All File Changes

v396_preview2 to v396_base (2020-03-23 to 2020-03-30) v396

• src/hg/cirm/gateway/htdocs/projects.html
  • lines changed 25, context: html, text, full: html, text
    9c21eb26b1ae190c7321be5f2f84b5ccb57f6482 Fri Mar 27 16:56:00 2020 -0700
    Add pyleSkeletalMuscle to project page and update tools page with NSFForest
  • lines changed 9, context: html, text, full: html, text
    72235220d5005556903abf2959870ff5d9d66781 Sun Mar 29 19:51:36 2020 -0700
    Update to NFS forest card box and pyle project page
• src/hg/cirm/gateway/htdocs/tools.html
  • lines changed 31, context: html, text, full: html, text
    9c21eb26b1ae190c7321be5f2f84b5ccb57f6482 Fri Mar 27 16:56:00 2020 -0700
    Add pyleSkeletalMuscle to project page and update tools page with NSFForest
  • lines changed 2, context: html, text, full: html, text
    72235220d5005556903abf2959870ff5d9d66781 Sun Mar 29 19:51:36 2020 -0700
    Update to NFS forest card box and pyle project page
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 3, context: html, text, full: html, text
    6ea7c4f34085dfc0f62ecf0dd5acc6adef2234d4 Thu Mar 26 14:40:42 2020 -0700
    Adding a comment to explain what the hgHubConnectDeveloperMode function does after code review, refs #25221
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 1, context: html, text, full: html, text
    c16b03ae8b5a84abbd8be623bcc3acf278f8fe56 Mon Mar 23 11:54:49 2020 -0700
    Add COVID-19 to Genomes dropdown menu. refs #25185
  • lines changed 1, context: html, text, full: html, text
    242384fe9d17cf69fcc1877842e75f534cd03e7e Mon Mar 23 12:26:23 2020 -0700
    Shortened menu item for hgTracks. refs #25185
  • lines changed 1, context: html, text, full: html, text
    2e2ca8d6f5b61f5891e7546ecb62337f49ad8c70 Thu Mar 26 14:05:58 2020 -0700
    Tweak menu drowdown, suggested by QA. refs #25185
  • lines changed 1, context: html, text, full: html, text
    eb94729439ab163fdec8c230272961eb91855de1 Mon Mar 30 08:59:29 2020 -0700
    Tweak COVID gateway page link label, as per input from Hiram, Ann. refs #25185
• src/hg/htdocs/training/index.html
  • lines changed 15, context: html, text, full: html, text
    f2e5eebf4a777d0bb005beadb594b4e8958bd7fe Tue Mar 24 16:54:47 2020 -0700
    added strikethroughs on some future workshops now cancelled or postponed. added genetic couselors meeting in november-- one can hope
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    c08af2897fd394984f965637ed91fb2a7cda299a Mon Mar 30 10:08:36 2020 -0700
    New version number v396
• src/hg/lib/asmEquivalent.as
  • lines changed 11, context: html, text, full: html, text
    c36eab92d8a9d8cdfd5b7a782b097a3e6f638441 Mon Mar 23 18:53:36 2020 -0700
    hgFixed.asmEquivalent table definition refs #21074
  • lines changed 3, context: html, text, full: html, text
    8479716afe2a31901141de47a23bcddf06325fa3 Thu Mar 26 17:28:55 2020 -0700
    unsigned int is a poor choice for numbers that need to have operations such as subtraction on them, MySQL keeps everything in unsigned int and is confused by negative results refs #21074
• src/hg/lib/asmEquivalent.c
  • lines changed 255, context: html, text, full: html, text
    8479716afe2a31901141de47a23bcddf06325fa3 Thu Mar 26 17:28:55 2020 -0700
    unsigned int is a poor choice for numbers that need to have operations such as subtraction on them, MySQL keeps everything in unsigned int and is confused by negative results refs #21074
• src/hg/lib/asmEquivalent.h
  • lines changed 101, context: html, text, full: html, text
    8479716afe2a31901141de47a23bcddf06325fa3 Thu Mar 26 17:28:55 2020 -0700
    unsigned int is a poor choice for numbers that need to have operations such as subtraction on them, MySQL keeps everything in unsigned int and is confused by negative results refs #21074
