All File Changes

v417_base to v418_preview (2021-07-05 to 2021-07-12) v418

• src/hg/hgBlat/hgBlat.c
  • lines changed 1, context: html, text, full: html, text
    f02bb3ce9489bb2c922188ebf94f52a0e80dd757 Mon Jul 5 10:45:34 2021 -0700
    change system() calls to pipeline() calls.
• src/hg/hgGene/rnaStructure.c
  • lines changed 13, context: html, text, full: html, text
    f02bb3ce9489bb2c922188ebf94f52a0e80dd757 Mon Jul 5 10:45:34 2021 -0700
    change system() calls to pipeline() calls.
  • lines changed 5, context: html, text, full: html, text
    4627c107f20b2ff3969114bcb619a0d02c0258a6 Fri Jul 9 12:58:00 2021 -0700
    replace a couple of calls to popen() with pipeline()
• src/hg/hgMirror/hgMirror
  • lines changed 2, context: html, text, full: html, text
    1a57630bdc45465db3b21ba99d8537d027ced0c9 Thu Jul 8 07:45:02 2021 -0700
    fixing GBIB problem due to cartVerstrion string, refs #27752
• src/hg/hgSession/backup.c
  • lines changed 12, context: html, text, full: html, text
    f02bb3ce9489bb2c922188ebf94f52a0e80dd757 Mon Jul 5 10:45:34 2021 -0700
    change system() calls to pipeline() calls.
• src/hg/hgSession/hgSession.c
  • lines changed 4, context: html, text, full: html, text
    f02bb3ce9489bb2c922188ebf94f52a0e80dd757 Mon Jul 5 10:45:34 2021 -0700
    change system() calls to pipeline() calls.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    d261f558e0a577ee269fe55215505668cdcb6f2a Wed Jul 7 07:09:11 2021 -0700
    Address several cases of possible uninitialized variables detected by -O3. None of these appear to be actually bugs due to the flow of the code
• src/hg/hgc/barChartClick.c
  • lines changed 6, context: html, text, full: html, text
    f02bb3ce9489bb2c922188ebf94f52a0e80dd757 Mon Jul 5 10:45:34 2021 -0700
    change system() calls to pipeline() calls.
• src/hg/hgc/hgc.c
  • lines changed 15, context: html, text, full: html, text
    f02bb3ce9489bb2c922188ebf94f52a0e80dd757 Mon Jul 5 10:45:34 2021 -0700
    change system() calls to pipeline() calls.
  • lines changed 3, context: html, text, full: html, text
    d261f558e0a577ee269fe55215505668cdcb6f2a Wed Jul 7 07:09:11 2021 -0700
    Address several cases of possible uninitialized variables detected by -O3. None of these appear to be actually bugs due to the flow of the code
• src/hg/hgc/rnaFoldClick.c
  • lines changed 9, context: html, text, full: html, text
    f02bb3ce9489bb2c922188ebf94f52a0e80dd757 Mon Jul 5 10:45:34 2021 -0700
    change system() calls to pipeline() calls.
  • lines changed 5, context: html, text, full: html, text
    4627c107f20b2ff3969114bcb619a0d02c0258a6 Fri Jul 9 12:58:00 2021 -0700
    replace a couple of calls to popen() with pipeline()
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 10, context: html, text, full: html, text
    566120e312927545a0dec54c6eb60a784ed996b7 Wed Jul 7 10:05:47 2021 -0700
    Adding a note about mean-whiskers on trackDbLibrary from MLQ input refs #27753
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 3, context: html, text, full: html, text
    d92fae77c81b3969405c288413a30f675ec324c3 Wed Jul 7 09:54:40 2021 -0700
    Adding a note about altColor on the wiggle.html page from MLQ input refs #27753
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 27, context: html, text, full: html, text
    5d40467bf390d16723a66826243f711a5cb739f7 Thu Jul 8 14:44:40 2021 -0700
    Updating news for the hg38 ncbiRefSeq track update, refs #27552
  • lines changed 0, context: html, text, full: html, text
    c517ad5ee34291fd8ea4c7543bdd4762f7a56bb2 Thu Jul 8 14:55:42 2021 -0700
    Editing newsarch.html due to a missing space between period and character, refs #27552
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    5d40467bf390d16723a66826243f711a5cb739f7 Thu Jul 8 14:44:40 2021 -0700
    Updating news for the hg38 ncbiRefSeq track update, refs #27552
