All File Changes

v383_preview2 to v383_base (2019-06-03 to 2019-06-10) v383

• confs/asia.hg.conf
  • lines changed 125, context: html, text, full: html, text
    92455293e28fff7df1afa1d925cdcb06fe5ebecb Sun Jun 9 01:11:37 2019 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta-public.hg.conf
  • lines changed 16, context: html, text, full: html, text
    92455293e28fff7df1afa1d925cdcb06fe5ebecb Sun Jun 9 01:11:37 2019 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgCollection/hgCollection.c
  • lines changed 4, context: html, text, full: html, text
    620af6412b4ca31db9608d127ec4b25c3445955a Mon Jun 3 17:28:38 2019 -0700
    don't crash if a track specifies a group that doesn't exist in hgCollection
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 25, context: html, text, full: html, text
    90782cab70bd2f2ee992b0a7f95b656c56fdbba1 Mon Jun 3 15:34:47 2019 -0700
    order public hubs by shortLabel
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 2, context: html, text, full: html, text
    b4b423e05131bd61d735915f088f066a8b950f1c Wed Jun 5 17:21:58 2019 -0700
    Adding CHO to release list #20540
• src/hg/htdocs/browserAgreement.html
  • lines changed 98, context: html, text, full: html, text
    1c1e57e11e060937653c32bed082331dcaa93107 Tue Jun 4 14:17:57 2019 -0700
    3-way browser genome release agreement
  • lines changed 7, context: html, text, full: html, text
    e107868e195088405fd83fa63173ecc25e4b05b2 Tue Jun 4 14:47:03 2019 -0700
    a few small changes
  • lines changed 10, context: html, text, full: html, text
    c83b36e5a03e866c7aafa7ffedd10a229640eef1 Wed Jun 5 06:51:38 2019 -0700
    removed some british-isms - amongst - and a few small grammar tweaks
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 5, context: html, text, full: html, text
    60e5a619892b6fd6329440071cc052a7950cc687 Wed Jun 5 17:17:47 2019 -0700
    Adding Cho to the credits page #20540
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 37, context: html, text, full: html, text
    79dec56e5e70c985527f73c0a292c70025609ee0 Wed Jun 5 16:57:31 2019 -0700
    Adding CHO release info #20540
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    95c2e36d2311f3cd0d188ff0641066778b3a9fd8 Wed Jun 5 17:05:14 2019 -0700
    Adding CHO announcement link #20540
• src/hg/inc/hui.h
  • lines changed 27, context: html, text, full: html, text
    06620d160679a0d2e77dedbe35b35edeea08c517 Mon Jun 3 16:17:48 2019 -0700
    Add checks to hubCheck and hgTrackUi for incorrect tag=val pairs in a subgroup line, refs #13428
• src/hg/inc/trackDb.h
  • lines changed 3, context: html, text, full: html, text
    8cc7dee111a52eed9f6e65a01e67730af13b43b4 Thu Jun 6 15:30:22 2019 -0700
    ongoing work on trackDb caching in shared memory
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    c81af79a92834c5685f102b581fe54986dc337ce Mon Jun 10 10:19:47 2019 -0700
    New version number v383
• src/hg/lib/hdb.c
  • lines changed 20, context: html, text, full: html, text
    8cc7dee111a52eed9f6e65a01e67730af13b43b4 Thu Jun 6 15:30:22 2019 -0700
    ongoing work on trackDb caching in shared memory
• src/hg/lib/hubConnect.c
  • lines changed 2, context: html, text, full: html, text
    06620d160679a0d2e77dedbe35b35edeea08c517 Mon Jun 3 16:17:48 2019 -0700
    Add checks to hubCheck and hgTrackUi for incorrect tag=val pairs in a subgroup line, refs #13428
• src/hg/lib/hui.c
  • lines changed 27, context: html, text, full: html, text
    06620d160679a0d2e77dedbe35b35edeea08c517 Mon Jun 3 16:17:48 2019 -0700
    Add checks to hubCheck and hgTrackUi for incorrect tag=val pairs in a subgroup line, refs #13428
  • lines changed 3, context: html, text, full: html, text
    c76af8b5689d4ea3b2c50448d607cc3aa84cbf9a Fri Jun 7 14:13:52 2019 -0700
    Fixing a few spots where I forgot to check for null subgroups earlier, refs #23556
• src/hg/lib/trackDbCustom.c
  • lines changed 70, context: html, text, full: html, text
    8cc7dee111a52eed9f6e65a01e67730af13b43b4 Thu Jun 6 15:30:22 2019 -0700
    ongoing work on trackDb caching in shared memory
• src/hg/lib/trackHub.c
  • lines changed 1, context: html, text, full: html, text
    8933db12a9efed4981ada1fcc16e51a364147b0a Tue Jun 4 16:57:53 2019 -0700
    look for BAM index by just adding .bai to the end of the bam file, and if that does NOT work , try replacing the old suffix (presumably .bam) with .bai and try that. Also, we weren't adding the whole URL to bigDataIndex in hubs, so now we do.
