All File Changes

v476_base to v477_preview (2025-01-13 to 2025-01-21) v477

• docs/gb101.md
  • lines changed 56, context: html, text, full: html, text
    5fb86269ebfbef64d7047b4943822ccd6f5365c0 Wed Jan 15 22:51:55 2025 -0800
    More work to the new gb101 new docs page, refs #30335
  • lines changed 5, context: html, text, full: html, text
    36c90af395efb0985f7f840005cb1ff9640d9d16 Mon Jan 20 09:19:13 2025 -0800
    Additional tweaks to the new docs page, more details in the ticket. Refs #30335
  • lines changed 1, context: html, text, full: html, text
    25394954ec94f6bd219b4bab65330b3cb7250893 Mon Jan 20 11:49:06 2025 -0800
    Fixing the basic tutorial link, refs #30335
  • lines changed 8, context: html, text, full: html, text
    b8749ace3d228c7b80f77948c523119c656051ea Mon Jan 20 12:02:40 2025 -0800
    Added some subtle lines to help visually divide the different workthrough sections. Refs #30335
• docs/index.md
  • lines changed 46, context: html, text, full: html, text
    0249444b9c89d4ce13a9c596e8baefffe7940f36 Mon Jan 20 11:43:31 2025 -0800
    First full draft of the tutorials landing page, refs #30335
• docs/staticPage.html
  • lines changed 13, context: html, text, full: html, text
    36c90af395efb0985f7f840005cb1ff9640d9d16 Mon Jan 20 09:19:13 2025 -0800
    Additional tweaks to the new docs page, more details in the ticket. Refs #30335
• docs/staticPage.lua
  • lines changed 21, context: html, text, full: html, text
    36c90af395efb0985f7f840005cb1ff9640d9d16 Mon Jan 20 09:19:13 2025 -0800
    Additional tweaks to the new docs page, more details in the ticket. Refs #30335
  • lines changed 7, context: html, text, full: html, text
    ba1c079db556eae13221bc6547b7be6abbbc8906 Tue Jan 21 05:04:54 2025 -0800
    fixing inline html in markdown, refs #30335
• src/hg/affyGnf/makefile
  • lines changed 2, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/gar/asr.cgi.pl
  • lines changed 2, context: html, text, full: html, text
    4888af47a6dceb9a40e20276c1acf861edf02479 Tue Jan 14 07:02:55 2025 -0800
    more useful to have the mail subject say assembly request rather than asr request refs #32596
• src/hg/hgHubConnect/hooks/testPostFinishHook.txt
  • lines changed 74, context: html, text, full: html, text
    b977befd83f4f7d99cfddb6b279b7c0b52665085 Mon Jan 13 12:53:05 2025 -0800
    Remove test hook files that were never meant to be committed, refs #35018
• src/hg/hgHubConnect/hooks/testPreCreateHook.txt
  • lines changed 44, context: html, text, full: html, text
    b977befd83f4f7d99cfddb6b279b7c0b52665085 Mon Jan 13 12:53:05 2025 -0800
    Remove test hook files that were never meant to be committed, refs #35018
• src/hg/hgHubConnect/makefile
  • lines changed 2, context: html, text, full: html, text
    6a9fee7fc8a682f48125eec21ea4fa767c8b6cab Fri Jan 17 10:58:20 2025 -0800
    Fix hgHubConnect hook targets to use '${MAKE}' instead of 'make'
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 9, context: html, text, full: html, text
    b7e0b5f7674dfa7600149aab93d79bed3c3b926a Mon Jan 13 17:40:22 2025 -0800
    When prefixing a file specified by the hubspace ui with the userDataDir, run realpath(3) on the file name to prevent looking up system files, refs #35018
  • lines changed 1, context: html, text, full: html, text
    a6e5c99f562491a34c8b1d69663b9a0c46c9adfe Tue Jan 14 15:19:38 2025 -0800
    Make hubspace tusd endpoint defined by hg.conf variable hubSpaceTusdEndpoint
  • lines changed 3, context: html, text, full: html, text
    6d748e8ea3c2a87f079e1e3dcd6b3f33c74ec76c Tue Jan 14 15:29:31 2025 -0800
    If someone calls generateApiKey without being logged in, generate an error message instead of just returning NULL
  • lines changed 12, context: html, text, full: html, text
    55de7ef426a462247f89f48afd9aa6a2eb2cdd19 Thu Jan 16 17:11:17 2025 -0800
    Remove a bunch of dead experimental hubspace code, and make sure to cgi-encode hub names, refs #35018
• src/hg/hgMirror/hgMirror
  • lines changed 1, context: html, text, full: html, text
    ad614fb3548131d4d8f6777a634f9b62516bf0eb Fri Jan 17 14:25:45 2025 -0800
    Minor change to hgMirror to support more restrictive permissions as we upgrade GBiB, no ticket
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 23, context: html, text, full: html, text
    f318a5ef17926efafcf8898bcfa5ec6bd8a57bf1 Mon Jan 13 13:37:17 2025 -0800
    Add a Download section when a download.html file is present in the org directory.