• src/hg/htdocs/license/index.html
  • lines changed 10, context: html, text, full: html, text
    25d1694a23073ae287b10376078a5e4888b49ea7 Tue Jul 6 12:52:18 2021 -0700
    small wording change. dropped a space from email address
• src/hg/htdocs/training/index.html
  • lines changed 22, context: html, text, full: html, text
    781c5b23930a2812568f69db962eb74193c1b928 Tue Jul 6 15:38:02 2021 -0700
    updating workshop schedule
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    09204bd4ac9403130d60c4dbf80a64cf360c6315 Wed Jul 7 12:55:36 2021 -0700
    adding VETC workshop
• src/hg/js/utils.js
  • lines changed 24, context: html, text, full: html, text
    58bdb6ef0be1f4f9f45157aa3b2c544ca1a92e57 Tue Jul 6 05:33:19 2021 -0700
    adding button click tracking to hgTracks, refs #27283
• src/hg/lib/googleAnalytics.c
  • lines changed 7, context: html, text, full: html, text
    58bdb6ef0be1f4f9f45157aa3b2c544ca1a92e57 Tue Jul 6 05:33:19 2021 -0700
    adding button click tracking to hgTracks, refs #27283
• src/hg/lib/gtexBoxplot.c
  • lines changed 7, context: html, text, full: html, text
    f02bb3ce9489bb2c922188ebf94f52a0e80dd757 Mon Jul 5 10:45:34 2021 -0700
    change system() calls to pipeline() calls.
• src/hg/lib/hubConnect.c
  • lines changed 16, context: html, text, full: html, text
    bbb7c4d70c083dc0285248a946892a5182da5e9f Thu Jul 8 13:04:25 2021 -0700
    use mysql advisory locks to avoid duplication of hubUrl in hubStatus
  • lines changed 1, context: html, text, full: html, text
    b85c7945f14c858bdd855fbdf2c5a55361052f28 Thu Jul 8 13:10:16 2021 -0700
    fix up misleading comment
• src/hg/lib/qaSeq.c
  • lines changed 2, context: html, text, full: html, text
    d261f558e0a577ee269fe55215505668cdcb6f2a Wed Jul 7 07:09:11 2021 -0700
    Address several cases of possible uninitialized variables detected by -O3. None of these appear to be actually bugs due to the flow of the code
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    ce206137add4e9417334363faeef58be09363972 Tue Jul 6 11:12:13 2021 -0700
    Native track 'url' settings should not get early expanded, refs #27752 and #27767
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 2, context: html, text, full: html, text
    4107737d94aaba086feffab7fa22ea7efd918d56 Tue Jul 6 12:38:07 2021 -0700
    now delivering GTF files for gene tracks in buildDir/genes/ refs #27512
• src/hg/makeDb/doc/hg19.txt
  • lines changed 1, context: html, text, full: html, text
    f2a0929905445624aa6ed01cbe74e0104876eb08 Tue Jul 6 13:54:31 2021 -0700
    Code review edits to hg19 makefile, updated name, refs #27805
• src/hg/makeDb/trackDb/dbSnpArchive.html
  • lines changed 15, context: html, text, full: html, text
    09a80236f1b65c47bb2887a2463986f152d2b191 Tue Jul 6 13:54:28 2021 -0700
    Code review changes to Data Access and longLabel refs #27802
• src/hg/makeDb/trackDb/human/hg19/dbSnpArchiveHg19.ra
  • lines changed 1, context: html, text, full: html, text
    09a80236f1b65c47bb2887a2463986f152d2b191 Tue Jul 6 13:54:28 2021 -0700
    Code review changes to Data Access and longLabel refs #27802
• src/hg/makeDb/trackDb/human/hg38/dbSnpArchiveHg38.ra
  • lines changed 1, context: html, text, full: html, text
    09a80236f1b65c47bb2887a2463986f152d2b191 Tue Jul 6 13:54:28 2021 -0700
    Code review changes to Data Access and longLabel refs #27802
• src/hg/makeDb/trackDb/mouse/mm10/dbSnpArchiveMm10.ra
  • lines changed 1, context: html, text, full: html, text
    09a80236f1b65c47bb2887a2463986f152d2b191 Tue Jul 6 13:54:28 2021 -0700
    Code review changes to Data Access and longLabel refs #27802
• src/hg/makeDb/trackDb/mouse/mm10/description.html
  • lines changed 1, context: html, text, full: html, text
    c089b265ce0161c75b39f142bf407155f3e2dc31 Wed Jul 7 11:15:21 2021 -0700
    Changing wording "native" since meaning was not completely clear.