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    3c53a67c75ff46566000137b4eb6dba7d1695b41 Thu Jun 6 09:05:40 2019 -0700
    added bisBis1 to hgwbeta.dbs and rr.dbs
• src/hg/makeDb/genbank/etc/rr.dbs
  • lines changed 1, context: html, text, full: html, text
    3c53a67c75ff46566000137b4eb6dba7d1695b41 Thu Jun 6 09:05:40 2019 -0700
    added bisBis1 to hgwbeta.dbs and rr.dbs
• src/hg/makeDb/hgLoadWiggle/makefile
  • lines changed 7, context: html, text, full: html, text
    7466895f92735f9a050b7080214195124b37e226 Wed Jun 5 17:32:18 2019 -0700
    add fixStepToBedGraph.pl and varStepToBedGraph.pl to build so they'll appear in userApps
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 3, context: html, text, full: html, text
    30f494c73af50b7879c6925c66c6c015fa217238 Wed Jun 5 10:11:06 2019 -0700
    Updating http to https for panTro3, uiLinks cronjob.
• src/hg/makeDb/trackDb/criGri/criGriChoV2/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    94b9335e46376b3c81b13638d965572fc639cabc Tue Jun 4 09:38:36 2019 -0700
    Changing ensembl linkout URL and modifying tracks #23540
• src/hg/makeDb/trackDb/human/encRegTfbsClustered.html
  • lines changed 1, context: html, text, full: html, text
    5cfc2f6577687733dcfc56c3f745e7799d200998 Tue Jun 4 15:59:41 2019 -0700
    Editing hg38 link on the encRegTfbsClustered.html page, refs #21139
• src/hg/makeDb/trackDb/human/encTfChipPk.html
  • lines changed 1, context: html, text, full: html, text
    3c4e6f0fa521b6534c5892e5db61b76eeca9b40a Tue Jun 4 15:50:55 2019 -0700
    Fixing link to hg38's Transcription Factor ChIP-seq Clusters tracks, refs #23243
• src/hg/makeDb/trackDb/human/hg19/mastermind.html
  • lines changed 87, context: html, text, full: html, text
    f5a6fb3df981f5ec1a2df4bed019b426bb25341f Fri Jun 7 02:27:58 2019 -0700
    preparing mastermind hg38 track and ottomatization by moving trackDb statements up one level. No redmine yet, as this is merely a move of existing information, not yet any change.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 24, context: html, text, full: html, text
    f5a6fb3df981f5ec1a2df4bed019b426bb25341f Fri Jun 7 02:27:58 2019 -0700
    preparing mastermind hg38 track and ottomatization by moving trackDb statements up one level. No redmine yet, as this is merely a move of existing information, not yet any change.
• src/hg/makeDb/trackDb/human/hg19/varsInPubs.html
  • lines changed 15, context: html, text, full: html, text
    f5a6fb3df981f5ec1a2df4bed019b426bb25341f Fri Jun 7 02:27:58 2019 -0700
    preparing mastermind hg38 track and ottomatization by moving trackDb statements up one level. No redmine yet, as this is merely a move of existing information, not yet any change.
• src/hg/makeDb/trackDb/human/mastermind.html
  • lines changed 87, context: html, text, full: html, text
    f5a6fb3df981f5ec1a2df4bed019b426bb25341f Fri Jun 7 02:27:58 2019 -0700
    preparing mastermind hg38 track and ottomatization by moving trackDb statements up one level. No redmine yet, as this is merely a move of existing information, not yet any change.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 25, context: html, text, full: html, text
    f5a6fb3df981f5ec1a2df4bed019b426bb25341f Fri Jun 7 02:27:58 2019 -0700
    preparing mastermind hg38 track and ottomatization by moving trackDb statements up one level. No redmine yet, as this is merely a move of existing information, not yet any change.
• src/hg/makeDb/trackDb/human/varsInPubs.html
  • lines changed 15, context: html, text, full: html, text
    f5a6fb3df981f5ec1a2df4bed019b426bb25341f Fri Jun 7 02:27:58 2019 -0700
    preparing mastermind hg38 track and ottomatization by moving trackDb statements up one level. No redmine yet, as this is merely a move of existing information, not yet any change.
• src/hg/makeDb/trackDb/xenTro/xenTro9/cons11way.html
  • lines changed 2, context: html, text, full: html, text
    5ad92bd8516d21a5fdada442ff93eb75f3e31256 Mon Jun 10 09:37:59 2019 -0700
    Updating redirected links for xenTro9 found by the uiLinks cronjob, no Redmine.
