All File Changes

v443_base to v444_preview (2023-01-30 to 2023-02-06) v444

• confs/hgwdev.hg.conf
  • lines changed 3, context: html, text, full: html, text
    793645fb163eae2b19431aabb7cb5da615a38dbd Sun Feb 5 01:11:24 2023 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 17, context: html, text, full: html, text
    e7c480dfff7785e7c2efd40aa13d55747affe961 Wed Feb 1 12:17:50 2023 -0800
    Added a DOI option to getTrackReferences and updated it's full-text link detection to match the current PubMed page structure. No ticket.
• src/hg/gar/rebuild.sh
  • lines changed 9, context: html, text, full: html, text
    eea1ea7511ae244feb7c92616d0d463896dc851d Thu Feb 2 13:22:59 2023 -0800
    send assemblyTable and requestTable listings out to hgdownload no redmine
• src/hg/hgGene/primers.c
  • lines changed 1, context: html, text, full: html, text
    96935ad6b01515061690f86a52bd4ed96f58e638 Mon Jan 30 07:37:39 2023 -0800
    addding a plug for view - in external tools to the new primer option on hgGene, refs #30545
• src/hg/hgTracks/chainSnakeTrack.c
  • lines changed 8, context: html, text, full: html, text
    1d5248e54214efc78f88eca4aa110bf0cc7e1a33 Wed Feb 1 15:45:06 2023 -0800
    don't require a twoBit in order to show snakes
  • lines changed 26, context: html, text, full: html, text
    edfe4db20446f5c266f2ba1155fc694d30fdf00c Fri Feb 3 09:10:41 2023 -0800
    ongoing work on snake display for chains
• src/hg/hgTracks/chainTrack.c
  • lines changed 9, context: html, text, full: html, text
    693a69d6c9bb0639e3b4e37581ade795b4c2a7c7 Wed Feb 1 15:18:33 2023 -0800
    add option to show chains as snakes under hg.conf control
• src/hg/hgTracks/hgTracks.c
  • lines changed 10, context: html, text, full: html, text
    ac2ff1a8119e79a5d98fcd06e7afd8a32c73d473 Wed Feb 1 08:25:31 2023 -0800
    adding query strand and position as color and mouseover to BLAT results tracks, refs #30578
  • lines changed 2, context: html, text, full: html, text
    75d8de13286a104c4396288110c69202a6cc2895 Fri Feb 3 15:18:34 2023 -0800
    Fix default tracks and default track order keyboard shortcuts, refs #30589
  • lines changed 1, context: html, text, full: html, text
    e889377237adcec49d42793348733de2461bbed1 Fri Feb 3 16:11:45 2023 -0800
    Don't submit() when doing refresh button click because it disables the track vis dropdowns, refs #30589
• src/hg/hgc/bamClick.c
  • lines changed 7, context: html, text, full: html, text
    3c28d2c5a4076d66b330f2c089b2485657fbe9f9 Mon Jan 30 18:10:51 2023 -0800
    Make sure the loop on aliasList stops when an item is found so that we have the right value of chromName when we need to search for paired items in an expanded range. refs #30566
• src/hg/hgc/barChartClick.c
  • lines changed 12, context: html, text, full: html, text
    668110379c7c18bc75dd2db8747821b387fb28d6 Fri Jan 27 10:22:57 2023 -0800
    Redraw barChart svgs on the client so the column widths can be wide enough for labels, refs #28439
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    ac2ff1a8119e79a5d98fcd06e7afd8a32c73d473 Wed Feb 1 08:25:31 2023 -0800
    adding query strand and position as color and mouseover to BLAT results tracks, refs #30578
  • lines changed 6, context: html, text, full: html, text
    edfe4db20446f5c266f2ba1155fc694d30fdf00c Fri Feb 3 09:10:41 2023 -0800
    ongoing work on snake display for chains
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 46, context: html, text, full: html, text
    345a74e5374d0661c43bd619450ea34372f3931f Tue Jan 31 10:50:49 2023 -0800
    Updating news and pennantIcons for the hg38 patch 14 announcement, refs #29964
  • lines changed 4, context: html, text, full: html, text
    68ea2e19f239f06bafd09853a0c1e4d4a991abc7 Tue Jan 31 13:26:41 2023 -0800
    Fixing GRC typo, refs #29964
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    345a74e5374d0661c43bd619450ea34372f3931f Tue Jan 31 10:50:49 2023 -0800
    Updating news and pennantIcons for the hg38 patch 14 announcement, refs #29964
• src/hg/inc/snakeUi.h
  • lines changed 1, context: html, text, full: html, text
    edfe4db20446f5c266f2ba1155fc694d30fdf00c Fri Feb 3 09:10:41 2023 -0800
    ongoing work on snake display for chains
• src/hg/js/hgTracks.js
  • lines changed 24, context: html, text, full: html, text
    1882b8518123019af079080747fa712cd0a75d65 Fri Jan 27 10:48:29 2023 -0800
    Add zoom to exon/codon feature to hgTracks right click menu, refs #2724