• src/hg/lib/asmEquivalent.sql
  • lines changed 18, context: html, text, full: html, text
    c36eab92d8a9d8cdfd5b7a782b097a3e6f638441 Mon Mar 23 18:53:36 2020 -0700
    hgFixed.asmEquivalent table definition refs #21074
  • lines changed 3, context: html, text, full: html, text
    8479716afe2a31901141de47a23bcddf06325fa3 Thu Mar 26 17:28:55 2020 -0700
    unsigned int is a poor choice for numbers that need to have operations such as subtraction on them, MySQL keeps everything in unsigned int and is confused by negative results refs #21074
• src/hg/lib/hic.c
  • lines changed 16, context: html, text, full: html, text
    823025651ec0baffef2fc7037f3b478d62dd4052 Thu Mar 26 14:28:25 2020 -0700
    Fixing libs build for machines without C++ libs; added USE_HIC option to makes, refs #24414
• src/hg/lib/makefile
  • lines changed 5, context: html, text, full: html, text
    823025651ec0baffef2fc7037f3b478d62dd4052 Thu Mar 26 14:28:25 2020 -0700
    Fixing libs build for machines without C++ libs; added USE_HIC option to makes, refs #24414
• src/hg/lib/straw/makefile
  • lines changed 1, context: html, text, full: html, text
    823025651ec0baffef2fc7037f3b478d62dd4052 Thu Mar 26 14:28:25 2020 -0700
    Fixing libs build for machines without C++ libs; added USE_HIC option to makes, refs #24414
• src/hg/makeDb/doc/asmHubs/mkAsmStats.pl
  • lines changed 36, context: html, text, full: html, text
    dff254260c6b5cb3ab0f2257775fce47bbbfa3ea Wed Mar 25 11:56:34 2020 -0700
    now staging on hgdownload.soe.ucsc.edu refs #24748
• src/hg/makeDb/doc/asmHubs/mkHubIndex.pl
  • lines changed 24, context: html, text, full: html, text
    dff254260c6b5cb3ab0f2257775fce47bbbfa3ea Wed Mar 25 11:56:34 2020 -0700
    now staging on hgdownload.soe.ucsc.edu refs #24748
• src/hg/makeDb/doc/asmHubs/trackData.pl
  • lines changed 51, context: html, text, full: html, text
    dff254260c6b5cb3ab0f2257775fce47bbbfa3ea Wed Mar 25 11:56:34 2020 -0700
    now staging on hgdownload.soe.ucsc.edu refs #24748
• src/hg/makeDb/doc/assemblyEquivalence/A.vs.B.sh
  • lines changed 46, context: html, text, full: html, text
    199b2d4113d9498515030061888af66cbf7e8246 Thu Mar 26 17:40:17 2020 -0700
    adding some of the scripts that do the comparisons refs #24547
• src/hg/makeDb/doc/assemblyEquivalence/README.txt
  • lines changed 193, context: html, text, full: html, text
    199b2d4113d9498515030061888af66cbf7e8246 Thu Mar 26 17:40:17 2020 -0700
    adding some of the scripts that do the comparisons refs #24547
• src/hg/makeDb/doc/assemblyEquivalence/allByAll.sh
  • lines changed 37, context: html, text, full: html, text
    199b2d4113d9498515030061888af66cbf7e8246 Thu Mar 26 17:40:17 2020 -0700
    adding some of the scripts that do the comparisons refs #24547
• src/hg/makeDb/doc/assemblyEquivalence/createNearMissRunList.pl
  • lines changed 68, context: html, text, full: html, text
    199b2d4113d9498515030061888af66cbf7e8246 Thu Mar 26 17:40:17 2020 -0700
    adding some of the scripts that do the comparisons refs #24547
• src/hg/makeDb/doc/assemblyEquivalence/exact.sh
  • lines changed 39, context: html, text, full: html, text
    199b2d4113d9498515030061888af66cbf7e8246 Thu Mar 26 17:40:17 2020 -0700
    adding some of the scripts that do the comparisons refs #24547
• src/hg/makeDb/doc/assemblyEquivalence/exactTableTsv.pl
  • lines changed 56, context: html, text, full: html, text
    199b2d4113d9498515030061888af66cbf7e8246 Thu Mar 26 17:40:17 2020 -0700
    adding some of the scripts that do the comparisons refs #24547
• src/hg/makeDb/doc/assemblyEquivalence/runOne
  • lines changed 90, context: html, text, full: html, text
