All File Changes

v458_preview to v458_preview2 (2023-11-27 to 2023-12-04) v458

• docs/gb101.html
  • lines changed 118, context: html, text, full: html, text
    30a93b60b63adec2bcc12b82694f9be164b87b03 Wed Nov 29 16:39:15 2023 -0800
    adding new tutorial files, refs #30335
• docs/index.md
  • lines changed 40, context: html, text, full: html, text
    7e9ec699b6d233213aca70776b2e89a0cc02f976 Wed Nov 29 13:41:32 2023 -0800
    first test of a markdown based docs directory, no redmine yet
• docs/makefile
  • lines changed 18, context: html, text, full: html, text
    7e9ec699b6d233213aca70776b2e89a0cc02f976 Wed Nov 29 13:41:32 2023 -0800
    first test of a markdown based docs directory, no redmine yet
• docs/new_home.html
  • lines changed 103, context: html, text, full: html, text
    30a93b60b63adec2bcc12b82694f9be164b87b03 Wed Nov 29 16:39:15 2023 -0800
    adding new tutorial files, refs #30335
• docs/staticPage.html
  • lines changed 24, context: html, text, full: html, text
    7e9ec699b6d233213aca70776b2e89a0cc02f976 Wed Nov 29 13:41:32 2023 -0800
    first test of a markdown based docs directory, no redmine yet
• docs/staticPage.lua
  • lines changed 437, context: html, text, full: html, text
    7e9ec699b6d233213aca70776b2e89a0cc02f976 Wed Nov 29 13:41:32 2023 -0800
    first test of a markdown based docs directory, no redmine yet
• src/hg/cirm/cdw/cdwReallyRemoveDataset/cdwReallyRemoveDataset.c
  • lines changed 51, context: html, text, full: html, text
    310ed9324362faacfdf0ca7d0cd011605ce2e750 Tue Nov 28 03:05:06 2023 -0800
    Improving ability to restore symlinked files back into their wrangle or submit directories so they are not lost. Includes special files such as 2bit under the path "". Handles either one dataset at a time, or can with great care be used to restore all files for all sets. Great care must be used with this command, and observe many caviots as well. We have no real way to preserve our symlinks other than this.
• src/hg/cirm/cdw/cdwUnlockSubmittedFile/cdwUnlockSubmittedFile.c
  • lines changed 3, context: html, text, full: html, text
    310ed9324362faacfdf0ca7d0cd011605ce2e750 Tue Nov 28 03:05:06 2023 -0800
    Improving ability to restore symlinked files back into their wrangle or submit directories so they are not lost. Includes special files such as 2bit under the path "". Handles either one dataset at a time, or can with great care be used to restore all files for all sets. Great care must be used with this command, and observe many caviots as well. We have no real way to preserve our symlinks other than this.
• src/hg/cirm/cdw/inc/cdwLib.h
  • lines changed 4, context: html, text, full: html, text
    310ed9324362faacfdf0ca7d0cd011605ce2e750 Tue Nov 28 03:05:06 2023 -0800
    Improving ability to restore symlinked files back into their wrangle or submit directories so they are not lost. Includes special files such as 2bit under the path "". Handles either one dataset at a time, or can with great care be used to restore all files for all sets. Great care must be used with this command, and observe many caviots as well. We have no real way to preserve our symlinks other than this.
• src/hg/cirm/cdw/lib/cdwLib.c
  • lines changed 27, context: html, text, full: html, text
    310ed9324362faacfdf0ca7d0cd011605ce2e750 Tue Nov 28 03:05:06 2023 -0800
    Improving ability to restore symlinked files back into their wrangle or submit directories so they are not lost. Includes special files such as 2bit under the path "". Handles either one dataset at a time, or can with great care be used to restore all files for all sets. Great care must be used with this command, and observe many caviots as well. We have no real way to preserve our symlinks other than this.