• src/hg/js/hgc.js
  • lines changed 51, context: html, text, full: html, text
    668110379c7c18bc75dd2db8747821b387fb28d6 Fri Jan 27 10:22:57 2023 -0800
    Redraw barChart svgs on the client so the column widths can be wide enough for labels, refs #28439
• src/hg/lib/barChartUi.c
  • lines changed 11, context: html, text, full: html, text
    c777a406269f3c9a4a6144c53213e25402f10b89 Fri Jan 27 10:29:01 2023 -0800
    faceted bar chart hgTrackUi pages are broken in the hgTracks hgTrackUi pop up. don't do the faceted selection part when we are in a pop up, refs #30102
• src/hg/lib/dupTrack.c
  • lines changed 1, context: html, text, full: html, text
    ab5e0ceb76e4abc3fd00d225f758a88f3c8fca34 Thu Feb 2 14:44:56 2023 -0800
    changed it so by default users can duplicate tracks
• src/hg/lib/hCommon.c
  • lines changed 1, context: html, text, full: html, text
    cb2521855378f51cc79a579faaa57a48ece6faed Wed Feb 1 03:18:46 2023 -0800
    fixing hgc crash when protocol is not https, refs #30545
• src/hg/lib/hui.c
  • lines changed 24, context: html, text, full: html, text
    693a69d6c9bb0639e3b4e37581ade795b4c2a7c7 Wed Feb 1 15:18:33 2023 -0800
    add option to show chains as snakes under hg.conf control
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    8ee7c8aa28f59334f4a99f7dbe8395bf884a4886 Tue Jan 31 10:32:08 2023 -0800
    adding GCA_000300575.2_ASM30057v2 basidiomycete A.bisporus (H97 2016) per user request refs #29545
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    f2a57847f1a0a95ccaac0f31f79b1438cfee7452 Wed Feb 1 15:11:12 2023 -0800
    add the California mussel for the CCGP project no redmine
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    ff9640d3cacadb3a108731e806a471d6d69ca293 Thu Feb 2 14:25:03 2023 -0800
    adding in some CCGP genome builds no redmine
• src/hg/makeDb/doc/ccgpAsmHub/ccgp.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    36ae2af1b2a0d3199292a8b2dfcee385855f140d Tue Jan 31 14:52:53 2023 -0800
    starting the CCGP GenArk hub collection no redmine
  • lines changed 12, context: html, text, full: html, text
    f066a3c7e3410f07595c5039b285f79da29c09c5 Thu Feb 2 14:48:01 2023 -0800
    adding some assemblies to CCGP no redmine
• src/hg/makeDb/doc/ccgpAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    36ae2af1b2a0d3199292a8b2dfcee385855f140d Tue Jan 31 14:52:53 2023 -0800
    starting the CCGP GenArk hub collection no redmine
• src/hg/makeDb/doc/ccgpAsmHub/makefile
  • lines changed 23, context: html, text, full: html, text
    36ae2af1b2a0d3199292a8b2dfcee385855f140d Tue Jan 31 14:52:53 2023 -0800
    starting the CCGP GenArk hub collection no redmine
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    8ee7c8aa28f59334f4a99f7dbe8395bf884a4886 Tue Jan 31 10:32:08 2023 -0800
    adding GCA_000300575.2_ASM30057v2 basidiomycete A.bisporus (H97 2016) per user request refs #29545
• src/hg/makeDb/doc/hg38/patchUpdate.14.txt
  • lines changed 3, context: html, text, full: html, text
    ee4c78e5d1d630be90e7ca6bc0c076fa0ffd3464 Wed Feb 1 16:07:41 2023 -0800
    minor makedoc update for final hg38 p14 patch.
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    f2a57847f1a0a95ccaac0f31f79b1438cfee7452 Wed Feb 1 15:11:12 2023 -0800
    add the California mussel for the CCGP project no redmine
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 6, context: html, text, full: html, text
    a3681e7888030cebc1023f74d77158862dd39a51 Tue Jan 31 11:45:57 2023 -0800
    catching up a number of recent additions no redmine
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    2dd607cbec07de1fe0ccf93b835fd19bcb147d76 Tue Jan 31 11:48:33 2023 -0800
    the extra one GCA_009914755.4_T2T-CHM13v2.0 is required since it is artifically added no redmine
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    e3f062b5aadf38361ca54bd25b6604bd5610dad8 Tue Jan 31 10:33:50 2023 -0800
    the GRCh38 versions are now legacy so as not to compete with hg38.p14 and a fungus has become obsolete per user request refs #29545
• src/hg/makeDb/makeGencodeKnownGene/makeGencodeKnownGene.c
  • lines changed 6, context: html, text, full: html, text
    5765efc706b41b9528d3a2a17a865f898473ce05 Wed Feb 1 13:14:08 2023 -0800
    fix a bug in calculating knownCanonical that b0b reported that was the result of a bone-headed parsing of the hash structure. While I was in there I prioritized MANE membership over the appris tags.