    199b2d4113d9498515030061888af66cbf7e8246 Thu Mar 26 17:40:17 2020 -0700
    adding some of the scripts that do the comparisons refs #24547
• src/hg/makeDb/doc/wuhCor1/crisprDet.txt
  • lines changed 4, context: html, text, full: html, text
    1e8cea555cb8e85aa840455926f5b2791982ab4a Fri Mar 27 07:51:50 2020 -0700
    adding CRISPR detection makedocs, refs #25247
• src/hg/makeDb/doc/wuhCor1/initialBuild.txt
  • lines changed 12, context: html, text, full: html, text
    52cd038bf4ae7872e59bc00bf22ab385492274ad Tue Mar 24 09:20:04 2020 -0700
    add search to ncbiGeneBGP
  • lines changed 9, context: html, text, full: html, text
    7fbb410aed66eb788b0c4d51f97f7c22ba0a40f6 Thu Mar 26 11:15:09 2020 -0700
    some tweaks in response to code review
• src/hg/makeDb/doc/wuhCor1/uniprot.txt
  • lines changed 12, context: html, text, full: html, text
    6abef9bb8be196d31e998a48558706db8e9d0e3b Thu Mar 26 10:38:06 2020 -0700
    makedoc for uniprot track, refs #25192
• src/hg/makeDb/hgLoadOut/hgLoadOut.c
  • lines changed 4, context: html, text, full: html, text
    e5dd7551b8031d28ac2f56c3e91f6d4c3db29ff2 Tue Mar 24 14:28:47 2020 -0700
    handle slighly different header created by some version of RepeatMasker
  • lines changed 1, context: html, text, full: html, text
    d67a231901dbbddbb17e7bb6a379feacdd87c9b4 Thu Mar 26 11:36:28 2020 -0700
    add another special case for recognizing a *.out file (from github https://github.com/ucscGenomeBrowser/kent/issues/31#issuecomment-602864913
• src/hg/makeDb/trackDb/geneid.html
  • lines changed 1, context: html, text, full: html, text
    0a3317c8146a8ef5037383526255b1baf389f8a4 Wed Mar 25 09:17:43 2020 -0700
    Updating a redirected link for apiMel2, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    e3f4dbfc2a5584535939332e5250e5e5ad68f7da Mon Mar 23 13:02:30 2020 -0700
    Hiding dbSNP 152 by default hg19 hg38 NoRM
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
  • lines changed 1, context: html, text, full: html, text
    1a9aa64a6b06ec13fd6d5a60c027bb1e2dcd2d60 Wed Mar 25 09:44:16 2020 -0700
    improving name of the uniprot chains track, no redmine, email from Jason Fernandes
• src/hg/makeDb/trackDb/virus/wuhCor1/cons44way.html
  • lines changed 9, context: html, text, full: html, text
    b65dff48f2876dc704c51f70c2bb7eeda6edfc35 Mon Mar 23 13:32:51 2020 -0700
    Fixing line lengths that were longer than 100 characters, refs #25187
• src/hg/makeDb/trackDb/virus/wuhCor1/crisprDet.html
  • lines changed 61, context: html, text, full: html, text
    1e8cea555cb8e85aa840455926f5b2791982ab4a Fri Mar 27 07:51:50 2020 -0700
    adding CRISPR detection makedocs, refs #25247
  • lines changed 1, context: html, text, full: html, text
    e8d0372512ad2173647348224f61a9d765963456 Fri Mar 27 08:23:06 2020 -0700
    adding funding disclaimer to new cov2 track docs pages
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
  • lines changed 10, context: html, text, full: html, text
    ac8b02729ccc78082ba75ca2243322520b5fb856 Mon Mar 23 12:38:01 2020 -0700
    Added Wikipedia link and funding blurb, input from JK. refs #25185
  • lines changed 9, context: html, text, full: html, text
    0a4f9c15b35990fa7adbd9cbb26e66f93fe9a9e5 Thu Mar 26 10:32:18 2020 -0700
    Improve other resources links, input from Max. refs #25185
  • lines changed 43, context: html, text, full: html, text
    7b02f9f43ad30760fb13f10c4e6c502fe98d11d0 Thu Mar 26 10:39:31 2020 -0700
    Move more new links and graphic ahead of boring assembly info on page, as per MH. refs #25185
  • lines changed 2, context: html, text, full: html, text
    19d834ec878db855e2da3fee9cef585ccdf17931 Thu Mar 26 10:56:09 2020 -0700
    Updating virus name to SARS-CoV-2.