• src/hg/genePredToMafFrames/finishMafFrames.c
  • lines changed 1, context: html, text, full: html, text
    8478bcb501f8c278278f63466d44501f3ca3f951 Tue Nov 28 01:37:05 2023 -0800
    make frameIncr function available to other code
• src/hg/genePredToMafFrames/frameIncr.h
  • lines changed 20, context: html, text, full: html, text
    8478bcb501f8c278278f63466d44501f3ca3f951 Tue Nov 28 01:37:05 2023 -0800
    make frameIncr function available to other code
• src/hg/genePredToMafFrames/makefile
  • lines changed 2, context: html, text, full: html, text
    8478bcb501f8c278278f63466d44501f3ca3f951 Tue Nov 28 01:37:05 2023 -0800
    make frameIncr function available to other code
• src/hg/genePredToMafFrames/mkMafFrames.c
  • lines changed 1, context: html, text, full: html, text
    8478bcb501f8c278278f63466d44501f3ca3f951 Tue Nov 28 01:37:05 2023 -0800
    make frameIncr function available to other code
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 7, context: html, text, full: html, text
    5ab5c95ea6e32a833ae923d7e212c99dd7285aa6 Fri Dec 1 07:01:47 2023 -0800
    prefer static_dot over sys-wide dot, refs #32691
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 45, context: html, text, full: html, text
    eeac40956b3dd6611f58aeb847ff5c404d3ce883 Fri Dec 1 09:05:41 2023 -0800
    Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file. This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it. Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 101, context: html, text, full: html, text
    eeac40956b3dd6611f58aeb847ff5c404d3ce883 Fri Dec 1 09:05:41 2023 -0800
    Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file. This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it. Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 1, context: html, text, full: html, text
    b0039dec371d7665e25e2e39b0e79d3e33ba50a1 Tue Nov 28 13:54:07 2023 -0800
    Fix amino acid translation to support transcipts that have UTR portions and skip noncoding transcripts.
  • lines changed 2, context: html, text, full: html, text
    eeac40956b3dd6611f58aeb847ff5c404d3ce883 Fri Dec 1 09:05:41 2023 -0800
    Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file. This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it. Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).
• src/hg/hgPhyloPlace/phyloPlaceMain.c
  • lines changed 1, context: html, text, full: html, text
    eeac40956b3dd6611f58aeb847ff5c404d3ce883 Fri Dec 1 09:05:41 2023 -0800
    Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file. This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it. Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 18, context: html, text, full: html, text
    b0039dec371d7665e25e2e39b0e79d3e33ba50a1 Tue Nov 28 13:54:07 2023 -0800
    Fix amino acid translation to support transcipts that have UTR portions and skip noncoding transcripts.
  • lines changed 25, context: html, text, full: html, text
    ea80dbd18523cfb2ad1efd1306ac81d7e994f9c4 Fri Dec 1 09:01:56 2023 -0800
    Update RSV metadata for new clade system (RSV Genotyping Consensus Consortium lineages replace Ramaekers 2020 clades).
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 32, context: html, text, full: html, text
    eeac40956b3dd6611f58aeb847ff5c404d3ce883 Fri Dec 1 09:05:41 2023 -0800
    Support trees whose reference/root is not from a db or hub, but rather a custom .2bit file. This means that the selected pathogen may or may not also be a db/hub, so the selection interacts with the db cart variable but does not always match it. Also, in phyloPlace.c, update RSV metadata column headers (RGCC lineages replace Ramaekers 2020 clades).
• src/hg/hgTables/bigBed.c
  • lines changed 73, context: html, text, full: html, text
    259c477dd82ab1de43ddcf36f809a3bfe99a54da Mon Nov 27 14:29:32 2023 -0800
    In bigBedGetFilteredBedsOnRegions, use nameIndex when user pastes/uploads identifiers, so we don't time out on large bigBeds like dbSnp. refs #32625
• src/hg/hgTracks/config.c
  • lines changed 47, context: html, text, full: html, text
    bfeae54a099bf1a9e2f29252b0ee581d2862ebf7 Wed Nov 29 12:07:15 2023 -0800
    Make tooltip text size a configurable option in hgTracks config page, refs #32688
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    b7e6cbd6fbcccbe434e05fca0a014cb239775b27 Fri Dec 1 16:05:22 2023 -0800
    polishing up the HPRC rearrangements track
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 8, context: html, text, full: html, text