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 25, context: html, text, full: html, text
    40b8d62768262d2fb46e26c87a5ec948a6cb0251 Wed Dec 11 13:03:51 2024 -0800
    checking in some code to hgSuggest that supports javascript autocomplete when seaching for tracks in trackDb
• src/hg/hgTracks/chainTrack.c
  • lines changed 1, context: html, text, full: html, text
    a2a63c32665b60fedfddd190c68500d912e1c1bc Thu Jan 16 14:43:17 2025 -0800
    fix a bug with bigChains that are loaded on a native database. refs #35037
• src/hg/hgTracks/coverageTrack.c
  • lines changed 1, context: html, text, full: html, text
    bf391f48053823623796ee5531d3e2b97a57c20e Mon Jan 13 13:49:12 2025 -0800
    promote "show" visibility to full status as a visbility instead of aliasing it to "full" refs #35036
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    bf391f48053823623796ee5531d3e2b97a57c20e Mon Jan 13 13:49:12 2025 -0800
    promote "show" visibility to full status as a visbility instead of aliasing it to "full" refs #35036
• src/hg/hgc/gencodeClick.c
  • lines changed 1, context: html, text, full: html, text
    2fff52ac48b4fe50d2b9803baa4727f6e3c379d1 Tue Jan 14 22:54:58 2025 -0800
    Braney said the comments were superfluous.
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    2fff52ac48b4fe50d2b9803baa4727f6e3c379d1 Tue Jan 14 22:54:58 2025 -0800
    Braney said the comments were superfluous.
  • lines changed 2, context: html, text, full: html, text
    b72ba361879084edbe22cd18e39c000bc6ffa122 Wed Jan 15 12:15:28 2025 -0800
    remove old comment hgc.c
• src/hg/htdocs/FAQ/FAQcustom.html
  • lines changed 2, context: html, text, full: html, text
    dcb079b13428b8d0416d44ec2626482fab2f3e53 Wed Jan 15 15:23:45 2025 -0800
    minor corrections based on code review, refs #35025
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 24, context: html, text, full: html, text
    47acd546e8100165cc25e0070ba8c870a8fec275 Fri Jan 17 11:22:27 2025 -0800
    Cleaning up the news list to 5 items per column, and creating the new anchor for 2025 news. No RM.
  • lines changed 12, context: html, text, full: html, text
    2019790b4445ac76dfc6e591fc1575abac740b5a Fri Jan 17 18:24:02 2025 -0800
    Renaming DDG2P announcement to DECIPHER Population CNVs, refs #35053
• src/hg/htdocs/images/bluebarMenuGif.gif
  • lines changed 0, context: html, text, full: html, text
    2a9cc71802a1c48c2b166e370e434fa6ff026f63 Wed Jan 15 22:49:33 2025 -0800
    committing without the 7.2 mb gif file src/hg/htdocs/images/highlightZoomGif.gif
• src/hg/htdocs/images/configureGif.gif
  • lines changed 0, context: html, text, full: html, text
    2a9cc71802a1c48c2b166e370e434fa6ff026f63 Wed Jan 15 22:49:33 2025 -0800
    committing without the 7.2 mb gif file src/hg/htdocs/images/highlightZoomGif.gif
• src/hg/htdocs/images/gb101cheatSheet.png
  • lines changed 0, context: html, text, full: html, text
    2a9cc71802a1c48c2b166e370e434fa6ff026f63 Wed Jan 15 22:49:33 2025 -0800
    committing without the 7.2 mb gif file src/hg/htdocs/images/highlightZoomGif.gif
• src/hg/htdocs/images/gettingHelp.png
  • lines changed 0, context: html, text, full: html, text
    2a9cc71802a1c48c2b166e370e434fa6ff026f63 Wed Jan 15 22:49:33 2025 -0800
    committing without the 7.2 mb gif file src/hg/htdocs/images/highlightZoomGif.gif
• src/hg/htdocs/images/reverseStrand.png
  • lines changed 0, context: html, text, full: html, text
    2a9cc71802a1c48c2b166e370e434fa6ff026f63 Wed Jan 15 22:49:33 2025 -0800
    committing without the 7.2 mb gif file src/hg/htdocs/images/highlightZoomGif.gif
• src/hg/htdocs/images/rightClickAndGreyBarGif.gif
  • lines changed 0, context: html, text, full: html, text
    2a9cc71802a1c48c2b166e370e434fa6ff026f63 Wed Jan 15 22:49:33 2025 -0800
    committing without the 7.2 mb gif file src/hg/htdocs/images/highlightZoomGif.gif
• src/hg/htdocs/indexMeetings.html
  • lines changed 20, context: html, text, full: html, text
    1d9786b069a50ac0953e72d6666c3a8e362ee8da Fri Jan 17 11:33:33 2025 -0800
    Updating our home page meetings events.
