All File Changes

v414_preview2 to v414_base (2021-04-26 to 2021-05-03) v414

• install-hooks.sh
  • lines changed 7, context: html, text, full: html, text
    e0755a58af901c9a5f24b23f55a9780c5929c7b7 Thu Apr 29 02:05:28 2021 -0700
    adding pre-commit hook to help users find out that the file is too big before they commit, not after they push.
• pre-commit-prevent-large-files.sh
  • lines changed 47, context: html, text, full: html, text
    e0755a58af901c9a5f24b23f55a9780c5929c7b7 Thu Apr 29 02:05:28 2021 -0700
    adding pre-commit hook to help users find out that the file is too big before they commit, not after they push.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    7eef1a46688dd71170e83f6c6a5406cb9632ed35 Tue Apr 27 09:04:51 2021 -0700
    check for missing bigDataUrl setting in Snake tracks
  • lines changed 3, context: html, text, full: html, text
    423e2e498d9be057b15a342d1059b969ed303bad Tue Apr 27 17:54:55 2021 -0700
    Don't call halOpenLOD when bigDataUrl is NULL. This happens when hgTrackUi cfgHalSnake is called on a composite track in an assembly hub. It is not clear by this first check for isNameAtParentLevel does cause this function to skip the open. However, in previous versions of HAL, passing in a a NULL file name returned a file handle of -1. cfgHalSnake then continue to call HAL function s with -1, and they returned empty values. Amazing this ever worked
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    184d831562694d456477d60a8a4ccaf9eb5ef5b9 Tue Apr 27 09:19:02 2021 -0700
    change udctimeout text, refs #27460
• src/hg/htdocs/staff.html
  • lines changed 4, context: html, text, full: html, text
    d398a6bb06cf1f29afd803e47dae793102f6417a Mon Apr 26 16:30:43 2021 -0700
    squash merging old master branch changes to staff.html
• src/hg/htdocs/style/HGStyle.css
  • lines changed 5, context: html, text, full: html, text
    f5a2b354f78396b053aa31a78f7aa6fdd395c99a Tue Apr 27 06:10:50 2021 -0700
    making hgTracks warnings not destroy the page layout but look more like a normal dialog box. refs #27460
  • lines changed 2, context: html, text, full: html, text
    b70a6f4e7e5d17234be5fa3c2a9fafe721237baf Wed Apr 28 02:46:33 2021 -0700
    making warnbox a bit less wide, refs #27460
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    9f5beb3a14154081fa490588943fa4b7f4ab0662 Mon May 3 10:23:29 2021 -0700
    New version number v414
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    eab50a6724ab3744ac395aeb57cecdcddb4a24ed Tue Apr 27 14:19:39 2021 -0700
    adding GCA_002844635.1_USMARCv1.0 Sus scrofa per user request refs #27388
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
  • lines changed 2, context: html, text, full: html, text
    28d715eb50876f2554505716fbd18b41e4c37b66 Tue Apr 27 14:17:49 2021 -0700
    now with a genesGtf download file refs #27388
• src/hg/makeDb/doc/bosTau9/initialBuild.txt
  • lines changed 11, context: html, text, full: html, text
    9e1d18bbaeabc8922c4aba1baa71102a436d1cc2 Tue Apr 27 14:12:08 2021 -0700
    hive cleaning running cleanup step for crispr tracks no redmine
• src/hg/makeDb/doc/calJac4/initialBuild.txt
  • lines changed 10, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/doc/canFam4/initialBuild.txt
  • lines changed 9, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/doc/canFam5/initialBuild.txt
  • lines changed 7, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/doc/cotJap2/initialBuild.txt
  • lines changed 5, context: html, text, full: html, text
    9e1d18bbaeabc8922c4aba1baa71102a436d1cc2 Tue Apr 27 14:12:08 2021 -0700
    hive cleaning running cleanup step for crispr tracks no redmine
• src/hg/makeDb/doc/criGriChoV2/initialBuild.txt
  • lines changed 8, context: html, text, full: html, text
    9e1d18bbaeabc8922c4aba1baa71102a436d1cc2 Tue Apr 27 14:12:08 2021 -0700
    hive cleaning running cleanup step for crispr tracks no redmine
• src/hg/makeDb/doc/enhLutNer1/initialBuild.txt
  • lines changed 6, context: html, text, full: html, text
    9e1d18bbaeabc8922c4aba1baa71102a436d1cc2 Tue Apr 27 14:12:08 2021 -0700