    86076fbfc6172072b28fcb064f0e4c3e835201c2 Tue Nov 28 05:03:52 2023 -0800
    docing exonFrames, refs #32675
• src/hg/htdocs/goldenPath/help/covidBrowser.html
  • lines changed 12, context: html, text, full: html, text
    fbeaf51d42a4e9306db9a5761730af8189300a7e Fri Nov 24 06:59:47 2023 -0800
    chinafying all other video links, refs #32535
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 4, context: html, text, full: html, text
    fbeaf51d42a4e9306db9a5761730af8189300a7e Fri Nov 24 06:59:47 2023 -0800
    chinafying all other video links, refs #32535
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 21, context: html, text, full: html, text
    fbeaf51d42a4e9306db9a5761730af8189300a7e Fri Nov 24 06:59:47 2023 -0800
    chinafying all other video links, refs #32535
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 8, context: html, text, full: html, text
    fbeaf51d42a4e9306db9a5761730af8189300a7e Fri Nov 24 06:59:47 2023 -0800
    chinafying all other video links, refs #32535
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 27, context: html, text, full: html, text
    fbeaf51d42a4e9306db9a5761730af8189300a7e Fri Nov 24 06:59:47 2023 -0800
    chinafying all other video links, refs #32535
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 6, context: html, text, full: html, text
    977f55b39381863017d7fb6d245b8d6c9e82cd57 Wed Nov 29 11:20:11 2023 -0800
    Adding documentation for searching previous NM accessions, refs #26016
  • lines changed 14, context: html, text, full: html, text
    18bb1494b9c59d40aae9bb6fb3b49421bd3d9203 Thu Nov 30 02:48:34 2023 -0800
    docing chris new cool feature, refs #32487
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 38, context: html, text, full: html, text
    8cd99720275c9d69502aade7523349b92edf278b Thu Nov 30 10:29:32 2023 -0800
    News announcement for the HGVS search feature, refs #26016
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 4, context: html, text, full: html, text
    af1ee4ab704bbf67117d4841eb4bd14963289672 Tue Nov 28 13:24:43 2023 -0800
    OK to have a lang=en in html tag and do not need to declare type of script for javascript included refs #29545
  • lines changed 1, context: html, text, full: html, text
    e5d251ed7f70081803a4198cec5526c6a0f83f0e Tue Nov 28 13:30:55 2023 -0800
    the pipe symbol in the URL to googleapis should be encoded as %7C instead of plain text refs #29545
• src/hg/htdocs/inc/hgCollectionHelpInclude.html
  • lines changed 14, context: html, text, full: html, text
    fbeaf51d42a4e9306db9a5761730af8189300a7e Fri Nov 24 06:59:47 2023 -0800
    chinafying all other video links, refs #32535
• src/hg/htdocs/indexMeetings.html
  • lines changed 1, context: html, text, full: html, text
    9bd0924516399892c2a1ed1a6d6efb74685521a0 Wed Nov 29 12:08:40 2023 -0800
    tiny index change, refs #31573
  • lines changed 6, context: html, text, full: html, text
    0ac2c1b24a781e53cd893b2fcb10c73e884f53b4 Wed Nov 29 15:08:46 2023 -0800
    Adding one meeting b0b is attending, no RM.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    8cd99720275c9d69502aade7523349b92edf278b Thu Nov 30 10:29:32 2023 -0800
    News announcement for the HGVS search feature, refs #26016
• src/hg/htdocs/style/bootstrap-3-3-7.min.css
  • lines changed 6, context: html, text, full: html, text
    2da1218b7b6b8706fff2d1cc403f7af49366b76d Wed Nov 29 16:42:35 2023 -0800
    adding full bootstrap 3.3.7 css file for new tutorials, refs #30335
• src/hg/inc/frame.h
  • lines changed 20, context: html, text, full: html, text
    8478bcb501f8c278278f63466d44501f3ca3f951 Tue Nov 28 01:37:05 2023 -0800
    make frameIncr function available to other code
• src/hg/js/hgTracks.js
  • lines changed 7, context: html, text, full: html, text
    17b4f90dc72d71ecaa7a9e64db21c3521eb1233b Mon Nov 27 12:57:18 2023 -0800
    Add 'choose exon' option for genePred tracks that allows users to enter an exon number to jump to for the right clicked transcript, refs Max email
  • lines changed 2, context: html, text, full: html, text
    fc9b9989494d05bc2e5d9735feed48e3f95b6953 Wed Nov 29 09:44:39 2023 -0800
    Make zoom to codon available for bigGenePred tracks, refs #32487
• src/hg/js/utils.js
  • lines changed 6, context: html, text, full: html, text
    3ad75c6b034903a322a9680b0cb544be1c840b08 Mon Nov 27 11:31:10 2023 -0800
    Fix missing zoom to exon right click menu option after mouseover changes, refs #31365
  • lines changed 1, context: html, text, full: html, text