  • lines changed 2, context: html, text, full: html, text
    eed125acd098f76e253b4b84bd1b6706fcb0b740 Thu Mar 26 13:08:16 2020 -0700
    Fix link problem found by QA. refs #25185
  • lines changed 1, context: html, text, full: html, text
    189b75110dfcc5c22d4f175b16086a65aa61f757 Mon Mar 30 09:36:43 2020 -0700
    Update funding statement, as per AZ request. refs #25185
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.html
  • lines changed 4, context: html, text, full: html, text
    63bd15f1095ff7e49ee401533b6507ed830f1deb Tue Mar 24 04:55:11 2020 -0700
    Cov2 work: adding funding disclaimers to various help pages, making primers and uniprots docs nicer, adding help to conservation tracks and adding IEDB prefix to epitopes track. refs #25189, refs #25190, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/epitopes.ra
  • lines changed 1, context: html, text, full: html, text
    63bd15f1095ff7e49ee401533b6507ed830f1deb Tue Mar 24 04:55:11 2020 -0700
    Cov2 work: adding funding disclaimers to various help pages, making primers and uniprots docs nicer, adding help to conservation tracks and adding IEDB prefix to epitopes track. refs #25189, refs #25190, refs #25090
  • lines changed 2, context: html, text, full: html, text
    efeac498624f4d43d90025929406203e582a1f1f Fri Mar 27 03:45:24 2020 -0700
    adapting epitopes track labels a little, refs #25190 and adding crispr detection track (no redmine yet)
• src/hg/makeDb/trackDb/virus/wuhCor1/gordon.html
  • lines changed 31, context: html, text, full: html, text
    0e34add1cbdc6a3504f97eb89e6bbf21c1f577a2 Fri Mar 27 07:15:32 2020 -0700
    updating gordon wuhCor1 docs page, no redmine yet.
  • lines changed 4, context: html, text, full: html, text
    e8d0372512ad2173647348224f61a9d765963456 Fri Mar 27 08:23:06 2020 -0700
    adding funding disclaimer to new cov2 track docs pages
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGene.html
  • lines changed 1, context: html, text, full: html, text
    19d834ec878db855e2da3fee9cef585ccdf17931 Thu Mar 26 10:56:09 2020 -0700
    Updating virus name to SARS-CoV-2.
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGene.ra
  • lines changed 6, context: html, text, full: html, text
    52cd038bf4ae7872e59bc00bf22ab385492274ad Tue Mar 24 09:20:04 2020 -0700
    add search to ncbiGeneBGP
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.html
  • lines changed 32, context: html, text, full: html, text
    ed719932e7adfaf18a4749c173b22093cb133396 Mon Mar 23 17:23:14 2020 -0700
    Changing the NCBI genes desc page #25114
  • lines changed 1, context: html, text, full: html, text
    19d834ec878db855e2da3fee9cef585ccdf17931 Thu Mar 26 10:56:09 2020 -0700
    Updating virus name to SARS-CoV-2.