    hive cleaning running cleanup step for crispr tracks no redmine
• src/hg/makeDb/doc/gorGor6/initialBuild.txt
  • lines changed 8, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/doc/hg19.txt
  • lines changed 6, context: html, text, full: html, text
    9e1d18bbaeabc8922c4aba1baa71102a436d1cc2 Tue Apr 27 14:12:08 2021 -0700
    hive cleaning running cleanup step for crispr tracks no redmine
  • lines changed 5, context: html, text, full: html, text
    045df4f1b6993a988ad9076cf9880d61aadf0a8f Wed Apr 28 02:51:37 2021 -0700
    makedoc fix for revel, #27142
• src/hg/makeDb/doc/hg38/cactus241way.txt
  • lines changed 65, context: html, text, full: html, text
    e941783cbc9cd3ec6af5f75b6969554fba9282e1 Thu Apr 29 23:05:28 2021 -0700
    adding frames procedure refs #11636
• src/hg/makeDb/doc/hg38/crispr.txt
  • lines changed 6, context: html, text, full: html, text
    0f52e6e2738f1a2a84e178d24e144efdeeb81a36 Tue Apr 27 14:14:21 2021 -0700
    running cleanup step on crispr tracks no redmine
• src/hg/makeDb/doc/hg38/crisprAll.txt
  • lines changed 7, context: html, text, full: html, text
    0f52e6e2738f1a2a84e178d24e144efdeeb81a36 Tue Apr 27 14:14:21 2021 -0700
    running cleanup step on crispr tracks no redmine
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 2, context: html, text, full: html, text
    d4d57b07f6ef7aea3f07012a1f13abf642579d29 Tue Apr 27 14:15:38 2021 -0700
    correct name on lastz work directory refs #27321
• src/hg/makeDb/doc/mm10.txt
  • lines changed 116, context: html, text, full: html, text
    80a6b42f5687642d83715afc58c46a095610c2dc Tue Apr 27 08:10:49 2021 -0700
    liftOver chainNet to GCF_900094665.1 per user request and cleaning hive of crispr results refs #27344
• src/hg/makeDb/doc/mm39/initialBuild.txt
  • lines changed 7, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/doc/mm39/lastzRuns.txt
  • lines changed 9, context: html, text, full: html, text
    44a2961414996cf4348b33a8c7daceacd3a3456e Tue Apr 27 14:50:55 2021 -0700
    completed lastz/chain/net to mm10 mm39 hg38 for rn7 release refs #26682
• src/hg/makeDb/doc/panPan3/initialBuild.txt
  • lines changed 7, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/doc/regenCho1/initialBuild.txt
  • lines changed 7, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/doc/regenRn1/initialBuild.txt
  • lines changed 7, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/doc/rn7/initialBuild.txt
  • lines changed 7, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/doc/rn7/lastzRuns.txt
  • lines changed 73, context: html, text, full: html, text
    f13110a42ef4ef8ef9953b31c797022aa7a4f2ff Wed Apr 28 11:47:54 2021 -0700
    beginning lastz chainNet runs for 45-way no redmine
• src/hg/makeDb/doc/staAur2/initialBuild.txt
  • lines changed 2, context: html, text, full: html, text
    e55f16028cef4f090371dafece16faf736596822 Mon Apr 26 14:53:09 2021 -0700
    fixup correct ports for blat server refs #26658
• src/hg/makeDb/doc/susScr11/lastzRuns.txt
  • lines changed 102, context: html, text, full: html, text
    835f3ad66aac1927fa501bad9511e56f62d706c4 Tue Apr 27 14:36:26 2021 -0700
    lastz chainNet run per user request refs #27388
• src/hg/makeDb/doc/transMapTracks.txt
  • lines changed 47, context: html, text, full: html, text
    098e7866ab59c5c6b0c4c77919350d637894d113 Wed Apr 28 00:38:42 2021 -0700
    transMap V6
• src/hg/makeDb/doc/wuhCor1/initialBuild.txt
  • lines changed 10, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/doc/xenTro10/initialBuild.txt
  • lines changed 6, context: html, text, full: html, text
    2e3edf11e977a5c3a12aa2e1fed9cbfa25ffe928 Mon Apr 26 15:02:21 2021 -0700
    cleaning up crisprAll working data about 326 Tb no redmine
• src/hg/makeDb/trackDb/drosophila/dm2/augustus.html
  • lines changed 1, context: html, text, full: html, text
    4820c9fbd52c3f5c670086a128eaa272bf0527ca Wed Apr 28 10:56:48 2021 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/bacEndPairs.html
  • lines changed 4, context: html, text, full: html, text