    172e34d4be1d144aad214488d90b35e0b96317d4 Tue Nov 28 10:38:22 2023 -0800
    Lower amount of time required to show a new mouseover once one is already visible, allows user to more quickly move the cursor back and forth over two adjacent items, refs Max and Mark email
  • lines changed 3, context: html, text, full: html, text
    bfeae54a099bf1a9e2f29252b0ee581d2862ebf7 Wed Nov 29 12:07:15 2023 -0800
    Make tooltip text size a configurable option in hgTracks config page, refs #32688
  • lines changed 11, context: html, text, full: html, text
    c11fa0744b12d0a369c0b73722afff9ced9764c5 Thu Nov 30 13:53:31 2023 -0800
    Fix over correction of timer controlling whether a second tooltip should show up. Make code for determining y position of tooltip aware of which direction the mouse enters from so as not to obscure the element to be moused over, refs Max email
  • lines changed 19, context: html, text, full: html, text
    3f45623e433942768d54a474f0e66709c1fad529 Fri Dec 1 11:18:12 2023 -0800
    Make tooltips go away when moving the mouse outside the window
• src/hg/lib/customTrack.c
  • lines changed 5, context: html, text, full: html, text
    ae327c5f42eddb3039d0c1b0182a61419b03c98f Fri Dec 1 09:23:18 2023 -0800
    When there is an error while loading customTracks, don't assume it's an unrecoverable file corruption problem; recently we have seen some out-of-mem and/or pthread_create issues. Don't remove the custom track file because it may be a saved session file shared by multiple sessions and users. Instead, ask the user to send us a session link. refs #32627
  • lines changed 7, context: html, text, full: html, text
    35104810b1eefd07d38383abefe90c24553cc146 Fri Dec 1 09:48:55 2023 -0800
    When loading of existing custom tracks fails, do not attempt to merge new custom tracks because we will lose all existing custom tracks. Leave the settings in the cart for next time. (forgot to include this in previous commit) refs #32627
• src/hg/makeDb/doc/asmHubs/commonHtml.pm
  • lines changed 3, context: html, text, full: html, text
    6e2ce95748a6b80895027e24e6f5086890d169bc Tue Nov 28 14:10:37 2023 -0800
    correct style statements in html elements for border and text alignment and do not declare type javascript refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 2, context: html, text, full: html, text
    4d8026612d9d5a30705394c18ab8948a8fb12e12 Wed Nov 29 11:16:09 2023 -0800
    adding a couple of VGP fish refs #29545
  • lines changed 3, context: html, text, full: html, text
    b65675bc7cab7726ddcc5de2fb46192460143f76 Thu Nov 30 12:26:13 2023 -0800
    update catching up for VGP assemblies refs #29545
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 19, context: html, text, full: html, text
    6e2ce95748a6b80895027e24e6f5086890d169bc Tue Nov 28 14:10:37 2023 -0800
    correct style statements in html elements for border and text alignment and do not declare type javascript refs #29545
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 1, context: html, text, full: html, text
    608a494f6dda29a4e7529680507ac894d78913fe Tue Nov 28 13:02:48 2023 -0800
    a less than bare character should be html encoded refs #29545
  • lines changed 18, context: html, text, full: html, text
    6e2ce95748a6b80895027e24e6f5086890d169bc Tue Nov 28 14:10:37 2023 -0800
    correct style statements in html elements for border and text alignment and do not declare type javascript refs #29545
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 13, context: html, text, full: html, text
    6e2ce95748a6b80895027e24e6f5086890d169bc Tue Nov 28 14:10:37 2023 -0800
    correct style statements in html elements for border and text alignment and do not declare type javascript refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    4d8026612d9d5a30705394c18ab8948a8fb12e12 Wed Nov 29 11:16:09 2023 -0800
    adding a couple of VGP fish refs #29545
  • lines changed 1, context: html, text, full: html, text
    b65675bc7cab7726ddcc5de2fb46192460143f76 Thu Nov 30 12:26:13 2023 -0800
    update catching up for VGP assemblies refs #29545
• src/hg/makeDb/doc/hg38/hprcInDel.txt
  • lines changed 1, context: html, text, full: html, text
    b7e6cbd6fbcccbe434e05fca0a014cb239775b27 Fri Dec 1 16:05:22 2023 -0800
    polishing up the HPRC rearrangements track
• src/hg/makeDb/doc/hs1/hoffmanMappability.txt
  • lines changed 31, context: html, text, full: html, text
    8413766c3b7cff4af51b8bb9937e34413cb46ad2 Thu Nov 30 09:26:07 2023 -0800
    Adding the umap mappability track to hs1, refs #32694
