All File Changes

v477_preview to v477_preview2 (2025-01-21 to 2025-01-27) v477

• confs/hgwbeta.hg.conf
  • lines changed 4, context: html, text, full: html, text
    512381f3f183b65eaab1d1a341f8510fb919e981 Sun Jan 26 01:11:15 2025 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    512381f3f183b65eaab1d1a341f8510fb919e981 Sun Jan 26 01:11:15 2025 -0800
    Installing updated hg.conf files from UCSC servers
• docs/gb101.md
  • lines changed 12, context: html, text, full: html, text
    4fc10f8d260d0f77816cbadd6f64541b49bb272b Mon Jan 27 09:49:27 2025 -0800
    adding images for new tutorial and tweaking makefile and lua file to including different bootstrap css file, refs #30335
• docs/index.md
  • lines changed 1, context: html, text, full: html, text
    8b1cb57aefa7b685016b223c6ccc23f6ba9555d7 Wed Jan 22 16:54:55 2025 -0800
    Feedback from CR, refs #35113
• docs/staticPage.lua
  • lines changed 1, context: html, text, full: html, text
    4fc10f8d260d0f77816cbadd6f64541b49bb272b Mon Jan 27 09:49:27 2025 -0800
    adding images for new tutorial and tweaking makefile and lua file to including different bootstrap css file, refs #30335
• src/browserbox/makefile
  • lines changed 11, context: html, text, full: html, text
    f86ab74eb6895232f4c9533d658afdc65b67b381 Tue Jan 21 16:17:09 2025 -0800
    Prefix makefile echo lines with @ to prevent double printing of messages, clarify message to state one does not need to do anything after running make alpha
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c
  • lines changed 1, context: html, text, full: html, text
    81dc9c6a4cd16bbd0fc9ef0bff84b38de7d0679d Wed Jan 22 14:13:50 2025 -0800
    Fixing warning about printing a potentially NULL string, no ticket
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    17cb537ae03617f211190c1d0950e0deff4a8c6e Wed Jan 22 05:02:11 2025 -0800
    broke the build, fixing hgCustom, refs #35085
• src/hg/hgTracks/config.c
  • lines changed 1, context: html, text, full: html, text
    03f4c6a87b2168f343110968b73cbcd52f34f450 Wed Jan 22 05:59:02 2025 -0800
    typo
• src/hg/hgTracks/vcfTrack.c
  • lines changed 4, context: html, text, full: html, text
    e630f719d5af868110150d1580807b685bf5c27b Fri Jan 24 16:32:03 2025 -0800
    Prevent off-by-one in loop which prevents writing off the end of an array, refs #35138
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    2d966bbfcec51fe47cb0d36791a20380eb034ba6 Wed Jan 22 04:58:31 2025 -0800
    broke the build, fixing hgc again, refs #35085
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 13, context: html, text, full: html, text
    048b2becc526e0ec8ef7d4a172543349e72d2020 Mon Jan 27 10:00:50 2025 -0800
    adding pointers to net construction example in GenomeWiki, refs #26358
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 3, context: html, text, full: html, text
    079452db1366f3fdeac159871bf2950ffc8fb48b Tue Jan 21 16:46:20 2025 -0800
    Adding setColorWith settings to all the docs. Refs #34958
• src/hg/htdocs/goldenPath/help/net.html
  • lines changed 4, context: html, text, full: html, text
    048b2becc526e0ec8ef7d4a172543349e72d2020 Mon Jan 27 10:00:50 2025 -0800
    adding pointers to net construction example in GenomeWiki, refs #26358
• src/hg/htdocs/goldenPath/help/trackDb/changes.html
  • lines changed 7, context: html, text, full: html, text
    8dee3260d13eec1c39191923ba758ad9e6b4dc0c Wed Jan 22 02:46:13 2025 -0800
    docing change to trackDb, refs #34958
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 4, context: html, text, full: html, text
    079452db1366f3fdeac159871bf2950ffc8fb48b Tue Jan 21 16:46:20 2025 -0800
    Adding setColorWith settings to all the docs. Refs #34958
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 18, context: html, text, full: html, text
    079452db1366f3fdeac159871bf2950ffc8fb48b Tue Jan 21 16:46:20 2025 -0800
    Adding setColorWith settings to all the docs. Refs #34958
• src/hg/htdocs/images/hgTracksSearchBarExample.png
  • lines changed 0, context: html, text, full: html, text
    4fc10f8d260d0f77816cbadd6f64541b49bb272b Mon Jan 27 09:49:27 2025 -0800