    4820c9fbd52c3f5c670086a128eaa272bf0527ca Wed Apr 28 10:56:48 2021 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/drosophila/dm2/picTar.html
  • lines changed 1, context: html, text, full: html, text
    4820c9fbd52c3f5c670086a128eaa272bf0527ca Wed Apr 28 10:56:48 2021 -0700
    Updating http to https for dm2, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 1, context: html, text, full: html, text
    3e199fc726891c23531debc08cbf365a271d30ef Tue Apr 27 11:38:02 2021 -0700
    Updating rn6 and rn7 chain/net default settings for other assemblies, refs #26682
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 1, context: html, text, full: html, text
    42491fb413e7e979a257865a901053d4bb4d00c4 Fri Apr 30 17:38:15 2021 -0700
    Cleaning up the hg38 and mm10 chain/net tracks refs #18071
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    dc121b5a9165050b75b4d6757a6265737876f135 Wed Apr 28 11:00:20 2021 -0700
    Adding pennantIcon for a news annoucnement, no Redmine.
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
  • lines changed 2, context: html, text, full: html, text
    099d84d6dc2220c2401bc5ff18bc026d8651fd37 Thu Apr 29 22:54:47 2021 -0700
    turn on frames view refs #11636
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
  • lines changed 18, context: html, text, full: html, text
    42491fb413e7e979a257865a901053d4bb4d00c4 Fri Apr 30 17:38:15 2021 -0700
    Cleaning up the hg38 and mm10 chain/net tracks refs #18071
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra
  • lines changed 2, context: html, text, full: html, text
    3e199fc726891c23531debc08cbf365a271d30ef Tue Apr 27 11:38:02 2021 -0700
    Updating rn6 and rn7 chain/net default settings for other assemblies, refs #26682
  • lines changed 17, context: html, text, full: html, text
    42491fb413e7e979a257865a901053d4bb4d00c4 Fri Apr 30 17:38:15 2021 -0700
    Cleaning up the hg38 and mm10 chain/net tracks refs #18071
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 6, context: html, text, full: html, text
    42491fb413e7e979a257865a901053d4bb4d00c4 Fri Apr 30 17:38:15 2021 -0700
    Cleaning up the hg38 and mm10 chain/net tracks refs #18071
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 17, context: html, text, full: html, text
    42491fb413e7e979a257865a901053d4bb4d00c4 Fri Apr 30 17:38:15 2021 -0700
    Cleaning up the hg38 and mm10 chain/net tracks refs #18071
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.chainNet.ra
  • lines changed 4, context: html, text, full: html, text
    3e199fc726891c23531debc08cbf365a271d30ef Tue Apr 27 11:38:02 2021 -0700
    Updating rn6 and rn7 chain/net default settings for other assemblies, refs #26682
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 2, context: html, text, full: html, text
    7a5bfc29ad23e75f1c2e7de49cab1de76af5cce0 Fri Apr 30 16:21:46 2021 -0700
    Making the descriptions for related tracks to make sure they are different, refs #25721
• src/hg/makeDb/trackDb/trackDb.transMap.ra
  • lines changed 135, context: html, text, full: html, text
    098e7866ab59c5c6b0c4c77919350d637894d113 Wed Apr 28 00:38:42 2021 -0700
    transMap V6
• src/hg/makeDb/trackDb/transMapV6.html
  • lines changed 25, context: html, text, full: html, text
    098e7866ab59c5c6b0c4c77919350d637894d113 Wed Apr 28 00:38:42 2021 -0700
    transMap V6
• src/hg/makeDb/trackDb/virus/wuhCor1/vaccines.ra
  • lines changed 1, context: html, text, full: html, text
    a6a3661b7418c7c908826e44e5d94e42dea079e4 Wed Apr 28 11:01:40 2021 -0700
    Changing the default base color for the vaccines track, refs #27312
• src/hg/mouseStuff/chainScore/chainScore.c
  • lines changed 30, context: html, text, full: html, text
    bd464ac7d3b30ad611826fb73c6f26ddaba52fce Thu May 17 13:12:51 2018 -0700
    Modernization: fixed compiler warnings; use 2bit instead of nib, verbose instead of uglyf. Added missing optionSpecs. This appears to be using old copied code and should use the lib function chainCalcScore instead; thanks Galt for finding that I left these changes off in a branch in 2018!