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.ra
  • lines changed 7, context: html, text, full: html, text
    52cd038bf4ae7872e59bc00bf22ab385492274ad Tue Mar 24 09:20:04 2020 -0700
    add search to ncbiGeneBGP
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html
  • lines changed 60, context: html, text, full: html, text
    79deaabec43414458c195d8b4b3abce6d0e75cd6 Mon Mar 23 17:35:56 2020 -0700
    Fleshing out nextstrain track details (thanks for starting those, Max!) refs #25188
  • lines changed 22, context: html, text, full: html, text
    4cc83524b64cfedc3898c869ada91c3734b22aab Wed Mar 25 11:46:20 2020 -0700
    Added links from clades back to Nextstrain, and from description page to Nextstrain situation report pages that used the clades. refs #25188
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    8cd41d8051583a144e2405ee0df4c90bf92881ff Wed Mar 25 14:29:04 2020 -0700
    Tree terminology correction from David. refs #25188
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    fc7f1b9f5e16f4128f56760ac87a5649ee422b9d Thu Mar 26 15:07:25 2020 -0700
    Add TreeTime date and administrative division (location) info for clades to nextstrainClade. refs #25188
  • lines changed 9, context: html, text, full: html, text
    93bd8f55e6b4435aa28fd103b2772add7d17ce93 Fri Mar 27 15:26:03 2020 -0700
    Adding Data Access section #25188
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    4e45781eb14c7d78b1ac1202661756b4c4edd05b Fri Mar 27 17:16:53 2020 -0700
    Changing desc pages #25188 #25189
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClades.html
  • lines changed 29, context: html, text, full: html, text
    79deaabec43414458c195d8b4b3abce6d0e75cd6 Mon Mar 23 17:35:56 2020 -0700
    Fleshing out nextstrain track details (thanks for starting those, Max!) refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainGene.html
  • lines changed 26, context: html, text, full: html, text
    79deaabec43414458c195d8b4b3abce6d0e75cd6 Mon Mar 23 17:35:56 2020 -0700
    Fleshing out nextstrain track details (thanks for starting those, Max!) refs #25188
  • lines changed 12, context: html, text, full: html, text
    93bd8f55e6b4435aa28fd103b2772add7d17ce93 Fri Mar 27 15:26:03 2020 -0700
    Adding Data Access section #25188
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    4e45781eb14c7d78b1ac1202661756b4c4edd05b Fri Mar 27 17:16:53 2020 -0700
    Changing desc pages #25188 #25189
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html
  • lines changed 97, context: html, text, full: html, text
    79deaabec43414458c195d8b4b3abce6d0e75cd6 Mon Mar 23 17:35:56 2020 -0700
    Fleshing out nextstrain track details (thanks for starting those, Max!) refs #25188
  • lines changed 6, context: html, text, full: html, text
    93bd8f55e6b4435aa28fd103b2772add7d17ce93 Fri Mar 27 15:26:03 2020 -0700
    Adding Data Access section #25188
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    4e45781eb14c7d78b1ac1202661756b4c4edd05b Fri Mar 27 17:16:53 2020 -0700
    Changing desc pages #25188 #25189
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainVars.html
  • lines changed 66, context: html, text, full: html, text
    79deaabec43414458c195d8b4b3abce6d0e75cd6 Mon Mar 23 17:35:56 2020 -0700
    Fleshing out nextstrain track details (thanks for starting those, Max!) refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/primers.html
  • lines changed 51, context: html, text, full: html, text
    63bd15f1095ff7e49ee401533b6507ed830f1deb Tue Mar 24 04:55:11 2020 -0700
    Cov2 work: adding funding disclaimers to various help pages, making primers and uniprots docs nicer, adding help to conservation tracks and adding IEDB prefix to epitopes track. refs #25189, refs #25190, refs #25090
  • lines changed 23, context: html, text, full: html, text
    f7969c11afbc35bf440738aceef6b1c7b3a252cd Wed Mar 25 05:08:17 2020 -0700
    fixing small type in uniprot wuhCor1 track, refs #25192
  • lines changed 16, context: html, text, full: html, text
    4e45781eb14c7d78b1ac1202661756b4c4edd05b Fri Mar 27 17:16:53 2020 -0700
    Changing desc pages #25188 #25189
• src/hg/makeDb/trackDb/virus/wuhCor1/rfam.html
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    a862248865ad974eac79080875c0c14955f385d0 Thu Mar 26 03:38:06 2020 -0700
    Adding rfam track created by Todd, no redmine yet.