    adding images for new tutorial and tweaking makefile and lua file to including different bootstrap css file, refs #30335
• src/hg/htdocs/images/trackSearchSimpleExample.png
  • lines changed 0, context: html, text, full: html, text
    4fc10f8d260d0f77816cbadd6f64541b49bb272b Mon Jan 27 09:49:27 2025 -0800
    adding images for new tutorial and tweaking makefile and lua file to including different bootstrap css file, refs #30335
• src/hg/htdocs/images/trackVisExamples.png
  • lines changed 0, context: html, text, full: html, text
    4fc10f8d260d0f77816cbadd6f64541b49bb272b Mon Jan 27 09:49:27 2025 -0800
    adding images for new tutorial and tweaking makefile and lua file to including different bootstrap css file, refs #30335
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    53cec0e344d474d5d46039f46bd3ecaab57d79b5 Tue Jan 21 17:10:19 2025 -0800
    Removing wuhCor1 from the dropdown menu, refs #34992
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    53cec0e344d474d5d46039f46bd3ecaab57d79b5 Tue Jan 21 17:10:19 2025 -0800
    Removing wuhCor1 from the dropdown menu, refs #34992
• src/hg/htdocs/style/makefile
  • lines changed 2, context: html, text, full: html, text
    4fc10f8d260d0f77816cbadd6f64541b49bb272b Mon Jan 27 09:49:27 2025 -0800
    adding images for new tutorial and tweaking makefile and lua file to including different bootstrap css file, refs #30335
• src/hg/js/hgMyData.js
  • lines changed 11, context: html, text, full: html, text
    72a39a73f65feecd86b7e6cf20bdd346fcad4868 Thu Jan 23 13:09:33 2025 -0800
    Fix bug in handling non alphanum characters in filenames in hubspace. I was mistakenly double encoding the filenames when creating trackDb stanzas. Also on client side, prevent users from even submitting files with weird characters to start with, refs #35064
• src/hg/js/hgTracks.js
  • lines changed 4, context: html, text, full: html, text
    276c430072309a1fb8a1da9a905a6172594d5276 Thu Jan 23 10:15:11 2025 -0800
    Replace '.' with '\.' in some row selectors in hgTracks.js so the hide track set menu item shows up
• src/hg/js/tutorials/basicTutorial.js
  • lines changed 1, context: html, text, full: html, text
    987b763584ce86509e83db6c0e4cbabcbe435f52 Wed Jan 22 19:11:59 2025 -0800
    Making the 'Reverse' tooltip attach to the 'Reverse' button on hgTracks. Found the issue when making a GIF for the PAG presentation, refs #35123
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    110a67256f2038b6216c448e86967dc763efc8c8 Sun Jan 26 12:57:24 2025 -0800
    properly deal with tvShow when ranking visibilities refs #35137
• src/hg/lib/tests/customTrackTester.c
  • lines changed 5, context: html, text, full: html, text
    576f9b015b0d3df408c6f1323b7247096c80193f Wed Jan 22 05:04:30 2025 -0800
    broke the build, fixing customTrackTester, refs #35085
• src/hg/lib/userdata.c
  • lines changed 8, context: html, text, full: html, text
    72a39a73f65feecd86b7e6cf20bdd346fcad4868 Thu Jan 23 13:09:33 2025 -0800
    Fix bug in handling non alphanum characters in filenames in hubspace. I was mistakenly double encoding the filenames when creating trackDb stanzas. Also on client side, prevent users from even submitting files with weird characters to start with, refs #35064
  • lines changed 6, context: html, text, full: html, text
    28ac91cd29f92b006199680053b5b93c42f27c74 Fri Jan 24 17:11:10 2025 -0800
    When hubspace UI requests to remove a file, ensure realpath gets called on the requested file and check that the file is belonging to the userName, right before deletion, refs #35109
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    a7941c8b389f35cf00152b778596472530450989 Fri Jan 24 15:54:17 2025 -0800
    adding a sea turtle per user request refs #35104
• src/hg/makeDb/doc/hg19.txt
  • lines changed 17, context: html, text, full: html, text
    ee98569fb749e16cf3e4601a7cef331432d062f8 Tue Jan 21 10:25:19 2025 -0800
    adding alphaMissense
  • lines changed 3, context: html, text, full: html, text
    66a5094b52b1b49a14b72ddd612f6f08257f4c92 Fri Jan 24 11:03:50 2025 -0800