  • lines changed 12, context: html, text, full: html, text
    4ea2d7c77204dff2cae4a4218de8f37c2162154d Mon Apr 26 16:08:50 2021 -0700
    fixing compiler complaints on chainScore
  • lines changed 282, context: html, text, full: html, text
    517eb6200c1b9aa830f9d018b193ce47feb4c2a0 Tue Apr 27 16:45:08 2021 -0700
    Some revamping of chainScore to handle compiler errors and to refactor to use existing library functions. No redmine.
• src/hg/mouseStuff/chainScore/makefile
  • lines changed 14, context: html, text, full: html, text
    b9232de5fd4b6b86b6478c4631462450d8c74b84 Wed Apr 28 12:14:32 2021 -0700
    chainScore makefile was old and needed updating
• src/hg/mouseStuff/makefile
  • lines changed 1, context: html, text, full: html, text
    517eb6200c1b9aa830f9d018b193ce47feb4c2a0 Tue Apr 27 16:45:08 2021 -0700
    Some revamping of chainScore to handle compiler errors and to refactor to use existing library functions. No redmine.
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 2, context: html, text, full: html, text
    67834b02649fc82ec728bd72a50309d87128007d Fri Apr 30 21:41:59 2021 -0700
    correct featureBits result file name refs #26682
• src/hg/utils/automation/pairLastz.sh
  • lines changed 434, context: html, text, full: html, text
    6348b62549ccdad39b50fb4fd493d593b44ab31d Fri Apr 30 13:41:29 2021 -0700
    a supervisor script to the doBlastzChainNet script to run everything refs #26682
  • lines changed 19, context: html, text, full: html, text
    67834b02649fc82ec728bd72a50309d87128007d Fri Apr 30 21:41:59 2021 -0700
    correct featureBits result file name refs #26682
  • lines changed 1, context: html, text, full: html, text
    c4e2ae3a2c37b244143589fbeda66de7e52f4ad7 Fri Apr 30 21:43:40 2021 -0700
    correct usage message refs #26682
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 8, context: html, text, full: html, text
    8446663b24ef2f8db0695d970f7c6b4a03a9949f Mon Apr 26 15:33:26 2021 -0700
    Use matUtils annotate new options -m and -D to get mutations and details files.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    9f5beb3a14154081fa490588943fa4b7f4ab0662 Mon May 3 10:23:29 2021 -0700
    New version number v414
• src/lib/htmshell.c
  • lines changed 1, context: html, text, full: html, text
    b70a6f4e7e5d17234be5fa3c2a9fafe721237baf Wed Apr 28 02:46:33 2021 -0700
    making warnbox a bit less wide, refs #27460
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    03fc3b991f682c9170969e9f64cde00d9fbfa445 Mon May 3 10:18:55 2021 -0700
    v414 final build, refs #27418

• lines changed: 1676
• files changed: 68