• src/hg/htdocs/indexNews.html
  • lines changed 1, context: html, text, full: html, text
    2019790b4445ac76dfc6e591fc1575abac740b5a Fri Jan 17 18:24:02 2025 -0800
    Renaming DDG2P announcement to DECIPHER Population CNVs, refs #35053
• src/hg/inc/customFactory.h
  • lines changed 2, context: html, text, full: html, text
    d0c37ab6f0269c790d237ea37f9d4873136aec97 Tue Jan 21 02:16:18 2025 -0800
    defaulting to filename when there is no browser line, refs #35085
• src/hg/inc/hui.h
  • lines changed 2, context: html, text, full: html, text
    bf391f48053823623796ee5531d3e2b97a57c20e Mon Jan 13 13:49:12 2025 -0800
    promote "show" visibility to full status as a visbility instead of aliasing it to "full" refs #35036
• src/hg/inc/userdata.h
  • lines changed 3, context: html, text, full: html, text
    a6e5c99f562491a34c8b1d69663b9a0c46c9adfe Tue Jan 14 15:19:38 2025 -0800
    Make hubspace tusd endpoint defined by hg.conf variable hubSpaceTusdEndpoint
  • lines changed 27, context: html, text, full: html, text
    55de7ef426a462247f89f48afd9aa6a2eb2cdd19 Thu Jan 16 17:11:17 2025 -0800
    Remove a bunch of dead experimental hubspace code, and make sure to cgi-encode hub names, refs #35018
• src/hg/js/external/tus.js
  • lines changed 4973, context: html, text, full: html, text
    3243eb0034564ee8a123d99ba186fea78c06d09d Mon Jan 13 14:05:01 2025 -0800
    Remove tus javascript library now that we are using uppy to manage uploads, refs #35018
• src/hg/js/hgMyData.js
  • lines changed 3, context: html, text, full: html, text
    14f0e7fd728cdbfae3389e494fd98bc4a29d5c4f Tue Jan 14 13:53:59 2025 -0800
    Update history state on row removal in hubSpace UI so after removing a file, clicking a link to view a separate file in the genome browser and then hitting the web browser back button shows the correct state
  • lines changed 5, context: html, text, full: html, text
    b17e57befc1ec01135c98e91d93e5692b1b0f523 Tue Jan 14 14:06:59 2025 -0800
    Oops print numbers in 'byte' sizes rather than metric sizes, refs #35018
  • lines changed 14, context: html, text, full: html, text
    d8c1e04bf62d885bad423a5f8ad7222421a15cc0 Tue Jan 14 14:49:21 2025 -0800
    After an upload or upload batch is done, clear the uppy state so that when the upload button is clicked again you don't have to click 'done' first, refs #35018
  • lines changed 4, context: html, text, full: html, text
    a6e5c99f562491a34c8b1d69663b9a0c46c9adfe Tue Jan 14 15:19:38 2025 -0800
    Make hubspace tusd endpoint defined by hg.conf variable hubSpaceTusdEndpoint
  • lines changed 5, context: html, text, full: html, text
    e990c76fb9538fc05ace961289390d88f2ecec84 Tue Jan 14 15:40:36 2025 -0800
    Remove orphaned defaultFileType function, refs #35018
  • lines changed 2, context: html, text, full: html, text
    135003b02fd3d3cd21400ea5b1bb58a385892efb Tue Jan 14 15:46:05 2025 -0800
    Change for..in loop to for..of, refs #35018
  • lines changed 2, context: html, text, full: html, text
    fc715fcc5977edc36a079b3a1a9da5534ddec030 Tue Jan 14 15:57:02 2025 -0800
    Add stopPropagation() call when the convenient view button link is clicked in hubspace, refs #35018
• src/hg/js/subCfg.js
  • lines changed 25, context: html, text, full: html, text
    b56b616deec9a8b92b3abaf45b78e06d973a6517 Mon Jan 13 10:24:56 2025 -0800
    addressing various issues on the hgTrackUi config page that have to do with visibility interactions between composite parents and children, refs #4042
• src/hg/lib/customFactory.c
  • lines changed 9, context: html, text, full: html, text
    d0c37ab6f0269c790d237ea37f9d4873136aec97 Tue Jan 21 02:16:18 2025 -0800
    defaulting to filename when there is no browser line, refs #35085
  • lines changed 7, context: html, text, full: html, text
    4466547a6c6f13857b62d5bd98c7341cf1376500 Tue Jan 21 02:23:42 2025 -0800
    also setting custom track name, in addition to track description, refs #35085
• src/hg/lib/customTrack.c
  • lines changed 2, context: html, text, full: html, text
    d0c37ab6f0269c790d237ea37f9d4873136aec97 Tue Jan 21 02:16:18 2025 -0800