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 45, context: html, text, full: html, text
    06620d160679a0d2e77dedbe35b35edeea08c517 Mon Jun 3 16:17:48 2019 -0700
    Add checks to hubCheck and hgTrackUi for incorrect tag=val pairs in a subgroup line, refs #13428
• src/hg/utils/otto/omim/checkOmimUpload.sh
  • lines changed 1, context: html, text, full: html, text
    47f99864fd3008d6343aeab050b4a5a261d90700 Tue Jun 4 09:49:49 2019 -0700
    Updating mysqlbeta to hgwbeta in omim cronjob, no refs
• src/inc/localmem.h
  • lines changed 6, context: html, text, full: html, text
    8cc7dee111a52eed9f6e65a01e67730af13b43b4 Thu Jun 6 15:30:22 2019 -0700
    ongoing work on trackDb caching in shared memory
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    c81af79a92834c5685f102b581fe54986dc337ce Mon Jun 10 10:19:47 2019 -0700
    New version number v383
• src/lib/bamFile.c
  • lines changed 18, context: html, text, full: html, text
    8933db12a9efed4981ada1fcc16e51a364147b0a Tue Jun 4 16:57:53 2019 -0700
    look for BAM index by just adding .bai to the end of the bam file, and if that does NOT work , try replacing the old suffix (presumably .bam) with .bai and try that. Also, we weren't adding the whole URL to bigDataIndex in hubs, so now we do.
• src/lib/basicBed.c
  • lines changed 1, context: html, text, full: html, text
    05664e5f0416e06ee981821f7cc26f16ff1a5138 Fri Jun 7 02:29:45 2019 -0700
    small improvement to BED parser error message, no redmine
• src/lib/localmem.c
  • lines changed 18, context: html, text, full: html, text
    8cc7dee111a52eed9f6e65a01e67730af13b43b4 Thu Jun 6 15:30:22 2019 -0700
    ongoing work on trackDb caching in shared memory
• src/oneShot/chrisCrawl/chrisCrawl.c
  • lines changed 386, context: html, text, full: html, text
    532835069d106de1a41a4a525a8d9c3023e815ae Thu Jun 6 16:07:57 2019 -0700
    Adding small program to kind of clean up an error log and get a list of functions implicated in stack dumps
• src/oneShot/chrisCrawl/makefile
  • lines changed 3, context: html, text, full: html, text
    532835069d106de1a41a4a525a8d9c3023e815ae Thu Jun 6 16:07:57 2019 -0700
    Adding small program to kind of clean up an error log and get a list of functions implicated in stack dumps
• src/utils/qa/bigPush.sh
  • lines changed 4, context: html, text, full: html, text
    91cecec4e65aa52dfa528d17a1fba9e1b7672381 Tue Jun 4 13:41:15 2019 -0700
    Updating scripts to point to new beta machine #23616
• src/utils/qa/checkGbdbDiffs.csh
  • lines changed 1, context: html, text, full: html, text
    e71fc9753db2aa4e17edd269c0145449814dc93c Tue Jun 4 09:38:10 2019 -0700
    Adding a slash to a find command in /gbdb/ that was impacted by new hgwbeta.
• src/utils/qa/copyHgcentral
  • lines changed 6, context: html, text, full: html, text
    91cecec4e65aa52dfa528d17a1fba9e1b7672381 Tue Jun 4 13:41:15 2019 -0700
    Updating scripts to point to new beta machine #23616
• src/utils/qa/knownGene.csh
  • lines changed 1, context: html, text, full: html, text
    91cecec4e65aa52dfa528d17a1fba9e1b7672381 Tue Jun 4 13:41:15 2019 -0700
    Updating scripts to point to new beta machine #23616
• src/utils/qa/qaConfig.bash
  • lines changed 1, context: html, text, full: html, text
    f787d70c11574d33f56d2e1020dce2d100487b34 Mon Jun 3 13:13:34 2019 -0700
    Updating the name of the MariaDb host to the new 'hgwbeta' host for our QA shell scripts, no Redmine. (hgwbeta upgrade)
• src/utils/qa/qaConfig.csh
  • lines changed 1, context: html, text, full: html, text
    f787d70c11574d33f56d2e1020dce2d100487b34 Mon Jun 3 13:13:34 2019 -0700
    Updating the name of the MariaDb host to the new 'hgwbeta' host for our QA shell scripts, no Redmine. (hgwbeta upgrade)
• src/utils/qa/showTracks
  • lines changed 13, context: html, text, full: html, text
    91cecec4e65aa52dfa528d17a1fba9e1b7672381 Tue Jun 4 13:41:15 2019 -0700
    Updating scripts to point to new beta machine #23616
• src/utils/qa/updateTimesDb.sh
  • lines changed 4, context: html, text, full: html, text
    91cecec4e65aa52dfa528d17a1fba9e1b7672381 Tue Jun 4 13:41:15 2019 -0700
    Updating scripts to point to new beta machine #23616
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    2f0a5a11d50fa30e21f2229604096659e912e2a3 Mon Jun 10 10:18:07 2019 -0700
    v383 final build, refs #23583

• lines changed: 1283
• files changed: 52