• src/hg/makeDb/trackDb/human/genCC.html
  • lines changed 2, context: html, text, full: html, text
    a224faf89971608c75cd3c91ddc797da891bef2c Thu Feb 2 16:48:01 2023 -0800
    Adding more info in mouseOver requested by Ana, no RM.
• src/hg/makeDb/trackDb/human/genCC.ra
  • lines changed 1, context: html, text, full: html, text
    a224faf89971608c75cd3c91ddc797da891bef2c Thu Feb 2 16:48:01 2023 -0800
    Adding more info in mouseOver requested by Ana, no RM.
• src/hg/makeDb/trackDb/human/hg38/recombRate.ra
  • lines changed 1, context: html, text, full: html, text
    81e0d2a937916992f8ec951d650c8aa28f1a74d1 Mon Jan 30 10:51:58 2023 -0800
    Code review edit for the capitalization of G in genetic, refs #30536
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    c6642aa54d4b4ae266f75aa9ceca45c2e7cc3e22 Thu Feb 2 16:01:27 2023 -0800
    Adding the track description html to subtracks, refs #30044
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    345a74e5374d0661c43bd619450ea34372f3931f Tue Jan 31 10:50:49 2023 -0800
    Updating news and pennantIcons for the hg38 patch 14 announcement, refs #29964
• src/hg/utils/automation/asmHubChainNetTrackDb.sh
  • lines changed 1, context: html, text, full: html, text
    21f4b0da7fe6f8d64ba6d67cabb4bb464df44112 Tue Jan 31 12:21:53 2023 -0800
    correct symlink to ../trackData/ not to ../trackDb/ no redmine
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 6, context: html, text, full: html, text
    960327879cd684b279610a26bcd311625c401b02 Tue Jan 31 11:17:32 2023 -0800
    incorrect buildDir variable in the netSyntenic step fixed no redmine
• src/hg/utils/automation/doRecipBest.pl
  • lines changed 6, context: html, text, full: html, text
    5f82f3c44e6e68741fde81a878958cad5d327c6e Tue Jan 31 11:24:48 2023 -0800
    incorrect buildDir variable in the loadRBest step fixed no redmine
• src/hg/utils/otto/genArk/genArkListToSql.pl
  • lines changed 44, context: html, text, full: html, text
    c4c80a07b85c6aa44fa6f862536e297c8310a53a Thu Feb 2 12:37:12 2023 -0800
    adding otto cron scripts to keep the hgcentral.genark table up to date
• src/hg/utils/otto/genArk/updateHgcentral.sh
  • lines changed 113, context: html, text, full: html, text
    c4c80a07b85c6aa44fa6f862536e297c8310a53a Thu Feb 2 12:37:12 2023 -0800
    adding otto cron scripts to keep the hgcentral.genark table up to date
  • lines changed 11, context: html, text, full: html, text
    70124b0bcc90d53de666f37cccd6b1a4356161de Thu Feb 2 12:45:54 2023 -0800
    correctly check for an unbound variable no redmine
• src/hg/utils/otto/otto.crontab
  • lines changed 7, context: html, text, full: html, text
    105fed4179457f1d6ae6fb3daa94cd0cd0270451 Thu Feb 2 12:48:45 2023 -0800
    catch up with current crontab in otto user no redmine
  • lines changed 1, context: html, text, full: html, text
    230381336761678f15ec2bb28751ce9d558fbd3c Thu Feb 2 12:52:08 2023 -0800
    restore Lou's edit of 03 Jan to reduce frequency of lrgWrapper no redmine
  • lines changed 4, context: html, text, full: html, text
    2a1eb01eec5310638a682d97ef6e6e0204062bca Thu Feb 2 12:59:26 2023 -0800
    adding GenArk updating hgcentral.genark table once a week no redmine
• src/utils/chromToUcsc/chromToUcsc
  • lines changed 2, context: html, text, full: html, text
    49340bc650cba71856dc15f8972b804faf0035ec Thu Feb 2 11:20:54 2023 +0100
    modifying the -k docs for chromToUcsc, refs #30567
• src/utils/qa/searchedTermsCron.py
  • lines changed 6, context: html, text, full: html, text
    08f5e3bad3f8c53aae20321ccd4f5284c18da46d Thu Feb 2 13:03:11 2023 -0800
    Fixing script to have the current year for error logs and adding loop to get asiaNode 5 latest error logs, refs #30372
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    c5debff223dd6b551e14e045aa9f3f8b093b8ac0 Mon Feb 6 10:08:54 2023 -0800
    v444 preview1, refs #30497

• lines changed: 579
• files changed: 55