    defaulting to filename when there is no browser line, refs #35085
• src/hg/lib/hubConnect.c
  • lines changed 2, context: html, text, full: html, text
    5cedb50e1dadbb9458af75635eb78dbd65db730c Tue Jan 14 12:26:55 2025 -0800
    don't crash if a hub track doesn't have a bigDataUrl refs #34954
• src/hg/lib/hui.c
  • lines changed 5, context: html, text, full: html, text
    bf391f48053823623796ee5531d3e2b97a57c20e Mon Jan 13 13:49:12 2025 -0800
    promote "show" visibility to full status as a visbility instead of aliasing it to "full" refs #35036
• src/hg/lib/straw/makefile
  • lines changed 2, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/lib/userdata.c
  • lines changed 11, context: html, text, full: html, text
    b7e0b5f7674dfa7600149aab93d79bed3c3b926a Mon Jan 13 17:40:22 2025 -0800
    When prefixing a file specified by the hubspace ui with the userDataDir, run realpath(3) on the file name to prevent looking up system files, refs #35018
  • lines changed 9, context: html, text, full: html, text
    b50eb72560c220a7d4bb6856cedfe1e23fd1d2bf Tue Jan 14 16:08:32 2025 -0800
    oops I deleted the web accessible file uploads location not the tusd endpoint location, refs Hiram email
  • lines changed 110, context: html, text, full: html, text
    55de7ef426a462247f89f48afd9aa6a2eb2cdd19 Thu Jan 16 17:11:17 2025 -0800
    Remove a bunch of dead experimental hubspace code, and make sure to cgi-encode hub names, refs #35018
  • lines changed 11, context: html, text, full: html, text
    90a4b891ec9646bb4f4448a2bf53e714a8aa4492 Fri Jan 17 11:55:54 2025 -0800
    When creating track stanzas after uploading a file to hubspace, wrap the bigBedFileOpen call in an errCatch so that if the file is actually not a bigBed, the user doesn't encounter some mysterious behavior when bigBedFileOpen errAborts, refs #35064
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 4, context: html, text, full: html, text
    47a1923ca3817900bbd90d07d9a073719a0a7f32 Tue Jan 14 14:35:05 2025 -0800
    adding a couple per user request refs #29545
  • lines changed 3, context: html, text, full: html, text
    d2353c8c3ff43dc95f0fb2a13e5d0592c7521a25 Mon Jan 20 09:28:40 2025 -0800
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 1, context: html, text, full: html, text
    0bb1aded8773d1762002ee556834f582252e0711 Tue Jan 14 16:08:12 2025 -0800
    legacy reached a new low with a virus no redmine
• src/hg/makeDb/doc/hg19.txt
  • lines changed 37, context: html, text, full: html, text
    2f75ea14748d867f3ab9f56ccaa69bc74e9486a3 Tue Jan 14 22:35:06 2025 -0800
    Renaming/updating DDG2P track to DECIPHER Population CNVs, refs #35053
• src/hg/makeDb/doc/hg38/decipher.txt
  • lines changed 37, context: html, text, full: html, text
    2f75ea14748d867f3ab9f56ccaa69bc74e9486a3 Tue Jan 14 22:35:06 2025 -0800
    Renaming/updating DDG2P track to DECIPHER Population CNVs, refs #35053
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    47a1923ca3817900bbd90d07d9a073719a0a7f32 Tue Jan 14 14:35:05 2025 -0800
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    47a1923ca3817900bbd90d07d9a073719a0a7f32 Tue Jan 14 14:35:05 2025 -0800
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    47a1923ca3817900bbd90d07d9a073719a0a7f32 Tue Jan 14 14:35:05 2025 -0800
    adding a couple per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    d2353c8c3ff43dc95f0fb2a13e5d0592c7521a25 Mon Jan 20 09:28:40 2025 -0800
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    47a1923ca3817900bbd90d07d9a073719a0a7f32 Tue Jan 14 14:35:05 2025 -0800
    adding a couple per user request refs #29545
• src/hg/makeDb/outside/pseudogenes/pseudoPipeParents.py
  • lines changed 115, context: html, text, full: html, text
    c545301381d0663f19215c3642acfea9b24d407d Tue Jan 7 13:09:28 2025 -0800
    Yale pseudogene and parents composite track (pseudoPipe)
• src/hg/makeDb/outside/pseudogenes/pseudoPipeToBed.py
  • lines changed 143, context: html, text, full: html, text
    c545301381d0663f19215c3642acfea9b24d407d Tue Jan 7 13:09:28 2025 -0800
