specified as track type
• src/hg/lib/hui.c
  • lines changed 16, context: html, text, full: html, text
    d409d8e8e6c09a6a668752d9d811c95da0873dc5 Mon Nov 13 23:07:24 2023 -0800
    adding info bubbles to hgLiftOver, refs #32011
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 28, context: html, text, full: html, text
    8226768e453e0e5c300bce7266ca658566f531c1 Tue Nov 14 11:31:49 2023 -0800
    a RefSeq update bringing in about 26 assemblies refs #29545
  • lines changed 34, context: html, text, full: html, text
    d7f16ed60951554dc44e4ef0833c92343e7077f4 Fri Nov 17 15:10:04 2023 -0800
    update to catch up some VGP assemblies refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8226768e453e0e5c300bce7266ca658566f531c1 Tue Nov 14 11:31:49 2023 -0800
    a RefSeq update bringing in about 26 assemblies refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    d7f16ed60951554dc44e4ef0833c92343e7077f4 Fri Nov 17 15:10:04 2023 -0800
    update to catch up some VGP assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    d7f16ed60951554dc44e4ef0833c92343e7077f4 Fri Nov 17 15:10:04 2023 -0800
    update to catch up some VGP assemblies refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    8226768e453e0e5c300bce7266ca658566f531c1 Tue Nov 14 11:31:49 2023 -0800
    a RefSeq update bringing in about 26 assemblies refs #29545
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 5, context: html, text, full: html, text
    0853d1cdfb0165451ebf726bc0579602ba756002 Thu Nov 16 09:19:31 2023 -0800
    gnomAD fixed their chrY variants for their v4 release, add them in, refs Max email, #32545
• src/hg/makeDb/doc/hg38/tabulaSapiens.txt
  • lines changed 26, context: html, text, full: html, text
    cb2db10ee029b7dfed6b003d2a4bdf29ec0e99a7 Wed Nov 15 21:17:21 2023 -0800
    work on tabula-sapiens, but it is not done
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    d7f16ed60951554dc44e4ef0833c92343e7077f4 Fri Nov 17 15:10:04 2023 -0800
    update to catch up some VGP assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 32, context: html, text, full: html, text
    d7f16ed60951554dc44e4ef0833c92343e7077f4 Fri Nov 17 15:10:04 2023 -0800
    update to catch up some VGP assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    8226768e453e0e5c300bce7266ca658566f531c1 Tue Nov 14 11:31:49 2023 -0800
    a RefSeq update bringing in about 26 assemblies refs #29545
  • lines changed 31, context: html, text, full: html, text
    d7f16ed60951554dc44e4ef0833c92343e7077f4 Fri Nov 17 15:10:04 2023 -0800
    update to catch up some VGP assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8226768e453e0e5c300bce7266ca658566f531c1 Tue Nov 14 11:31:49 2023 -0800
    a RefSeq update bringing in about 26 assemblies refs #29545
  • lines changed 9, context: html, text, full: html, text
    fe29fb0e1302156c2dc0a3344618059bf630c88c Tue Nov 14 13:31:50 2023 -0800
    a RefSeq update brings in a number of new assemblies refs #29545
  • lines changed 8, context: html, text, full: html, text
    d7f16ed60951554dc44e4ef0833c92343e7077f4 Fri Nov 17 15:10:04 2023 -0800
    update to catch up some VGP assemblies refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    8226768e453e0e5c300bce7266ca658566f531c1 Tue Nov 14 11:31:49 2023 -0800
    a RefSeq update bringing in about 26 assemblies refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    d7f16ed60951554dc44e4ef0833c92343e7077f4 Fri Nov 17 15:10:04 2023 -0800
    update to catch up some VGP assemblies refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    8226768e453e0e5c300bce7266ca658566f531c1 Tue Nov 14 11:31:49 2023 -0800
    a RefSeq update bringing in about 26 assemblies refs #29545
  • lines changed 8, context: html, text, full: html, text
    d7f16ed60951554dc44e4ef0833c92343e7077f4 Fri Nov 17 15:10:04 2023 -0800
    update to catch up some VGP assemblies refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8226768e453e0e5c300bce7266ca658566f531c1 Tue Nov 14 11:31:49 2023 -0800
    a RefSeq update bringing in about 26 assemblies refs #29545
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 2, context: html, text, full: html, text
    0853d1cdfb0165451ebf726bc0579602ba756002 Thu Nov 16 09:19:31 2023 -0800
    gnomAD fixed their chrY variants for their v4 release, add them in, refs Max email, #32545
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 2, context: html, text, full: html, text
    4ef80e66feef2a31d26d764f64e545883240213a Tue Nov 14 16:50:52 2023 -0800
    renaming hprc double track, refs #31561
• src/hg/makeDb/trackDb/human/refSeqComposite.html
  • lines changed 3, context: html, text, full: html, text
    dd87117369624a1c9662d47db73146b78f98c2ca Fri Nov 17 07:47:02 2023 -0800
    after discussion with Francoise at NCBI, adapting refseq track docs a little
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    a743fa87e218b7d9219a0878db8ec8357a349e8f Mon Nov 20 12:57:14 2023 -0800
    New version number v457
• src/product/installer/browserSetup.sh
  • lines changed 1, context: html, text, full: html, text
    59124205fd38e7898cd2924316d3fcb119b14bcc Fri Nov 17 07:53:35 2023 -0800
    hiding OMIM tracks in gbib, email from Alexander Stuy
  • lines changed 47, context: html, text, full: html, text
    cb3778318684da37020f3a857d5d601e893b3d0b Fri Nov 17 18:44:53 2023 -0800
    applying patch received from alex Stuy, no redmine
• src/utils/qa/checkHTTPS
  • lines changed 6, context: html, text, full: html, text
    004fb23971f2d9e6186785612b5eebe6340494d4 Tue Nov 14 15:18:02 2023 -0800
    Removed hgdownload2 on 11/14/23 after consulting the admins and they sharing it is offline.
  • lines changed 6, context: html, text, full: html, text
    57b5255edd9b281dbb9eba60f685af66d7389b9e Tue Nov 14 15:45:34 2023 -0800
    Re-adding hgdownload2, the admins have fixed the issue.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    b803a504d93249623a7089ed188f65be43fe66af Mon Nov 20 12:56:09 2023 -0800
    v457 final build, refs #32573

• lines changed: 474
• files changed: 52