    Staging the VarChat track, refs #35081
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    f422617243b87c9c932331c7bbaba93c5a8381a6 Fri Jan 24 16:40:27 2025 -0800
    Adding the v101 COSMIC track for hg38/hg19, refs #34904
• src/hg/makeDb/doc/hg38/alphaMissense.txt
  • lines changed 11, context: html, text, full: html, text
    f7577fc37cbcba25eac796f12e81ac0235f77c0c Tue Jan 21 11:03:16 2025 -0800
    fixing wrongly named copy of alphaMissense.txt
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 7402, context: html, text, full: html, text
    ee98569fb749e16cf3e4601a7cef331432d062f8 Tue Jan 21 10:25:19 2025 -0800
    adding alphaMissense
  • lines changed 7402, context: html, text, full: html, text
    f7577fc37cbcba25eac796f12e81ac0235f77c0c Tue Jan 21 11:03:16 2025 -0800
    fixing wrongly named copy of alphaMissense.txt
  • lines changed 20, context: html, text, full: html, text
    f422617243b87c9c932331c7bbaba93c5a8381a6 Fri Jan 24 16:40:27 2025 -0800
    Adding the v101 COSMIC track for hg38/hg19, refs #34904
• src/hg/makeDb/doc/hg38/varChat.txt
  • lines changed 6, context: html, text, full: html, text
    66a5094b52b1b49a14b72ddd612f6f08257f4c92 Fri Jan 24 11:03:50 2025 -0800
    Staging the VarChat track, refs #35081
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    a7941c8b389f35cf00152b778596472530450989 Fri Jan 24 15:54:17 2025 -0800
    adding a sea turtle per user request refs #35104
• src/hg/makeDb/outside/alphaMissense/alphaMissenseToWig.py
  • lines changed 71, context: html, text, full: html, text
    ee98569fb749e16cf3e4601a7cef331432d062f8 Tue Jan 21 10:25:19 2025 -0800
    adding alphaMissense
• src/hg/makeDb/scripts/wigColorByColors/makeWigColorByRevelCadd.py
  • lines changed 13, context: html, text, full: html, text
    7046bad2efe40b36e3ebd4999e6caf30223ef0d1 Fri Jan 24 11:09:55 2025 -0800
    Merging Jeltje's changes to my tree, these were done to add colors to the alphaMissense bigWig, refs #32269
• src/hg/makeDb/trackDb/human/TFrPeakClusters.html
  • lines changed 90, context: html, text, full: html, text
    0acf7bb36b85100c30813e4c07a41a5b7e6b185b Fri Jan 24 11:08:31 2025 -0800
    I forgot to commit this page when I first staged the track, refs #34930
• src/hg/makeDb/trackDb/human/alphaMissense.html
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    ee98569fb749e16cf3e4601a7cef331432d062f8 Tue Jan 21 10:25:19 2025 -0800
    adding alphaMissense
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    02d07fdf331de9cdf04f74c5d9211800403dfa8b Tue Jan 21 10:52:51 2025 -0800
    basing alphaMissense html on revel
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    58e83e1a302e901ad4b97a529f15599f25f33e43 Tue Jan 21 11:58:49 2025 -0800
    alpha missense description
  • lines changed 13, context: html, text, full: html, text
    d36ce14a1f815d3b3bcdadf1972bba54eef120f8 Tue Jan 21 12:05:56 2025 -0800
    fix typos
  • lines changed 3, context: html, text, full: html, text
    4b874bc40240615779138005711f6fbe52640933 Tue Jan 21 12:21:39 2025 -0800
    capitalizing track name to match paper
• src/hg/makeDb/trackDb/human/alphaMissense.ra
  • lines changed 56, context: html, text, full: html, text
    ee98569fb749e16cf3e4601a7cef331432d062f8 Tue Jan 21 10:25:19 2025 -0800
    adding alphaMissense
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    7b06a17cfb384c076be22ae972f1e9fccb6e0e66 Tue Jan 21 12:10:15 2025 -0800
    track spelling
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    00cad26cab0f06e8cc4c370396a4bc5362de3aaa Tue Jan 21 12:26:19 2025 -0800
    changing capitalization
• src/hg/makeDb/trackDb/human/hg19/cosmicMuts.html
  • lines changed 82, context: html, text, full: html, text
    f422617243b87c9c932331c7bbaba93c5a8381a6 Fri Jan 24 16:40:27 2025 -0800
    Adding the v101 COSMIC track for hg38/hg19, refs #34904
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    f422617243b87c9c932331c7bbaba93c5a8381a6 Fri Jan 24 16:40:27 2025 -0800
    Adding the v101 COSMIC track for hg38/hg19, refs #34904
• src/hg/makeDb/trackDb/human/hg38/cosmicMuts.html
  • lines changed 3, context: html, text, full: html, text