    Yale pseudogene and parents composite track (pseudoPipe)
• src/hg/makeDb/scripts/wigColorByColors/makeWigColorByRevelCadd.py
  • lines changed 95, context: html, text, full: html, text
    12d2b2963d2d5f23d53317bc0ec49e9c787ef4e7 Fri Jan 17 10:26:03 2025 -0800
    Committing the directory with wigColorBy script, refs #34732
• src/hg/makeDb/trackDb/human/decipher.ra
  • lines changed 5, context: html, text, full: html, text
    2f75ea14748d867f3ab9f56ccaa69bc74e9486a3 Tue Jan 14 22:35:06 2025 -0800
    Renaming/updating DDG2P track to DECIPHER Population CNVs, refs #35053
• src/hg/makeDb/trackDb/human/decipherContainer.html
  • lines changed 12, context: html, text, full: html, text
    2f75ea14748d867f3ab9f56ccaa69bc74e9486a3 Tue Jan 14 22:35:06 2025 -0800
    Renaming/updating DDG2P track to DECIPHER Population CNVs, refs #35053
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    2459380aabc15ba888dc1722040d93a12d2363a0 Fri Jan 17 16:09:13 2025 -0800
    Fixing the outlinks for vista which were resulting in a not found page, refs #35092
• src/hg/makeDb/trackDb/human/hg38/pseudogenes.html
  • lines changed 70, context: html, text, full: html, text
    c545301381d0663f19215c3642acfea9b24d407d Tue Jan 7 13:09:28 2025 -0800
    Yale pseudogene and parents composite track (pseudoPipe)
• src/hg/makeDb/trackDb/human/hg38/pseudogenes.ra
  • lines changed 52, context: html, text, full: html, text
    c545301381d0663f19215c3642acfea9b24d407d Tue Jan 7 13:09:28 2025 -0800
    Yale pseudogene and parents composite track (pseudoPipe)
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    c545301381d0663f19215c3642acfea9b24d407d Tue Jan 7 13:09:28 2025 -0800
    Yale pseudogene and parents composite track (pseudoPipe)
  • lines changed 1, context: html, text, full: html, text
    2459380aabc15ba888dc1722040d93a12d2363a0 Fri Jan 17 16:09:13 2025 -0800
    Fixing the outlinks for vista which were resulting in a not found page, refs #35092
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    58e55e6377a59c2e91d8188fc43e491af91ec4db Mon Dec 9 01:28:56 2024 -0800
    Adding varaico variants track
  • lines changed 1, context: html, text, full: html, text
    cce2450dd30e559efed599f6345bfa944f6e1236 Fri Jan 17 02:05:37 2025 -0800
    added release alpha to varaico
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 7, context: html, text, full: html, text
    34f7d6002403040f75eb892b9a67a436503a1a36 Mon Jan 13 15:04:08 2025 -0800
    Relating gnomAD constraints to the constraints metric superTrack, refs #29043
• src/hg/utils/agpCondense/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/automation/doCpgIslands.pl
  • lines changed 1, context: html, text, full: html, text
    160145e7459ad9c3252fa47ddff8c1db634688a0 Tue Jan 14 07:07:44 2025 -0800
    eliminate duplicate declaration of $fh no redmine
• src/hg/utils/automation/doTandemDup.pl
  • lines changed 1, context: html, text, full: html, text
    a20a64637b2a8bddd07aa4071beb839daa464230 Tue Jan 14 10:53:07 2025 -0800
    using the faster python kmerPrint.py no redmine
• src/hg/utils/automation/kmerPrint.py
  • lines changed 61, context: html, text, full: html, text
    d46e25fbafa02b136e9cdbb6eafcbf01583d2a8a Tue Jan 14 10:51:47 2025 -0800
    dramatically faster than the perl equivalent no redmine
• src/hg/utils/automation/makefile
  • lines changed 3, context: html, text, full: html, text
    a3a313b3fa4aa9c77d0b9827f8721ef57990bebd Tue Jan 14 12:24:02 2025 -0800
    no using kmerPrint.py in place of kmerPrint.pl no redmine