  • lines changed 14, context: html, text, full: html, text
    830b8d7f5182b7280ea07ef78df5b46cd1ee77a7 Wed Jul 7 11:23:35 2021 -0700
    Removing SQL command.
• src/hg/makeDb/trackDb/mouse/mm10/mm10Patch4.html
  • lines changed 652, context: html, text, full: html, text
    8de20827acd9ec78000adf56f604eacf2ed08160 Fri Jul 9 11:38:00 2021 -0700
    Removing old patching approach for mm10, these are not needed anymore with Angie's new patching approach
• src/hg/makeDb/trackDb/mouse/mm10/mm10Patch4.ra
  • lines changed 118, context: html, text, full: html, text
    8de20827acd9ec78000adf56f604eacf2ed08160 Fri Jul 9 11:38:00 2021 -0700
    Removing old patching approach for mm10, these are not needed anymore with Angie's new patching approach
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    88b886211cae937bfd8ddb600c43a4d5b7c9bc3c Fri Jul 9 12:26:43 2021 -0700
    more cleanup mm10Patch4 obsolete
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 57, context: html, text, full: html, text
    6ac74bb165759e57dc5cf57cd3eba54eaebc4a36 Mon Jul 5 13:28:45 2021 -0700
    adding zebrafish/T5D/GCA_018400075.1_ASM1840007v1 chainNets refs #27512
• src/hg/makeDb/trackDb/xenTro/xenTro10/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    c8457255c44aa0748ab27150d8d9dfe1c1ece404 Fri Jul 9 20:13:44 2021 -0700
    Added mm39 getChainLines.csh output to match the description page, refs #24693
• src/hg/utils/automation/asmHubChainNetTrackDb.pl
  • lines changed 124, context: html, text, full: html, text
    2ce16411b0f909e7e1dfd27a01af34316c260f2f Mon Jul 5 11:58:27 2021 -0700
    catching up the edge cases for pair wise alignment to assembly hub genome no redmine
  • lines changed 96, context: html, text, full: html, text
    d17fec88b0ca3f013cd98a01bd65a928ddb349e9 Mon Jul 5 13:07:20 2021 -0700
    now with syntenic and reciprocal best no redmine
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 5, context: html, text, full: html, text
    2ce16411b0f909e7e1dfd27a01af34316c260f2f Mon Jul 5 11:58:27 2021 -0700
    catching up the edge cases for pair wise alignment to assembly hub genome no redmine
  • lines changed 6, context: html, text, full: html, text
    2b42d05e58a971f49afdd6d52c2ad415e165add0 Tue Jul 6 12:37:28 2021 -0700
    create a GTF file for the xenoRefGene result refs #27512
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 30, context: html, text, full: html, text
    2ce16411b0f909e7e1dfd27a01af34316c260f2f Mon Jul 5 11:58:27 2021 -0700
    catching up the edge cases for pair wise alignment to assembly hub genome no redmine
• src/hg/utils/automation/doXenoRefGene.pl
  • lines changed 36, context: html, text, full: html, text
    2b42d05e58a971f49afdd6d52c2ad415e165add0 Tue Jul 6 12:37:28 2021 -0700
    create a GTF file for the xenoRefGene result refs #27512
• src/hg/utils/automation/pairLastz.sh
  • lines changed 52, context: html, text, full: html, text
    2ce16411b0f909e7e1dfd27a01af34316c260f2f Mon Jul 5 11:58:27 2021 -0700
    catching up the edge cases for pair wise alignment to assembly hub genome no redmine
• src/jkOwnLib/supStitch.c
  • lines changed 2, context: html, text, full: html, text
    d261f558e0a577ee269fe55215505668cdcb6f2a Wed Jul 7 07:09:11 2021 -0700
    Address several cases of possible uninitialized variables detected by -O3. None of these appear to be actually bugs due to the flow of the code
• src/jkOwnLib/trans3.c
  • lines changed 1, context: html, text, full: html, text
    d261f558e0a577ee269fe55215505668cdcb6f2a Wed Jul 7 07:09:11 2021 -0700
    Address several cases of possible uninitialized variables detected by -O3. None of these appear to be actually bugs due to the flow of the code
• src/lib/diGraph.c
  • lines changed 1, context: html, text, full: html, text
    d261f558e0a577ee269fe55215505668cdcb6f2a Wed Jul 7 07:09:11 2021 -0700
    Address several cases of possible uninitialized variables detected by -O3. None of these appear to be actually bugs due to the flow of the code
• src/lib/dnaMotif.c
  • lines changed 35, context: html, text, full: html, text
    f02bb3ce9489bb2c922188ebf94f52a0e80dd757 Mon Jul 5 10:45:34 2021 -0700
    change system() calls to pipeline() calls.