    f422617243b87c9c932331c7bbaba93c5a8381a6 Fri Jan 24 16:40:27 2025 -0800
    Adding the v101 COSMIC track for hg38/hg19, refs #34904
• src/hg/makeDb/trackDb/human/hg38/miRnaAtlas.html
  • lines changed 1, context: html, text, full: html, text
    9cbe13e094cb2e7362a6c86e323e04e9496d4452 Tue Jan 21 16:55:23 2025 -0800
    Fixing a tissue mRNA outlink that was broken, refs #34890
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 14, context: html, text, full: html, text
    f422617243b87c9c932331c7bbaba93c5a8381a6 Fri Jan 24 16:40:27 2025 -0800
    Adding the v101 COSMIC track for hg38/hg19, refs #34904
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    ee98569fb749e16cf3e4601a7cef331432d062f8 Tue Jan 21 10:25:19 2025 -0800
    adding alphaMissense
  • lines changed 20, context: html, text, full: html, text
    66a5094b52b1b49a14b72ddd612f6f08257f4c92 Fri Jan 24 11:03:50 2025 -0800
    Staging the VarChat track, refs #35081
• src/hg/makeDb/trackDb/human/varChat.html
  • lines changed 95, context: html, text, full: html, text
    66a5094b52b1b49a14b72ddd612f6f08257f4c92 Fri Jan 24 11:03:50 2025 -0800
    Staging the VarChat track, refs #35081
• src/hg/makeDb/trackDb/human/varsInPubs.html
  • lines changed 13, context: html, text, full: html, text
    66a5094b52b1b49a14b72ddd612f6f08257f4c92 Fri Jan 24 11:03:50 2025 -0800
    Staging the VarChat track, refs #35081
• src/hg/utils/automation/pairLastz.sh
  • lines changed 12, context: html, text, full: html, text
    782d5187d53d69015b8344ac83651bc0350a263e Wed Jan 22 12:08:11 2025 -0800
    be very specific which machines are used for which jobs no redmine
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    76851862dc74347ab9b57976ba99c2b30968c66b Fri Jan 24 11:43:09 2025 -0800
    beware multiple copies of the same lastz run, use the latest refs #35135
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    16c6d21c4dcd64186a91638db6a2241d7d3807e4 Thu Jan 23 14:21:57 2025 -0800
    Updating python version needed for some imports.
• src/inc/common.mk
  • lines changed 6, context: html, text, full: html, text
    45e522e373c59faefa8a961c2bb3d44c93e84877 Wed Jan 22 14:12:50 2025 -0800
    Revising server name tests after migration, more to come. refs #35048
• src/userApps/Makefile
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    23492f5ba1daa5245326bb308db5dc51a711d1a3 Sat Jan 25 08:54:35 2025 -0800
    fixup for new source file organization no redmine
• src/userApps/fetchKentSource.sh
  • lines changed 2, context: html, text, full: html, text
    23492f5ba1daa5245326bb308db5dc51a711d1a3 Sat Jan 25 08:54:35 2025 -0800
    fixup for new source file organization no redmine
• src/utils/qa/checkSessionsFromRR.py
  • lines changed 13, context: html, text, full: html, text
    60f6cb43588518973a7c814280a211b56cd269d8 Sat Jan 25 14:23:11 2025 -0800
    Removing unneeded selenium packages from the script and adding errors to skip, No RM
• src/utils/qa/hubPublicMail
  • lines changed 2, context: html, text, full: html, text
    d545453f0d97807bb471417a70e4a15db50fbe2a Wed Jan 22 12:28:51 2025 -0800
    Fixing a small bug where if the hub URL was http but the query to their server failed, it would still try to initialize text=f.txt even though the request never worked. The FTP example already had it in the proper location. No RM.
• src/utils/qa/qaTestScript.py
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    b78ce91d034bd072326bddbcc19be79ff1b0af58 Thu Jan 23 11:58:32 2025 -0800
    Updating the script due to the new Selenium version which deprecated previous methods, No RM
• src/utils/qa/weeklybld/buildEnv.csh
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    c36a1f7987a07375abe2fadd2ae37868ed179a96 Mon Jan 27 11:19:10 2025 -0800
    v477 preview2, refs #35106
• src/utils/trackDbIndexBb/tests/makefile
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    a620fd62f2b9b073ea74b8f9632a59180746bfdf Thu Jan 23 05:05:09 2025 -0800
    fixing build up for rocky9, no need for py2 anymore

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• files changed: 71