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra
  • lines changed 17, context: html, text, full: html, text
    76ef8274d883c50415b2370ce9a3ed761296cb62 Sat Mar 28 13:54:50 2020 -0700
    changing names of conservation tracks, again, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.44way.ra
  • lines changed 7, context: html, text, full: html, text
    63bd15f1095ff7e49ee401533b6507ed830f1deb Tue Mar 24 04:55:11 2020 -0700
    Cov2 work: adding funding disclaimers to various help pages, making primers and uniprots docs nicer, adding help to conservation tracks and adding IEDB prefix to epitopes track. refs #25189, refs #25190, refs #25090
  • lines changed 2, context: html, text, full: html, text
    79356d111b5208faecf0adadc57ac465edb1315a Fri Mar 27 07:13:02 2020 -0700
    tweaking colors of cov2 browser a little, no redmine
  • lines changed 16, context: html, text, full: html, text
    76ef8274d883c50415b2370ce9a3ed761296cb62 Sat Mar 28 13:54:50 2020 -0700
    changing names of conservation tracks, again, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
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    4cc83524b64cfedc3898c869ada91c3734b22aab Wed Mar 25 11:46:20 2020 -0700
    Added links from clades back to Nextstrain, and from description page to Nextstrain situation report pages that used the clades. refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    52cd038bf4ae7872e59bc00bf22ab385492274ad Tue Mar 24 09:20:04 2020 -0700
    add search to ncbiGeneBGP
  • lines changed 2, context: html, text, full: html, text
    7dfd4dc59dd43059c333f33feb256c66d772c825 Tue Mar 24 14:14:36 2020 -0700
    Pushing RR version of description page #25114
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    a862248865ad974eac79080875c0c14955f385d0 Thu Mar 26 03:38:06 2020 -0700
    Adding rfam track created by Todd, no redmine yet.
  • lines changed 14, context: html, text, full: html, text
    efeac498624f4d43d90025929406203e582a1f1f Fri Mar 27 03:45:24 2020 -0700
    adapting epitopes track labels a little, refs #25190 and adding crispr detection track (no redmine yet)
  • lines changed 4, context: html, text, full: html, text
    79356d111b5208faecf0adadc57ac465edb1315a Fri Mar 27 07:13:02 2020 -0700
    tweaking colors of cov2 browser a little, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.strainName44way.ra
  • lines changed 1, context: html, text, full: html, text
    63bd15f1095ff7e49ee401533b6507ed830f1deb Tue Mar 24 04:55:11 2020 -0700
    Cov2 work: adding funding disclaimers to various help pages, making primers and uniprots docs nicer, adding help to conservation tracks and adding IEDB prefix to epitopes track. refs #25189, refs #25190, refs #25090
  • lines changed 21, context: html, text, full: html, text
    76ef8274d883c50415b2370ce9a3ed761296cb62 Sat Mar 28 13:54:50 2020 -0700
    changing names of conservation tracks, again, refs #25090
  • lines changed 1, context: html, text, full: html, text
    ba187a92298451436bf12e9b02dc74b90667d6c8 Sat Mar 28 13:56:29 2020 -0700
    oops, forgot to hide conservation track, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
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    f7969c11afbc35bf440738aceef6b1c7b3a252cd Wed Mar 25 05:08:17 2020 -0700
    fixing small type in uniprot wuhCor1 track, refs #25192
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    1a9aa64a6b06ec13fd6d5a60c027bb1e2dcd2d60 Wed Mar 25 09:44:16 2020 -0700
    improving name of the uniprot chains track, no redmine, email from Jason Fernandes
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    135241bdf3f8a12e6726bd176523d5644f4990cd Thu Mar 26 03:51:00 2020 -0700
    removing links from uniprot track and fixing missing gene symbols, refs #25192
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    4b18b24370a1fceb71c89763f4a828d809fbbcd6 Thu Mar 26 04:24:38 2020 -0700
    removing empty tracks, refs #25192
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    efeac498624f4d43d90025929406203e582a1f1f Fri Mar 27 03:45:24 2020 -0700
    adapting epitopes track labels a little, refs #25190 and adding crispr detection track (no redmine yet)