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    2dcb37891539b5291a228543bbe951e599d8d75b Mon Nov 27 12:48:18 2023 -0800
    catch up the clouded leopard refs #29545
  • lines changed 1, context: html, text, full: html, text
    4d8026612d9d5a30705394c18ab8948a8fb12e12 Wed Nov 29 11:16:09 2023 -0800
    adding a couple of VGP fish refs #29545
  • lines changed 1, context: html, text, full: html, text
    58a7e78f00de4c0c7b6e82454d2cb4a28ef2d35e Wed Nov 29 12:19:12 2023 -0800
    adding GCA_019393635.1_mDroGli1.pri refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 7, context: html, text, full: html, text
    4d8026612d9d5a30705394c18ab8948a8fb12e12 Wed Nov 29 11:16:09 2023 -0800
    adding a couple of VGP fish refs #29545
  • lines changed 1, context: html, text, full: html, text
    b65675bc7cab7726ddcc5de2fb46192460143f76 Thu Nov 30 12:26:13 2023 -0800
    update catching up for VGP assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    b65675bc7cab7726ddcc5de2fb46192460143f76 Thu Nov 30 12:26:13 2023 -0800
    update catching up for VGP assemblies refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    b65675bc7cab7726ddcc5de2fb46192460143f76 Thu Nov 30 12:26:13 2023 -0800
    update catching up for VGP assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    14d09b34efe9b204e474eaed455471fcbb7fce8f Mon Nov 27 11:15:15 2023 -0800
    update adding a couple assemblies refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.taxId.asmId.class.txt
  • lines changed 3, context: html, text, full: html, text
    4e5750a7503e2489ca5be1c5dc51f461ee3f8421 Mon Nov 27 11:22:28 2023 -0800
    update brings in three new assemblies refs #29545
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 75, context: html, text, full: html, text
    b7e6cbd6fbcccbe434e05fca0a014cb239775b27 Fri Dec 1 16:05:22 2023 -0800
    polishing up the HPRC rearrangements track
• src/hg/makeDb/trackDb/human/hg38/hprcArrV1.html
  • lines changed 89, context: html, text, full: html, text
    b7e6cbd6fbcccbe434e05fca0a014cb239775b27 Fri Dec 1 16:05:22 2023 -0800
    polishing up the HPRC rearrangements track
• src/hg/makeDb/trackDb/human/hg38/hprcChainNet.ra
  • lines changed 1635, context: html, text, full: html, text
    ac7a713337149211893dc0eace64428fe67ff133 Fri Dec 1 14:22:35 2023 -0800
    replace the two tracks HPRC Chains and Nets by one single composite refs #31561
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    06892385ac11355c4469ec93d9714a9dbf7916f1 Fri Dec 1 14:28:04 2023 -0800
    will need to turn on some useful default set of tracks refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcVCF.html
  • lines changed 14, context: html, text, full: html, text
    d614c57bb718f9cfcaab8e6383a0e101f34e5670 Thu Nov 30 05:55:53 2023 -0800
    renaming and docing hprc vcf variants, refs #32288
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    62fe5de04f361d007d2492edade5a7f35f869f4a Fri Dec 1 07:13:07 2023 -0800
    adding docs to hprc vcf track, refs #32288
• src/hg/makeDb/trackDb/human/hg38/hprcVCF.ra
  • lines changed 15, context: html, text, full: html, text
    d614c57bb718f9cfcaab8e6383a0e101f34e5670 Thu Nov 30 05:55:53 2023 -0800
    renaming and docing hprc vcf variants, refs #32288
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
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    c57fe7f817a8918fac663b8f7b0e6a2f2af603f4 Fri Dec 1 17:42:51 2023 -0800
    spurious string in the middle of nowhere refs #31528
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    ac7a713337149211893dc0eace64428fe67ff133 Fri Dec 1 14:22:35 2023 -0800
    replace the two tracks HPRC Chains and Nets by one single composite refs #31561
• src/hg/makeDb/trackDb/human/hs1/hoffmanMappability.ra
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    8413766c3b7cff4af51b8bb9937e34413cb46ad2 Thu Nov 30 09:26:07 2023 -0800
    Adding the umap mappability track to hs1, refs #32694
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    2feb5fb91f6a27a8c3b394e5768d080a4f407a56 Thu Nov 30 09:47:55 2023 -0800
    Adding a pennantIcon for release date, refs #32694
• src/hg/makeDb/trackDb/human/hs1/html/mappability.html
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    8413766c3b7cff4af51b8bb9937e34413cb46ad2 Thu Nov 30 09:26:07 2023 -0800
    Adding the umap mappability track to hs1, refs #32694
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
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    8413766c3b7cff4af51b8bb9937e34413cb46ad2 Thu Nov 30 09:26:07 2023 -0800