• src/lib/fof.c
  • lines changed 4, context: html, text, full: html, text
    d261f558e0a577ee269fe55215505668cdcb6f2a Wed Jul 7 07:09:11 2021 -0700
    Address several cases of possible uninitialized variables detected by -O3. None of these appear to be actually bugs due to the flow of the code
• src/lib/obscure.c
  • lines changed 1, context: html, text, full: html, text
    d261f558e0a577ee269fe55215505668cdcb6f2a Wed Jul 7 07:09:11 2021 -0700
    Address several cases of possible uninitialized variables detected by -O3. None of these appear to be actually bugs due to the flow of the code
• src/lib/psGfx.c
  • lines changed 8, context: html, text, full: html, text
    f02bb3ce9489bb2c922188ebf94f52a0e80dd757 Mon Jul 5 10:45:34 2021 -0700
    change system() calls to pipeline() calls.
• src/product/installer/browserSetup.sh
  • lines changed 27, context: html, text, full: html, text
    00bd6030314d75c6fa7f81fd2434ee16cfd04943 Wed Jul 7 07:16:16 2021 -0700
    fixing gbic script output random error messages on startup by changing the entire error handling, refs #27795
  • lines changed 12, context: html, text, full: html, text
    94c916b927fe45291b61abe001b84a6be523a722 Wed Jul 7 07:42:33 2021 -0700
    breaking compatibility with ubuntu 14 again in gbic, but ubuntu 14 reaches it EOL in early 2022 and it does not seem possible to set passwords in a way that is compatible from mysql 5.6 up to mysql 8, refs #27795
• src/utils/browserRace
  • lines changed 88, context: html, text, full: html, text
    21a2ab63c1bfcd52087819669fb0cf615babe4f4 Fri Jul 9 01:07:19 2021 -0700
    adding little tool to compare browser timings, email thread with Braney, Mark, Hiram, Chris
• src/utils/hubPublicMail
  • lines changed 248, context: html, text, full: html, text
    d27aaec7fbbb9538cc65fdee35f7647d49246b50 Tue Jul 6 12:51:33 2021 +0200
    Wrote hubPublicMail monitor as requested by QA, refs #27779
• src/utils/makefile
  • lines changed 2, context: html, text, full: html, text
    d27aaec7fbbb9538cc65fdee35f7647d49246b50 Tue Jul 6 12:51:33 2021 +0200
    Wrote hubPublicMail monitor as requested by QA, refs #27779
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    feb78b2e26c14514a9c5b6957fafd27fecc0b4b2 Tue Jul 6 12:12:44 2021 -0400
    removed stray space that breaks makefile
  • lines changed 3, context: html, text, full: html, text
    ad5fb93ce662c0bd2ce1279eac38c26d5086cfd7 Tue Jul 6 11:12:34 2021 -0700
    tmp disable hubPublicMail until rules figured out
  • lines changed 4, context: html, text, full: html, text
    21a2ab63c1bfcd52087819669fb0cf615babe4f4 Fri Jul 9 01:07:19 2021 -0700
    adding little tool to compare browser timings, email thread with Braney, Mark, Hiram, Chris
  • lines changed 7, context: html, text, full: html, text
    d2048cbe73d85979b6975c2890c2dbc6342b6e3c Fri Jul 9 11:41:38 2021 -0700
    Moving hubPublicMail and browserRace utilities to the script section of the utils/makefile so make works
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    1c508af23b4d9f1f0156d2ffdf818bfd66e3c664 Mon Jul 12 10:13:26 2021 -0700
    v418 preview1, refs #27752

• lines changed: 1888
• files changed: 64