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    79356d111b5208faecf0adadc57ac465edb1315a Fri Mar 27 07:13:02 2020 -0700
    tweaking colors of cov2 browser a little, no redmine
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    52bcf27ac2a8c54573d4334093ec5be374684c11 Sat Mar 28 14:18:34 2020 -0700
    small rename of aa modifs track after email from Phil Berman, refs #25192
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    b88c4c7dfc4ebda2ee1daa62c2b3fc1c2f18406c Sat Mar 28 15:40:33 2020 -0700
    adding docs pages for uncomposited uniprot track, refs #25090
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    906da37654b6560c7d2fae3e0d2404dc64eeed34 Mon Mar 30 00:42:27 2020 -0700
    forgot mouse over field for cov-2 uniprot track, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2AliSwissprot.html
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    63bd15f1095ff7e49ee401533b6507ed830f1deb Tue Mar 24 04:55:11 2020 -0700
    Cov2 work: adding funding disclaimers to various help pages, making primers and uniprots docs nicer, adding help to conservation tracks and adding IEDB prefix to epitopes track. refs #25189, refs #25190, refs #25090
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    df8403b9311c8dea639311b38dcd9365b2dd7170 Thu Mar 26 10:43:20 2020 -0700
    adding small note to uniprot docs page
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    b9e6c6a709aab60f16a518738abd6bc70766f789 Thu Mar 26 10:56:58 2020 -0700
    Trimming up the wuhCor1 uniprot desc pages refs #25192
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    d02e2d7086f5472f7881677455b49dbd97629c27 Thu Mar 26 10:59:16 2020 -0700
    Trimming up the wuhCor1 uniprot desc pages refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2DisulfBond.html
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    b88c4c7dfc4ebda2ee1daa62c2b3fc1c2f18406c Sat Mar 28 15:40:33 2020 -0700
    adding docs pages for uncomposited uniprot track, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Domain.html
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    b88c4c7dfc4ebda2ee1daa62c2b3fc1c2f18406c Sat Mar 28 15:40:33 2020 -0700
    adding docs pages for uncomposited uniprot track, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Interest.html
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    63bd15f1095ff7e49ee401533b6507ed830f1deb Tue Mar 24 04:55:11 2020 -0700
    Cov2 work: adding funding disclaimers to various help pages, making primers and uniprots docs nicer, adding help to conservation tracks and adding IEDB prefix to epitopes track. refs #25189, refs #25190, refs #25090
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    b9e6c6a709aab60f16a518738abd6bc70766f789 Thu Mar 26 10:56:58 2020 -0700
    Trimming up the wuhCor1 uniprot desc pages refs #25192
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2LocSignal.html
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    b88c4c7dfc4ebda2ee1daa62c2b3fc1c2f18406c Sat Mar 28 15:40:33 2020 -0700
    adding docs pages for uncomposited uniprot track, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2LocTransMemb.html
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    b88c4c7dfc4ebda2ee1daa62c2b3fc1c2f18406c Sat Mar 28 15:40:33 2020 -0700
    adding docs pages for uncomposited uniprot track, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Modif.html
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    b88c4c7dfc4ebda2ee1daa62c2b3fc1c2f18406c Sat Mar 28 15:40:33 2020 -0700
    adding docs pages for uncomposited uniprot track, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Repeat.html
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    b88c4c7dfc4ebda2ee1daa62c2b3fc1c2f18406c Sat Mar 28 15:40:33 2020 -0700
    adding docs pages for uncomposited uniprot track, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/unipCov2Struct.html
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    b88c4c7dfc4ebda2ee1daa62c2b3fc1c2f18406c Sat Mar 28 15:40:33 2020 -0700
    adding docs pages for uncomposited uniprot track, refs #25090
• src/hg/makeDb/trackDb/virus/wuhCor1/uniprotCov2.html