• src/hg/utils/bedExtendRanges/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/bedMergeExpData/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/bedMergeOverlappingBlocks/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/bedRandom/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/blatServersCheck/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/cageSingleTrack/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/checkUrlsInTable/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/coloredExonToBed/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/findCutters/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/fiveCToBed/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/geoMirrorNode/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/gff3ToGenePred/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/gff3ToPsl/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/gffToBed/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/gtfToGenePred/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/hubCheck/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/liftUpBedFromTable/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/makeTableList/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/makeTrackIndex/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/mdbQuery/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/mutationClassifier/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/otto/clinvar/clinVarToBed
  • lines changed 2, context: html, text, full: html, text
    acfbaec13c08b80dc3c5138821a23ef4f905d573 Mon Jan 20 09:17:30 2025 -0800
    fixing color coding of CNVs in clinvar, refs #35062
• src/hg/utils/otto/ottoCompareGitVsHiveFiles.py
  • lines changed 1, context: html, text, full: html, text
    998833f3086db9b664f7998f1122e0a3ddfe8ff8 Mon Jan 20 09:15:04 2025 -0800
    Adding two more files to be ignored by the comparison script, no RM.
• src/hg/utils/overlapSelect/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/pslLiftSubrangeBlat/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/randFrag/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/refSeqGet/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/repeatSelect/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/rgdGeneXref2/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/sqlPerf/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/hg/utils/wigAsciiAverageOverBed/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/dataSim/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/gensub2/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/para/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/paraHub/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/paraHubStop/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/paraNode/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/paraNodeStart/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/paraNodeStatus/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/paraNodeStop/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/paraTestJob/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/parasol/parasol/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/tracks/makefile
  • lines changed 1, context: html, text, full: html, text
    3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800
    eliminate the duplication of the -lm library refs #35048
• src/utils/qa/checkSyncAndMetaDataAll.py
  • lines changed 2, context: html, text, full: html, text
    a3c5195d051868c371255e6fd6fb2fe81632ce44 Mon Jan 13 17:53:39 2025 -0800
    Updating the script to accommodate hgwbeta tables for hg19, no RM
• src/utils/qa/linkCheckExclude
  • lines changed 1, context: html, text, full: html, text
    14fc20805ee6a2ac014aee91c0a4f58dd9fe7960 Wed Jan 15 10:18:04 2025 -0800
    Adding the new assemblySearch.html to the list due to the cron outputting errors, No Redmine
• src/utils/qa/sendPublicHubAuthorsUsageStatistics.py
  • lines changed 123, context: html, text, full: html, text
    2424404585a3d8562fe2e94436fe3a32bab2980b Wed Jan 15 11:38:30 2025 -0800
    Script that calculates public hub usage, given a number of pre-generated hubPublic statistics files, then drafts and sends out emails to all public hubs informing them of their hub activity over the N time period. By default the sendEmail functions are all commented out so as not to accidentally spam our users. Refs #34421
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    c472d57e62e5b592212cd0fab2e1d80a4ce4f2ec Tue Jan 21 10:14:54 2025 -0800
    v477 preview1, refs #34963

• lines changed: 6501
• files changed: 135