    Adding the umap mappability track to hs1, refs #32694
• src/hg/pyLib/hgLib.py
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    a3f698ff4a4e761c2852870ccfb90af28cb6fe31 Thu Nov 30 04:48:39 2023 -0800
    reducing again the bottleneck warning trigger limits for hgGeneGraph, no redmine, email
• src/hg/pyLib/hgLib3.py
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    a3f698ff4a4e761c2852870ccfb90af28cb6fe31 Thu Nov 30 04:48:39 2023 -0800
    reducing again the bottleneck warning trigger limits for hgGeneGraph, no redmine, email
• src/hg/utils/automation/doAssemblyHub.pl
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    69bd7a8ab744d23ab1e364f1bdbcde1add08a6cf Thu Nov 30 14:42:50 2023 -0800
    do not use windowMasker when it claims to have masked everything refs #29545
• src/hg/utils/automation/doNcbiRefSeq.pl
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    1da1aecdb839e7ad81e55650cab403780076e198 Thu Nov 30 09:00:53 2023 -0800
    correct cleanup symLinks refs #29545
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.attrs
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    99682107a804fb410f20bdbe0c3f07d14c5fdb60 Mon Nov 27 18:45:55 2023 -0800
    update expected results due to change in behaivor in commit 677bb75aa7c1cbe71111e1a0ef1462f8277b6c9d; which improves the results on the degenrate NCBI cases handled by this case
• src/hg/utils/gff3ToGenePred/tests/expected/ncbiProblemsTest.gp
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    99682107a804fb410f20bdbe0c3f07d14c5fdb60 Mon Nov 27 18:45:55 2023 -0800
    update expected results due to change in behaivor in commit 677bb75aa7c1cbe71111e1a0ef1462f8277b6c9d; which improves the results on the degenrate NCBI cases handled by this case
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    6db87360227e298279ec6088c5e070f8c42e51b8 Tue Nov 14 17:11:45 2023 -0800
    Masking some additional locations in BA.2 (& onward), BA.2.86 and XCK.
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
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    3a74edab38d1a6e928729bc6b4feec3762ee2f40 Tue Nov 14 17:05:26 2023 -0800
    Don't offer uncompressed protobuf for download (only compressed). Also don't offer redundant .nextclade.pangolin version of same file.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    b80d731cca9f9a4b591fd60b7f6b1309e7a4cdbd Tue Nov 14 17:10:44 2023 -0800
    Added some more IDs by request.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    f3be5b0f7ad0fd1efbef1057ae5ed3799efcf5f7 Tue Nov 14 17:13:41 2023 -0800
    A few new lineages and a couple corrections: BA.2.86.1 no longer requires that last mutation and it has a descendant without it. B.1.637 needed some refinement after tree work.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    129db42d275d159115a7aef3d6377abb5d8e6c60 Tue Nov 14 17:08:20 2023 -0800
    Reduce number of threads for usher-sampled -- Cheng's suggestion after mysterious hang on 2023-10-05. Use new matUtils fix subcommand to get rid of annoying grandparent-reversions.
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
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    f1b5392d9fb6337cf2e2f9d55484a2950ebb3b37 Tue Nov 14 17:10:21 2023 -0800
    CNCB is now updating daily.
• src/product/installer/browserSetup.sh
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    417468b267382eaa03b7307439b4cb43aaab10f0 Fri Dec 1 02:22:41 2023 -0800
    hide some tracks on GBIC update, refs #32693
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    2e7b2a2a3e3bb68a9549c53f4dcbcd4a19f54761 Fri Dec 1 06:42:45 2023 -0800
    adding case that user has already downloaded non-assembly databases, bugfix for refs #32693
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    18b6d502e619fbc982e9bac1b5fc56050c3e821b Fri Dec 1 07:48:23 2023 -0800
    forgot hgFixed in last commit
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    e14db01e479c6605bb81b7199c9ed37ccab9ef5e Fri Dec 1 13:00:28 2023 -0800
    Add proteome to list of databases not to update trackDb, refs #32693
• src/utils/qa/weeklybld/buildEnv.csh
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    e90bc84829aaeb1c8a23e640909843468b414163 Mon Nov 27 10:52:34 2023 -0800
    v458 preview1, refs #32676
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    418575bfbbaf88277aeb9228216666ee88ad2068 Mon Dec 4 10:12:12 2023 -0800
    v458 preview2, refs #32676

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