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    63bd15f1095ff7e49ee401533b6507ed830f1deb Tue Mar 24 04:55:11 2020 -0700
    Cov2 work: adding funding disclaimers to various help pages, making primers and uniprots docs nicer, adding help to conservation tracks and adding IEDB prefix to epitopes track. refs #25189, refs #25190, refs #25090
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    b9e6c6a709aab60f16a518738abd6bc70766f789 Thu Mar 26 10:56:58 2020 -0700
    Trimming up the wuhCor1 uniprot desc pages refs #25192
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    b88c4c7dfc4ebda2ee1daa62c2b3fc1c2f18406c Sat Mar 28 15:40:33 2020 -0700
    adding docs pages for uncomposited uniprot track, refs #25090
• src/hg/utils/hubCheck/hubCheck.c
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    1925f0952661720e21caf1b7dbbea3db820b6610 Thu Mar 26 10:31:52 2020 -0700
    Fixing hubCheck htmlOut issue when a hub is missing a shortLabel, refs 24559 note 56
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    d0964dccfb4e1519574990aa210b953ace4c8851 Thu Mar 26 14:36:34 2020 -0700
    Fixing where I inadvertently deleted a comma in the last commit, and fixing some htmlEncoding errors after code review feedback, refs #25221
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
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    7b7e13b225417cda1b010036bb13394a8c1e790c Mon Mar 23 18:13:36 2020 -0700
    Updating nextstrainNcov/doUpdate.sh to produce less output and be smarter about the true file date. refs #25188
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    35899dd8b6349db50dd77a92398d356d9d3be47b Tue Mar 24 15:16:01 2020 -0700
    Make doUpdate silent when ncov.json has not been updated since the last build. refs #25188
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    fc7f1b9f5e16f4128f56760ac87a5649ee422b9d Thu Mar 26 15:07:25 2020 -0700
    Add TreeTime date and administrative division (location) info for clades to nextstrainClade. refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    39a6a0080ab48990a02c59d21a1566d25a0103fe Wed Mar 25 15:28:33 2020 -0700
    Add sample date (just month and day; GISAID sample name ends in year) to sample labels in VCF (David request). refs #25188
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    3aec6ebceadc5dee647d4c1b294b3a3d81a391e6 Wed Mar 25 17:38:38 2020 -0700
    Clade variant list format change from David: ;-separated for different nodes, ,-sep for within node; also added amino acid changes when applicable. refs #25188
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    fc7f1b9f5e16f4128f56760ac87a5649ee422b9d Thu Mar 26 15:07:25 2020 -0700
    Add TreeTime date and administrative division (location) info for clades to nextstrainClade. refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrainClade.as
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    4b20c7547572d8795b5a6675c45e44491b23b42d Wed Mar 25 14:30:12 2020 -0700
    Clade variant terminology change from David. refs #25188
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    fc7f1b9f5e16f4128f56760ac87a5649ee422b9d Thu Mar 26 15:07:25 2020 -0700
    Add TreeTime date and administrative division (location) info for clades to nextstrainClade. refs #25188
• src/inc/common.mk
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    823025651ec0baffef2fc7037f3b478d62dd4052 Thu Mar 26 14:28:25 2020 -0700
    Fixing libs build for machines without C++ libs; added USE_HIC option to makes, refs #24414
• src/inc/srcVersion.h
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    c08af2897fd394984f965637ed91fb2a7cda299a Mon Mar 30 10:08:36 2020 -0700
    New version number v396
• src/parasol/makefile
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    62e31071c76e4ed5ef4bc6b0f86b5a011edf803a Thu Mar 26 17:33:25 2020 -0400
    fixed make clean on os/x where it creates foo.dSYM directories
• src/utils/qa/weeklybld/buildEnv.csh
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    ce22187a6a9967194493c246fa5efe11f9266b7c Mon Mar 30 10:07:16 2020 -0700
    v396 final build, refs #25191

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