All File Changes

v417_preview2 to v417_base (2021-06-28 to 2021-07-05) v417

• confs/asia.hg.conf
  • lines changed 3, context: html, text, full: html, text
    911e34eb6778518e1eb35bae4d2cf8700f48287a Sun Jul 4 01:12:42 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    911e34eb6778518e1eb35bae4d2cf8700f48287a Sun Jul 4 01:12:42 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    911e34eb6778518e1eb35bae4d2cf8700f48287a Sun Jul 4 01:12:42 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 2, context: html, text, full: html, text
    1260e14f28ea8d0cf961cc3160862bf5307d684d Thu Jul 1 11:17:04 2021 -0700
    Oops, forgot to load needed JS files for results page, so when there was an error and we show the inputForm for the user to try again, the loadingImg was not initialized correctly.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 17, context: html, text, full: html, text
    0a01cd0845e94f390d6522016c6caf247ba36b96 Thu Jul 1 17:25:59 2021 -0700
    Adding Auspice colorings contributed by @babarlelephant in github PR #57.
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    8902e1619dfd0047ae546c3ed604841f3b9ba78c Tue Jun 29 07:01:09 2021 -0700
    changing udcTimeout warning text, refs #27677
• src/hg/hgTracks/simpleTracks.c
  • lines changed 4, context: html, text, full: html, text
    edd385f31b97ea6b5a9a0b6ccfcaaeff3c5afb74 Sat Jul 3 10:44:16 2021 -0700
    fix up logo drawing in hgTracks
• src/hg/hgc/barChartClick.c
  • lines changed 9, context: html, text, full: html, text
    e5705b39b450c584576d183175f6b2656420bd88 Tue Jun 29 17:06:31 2021 -0700
    change barChartClick to use the pipeline library instead of system()
• src/hg/hgc/lowelab.c
  • lines changed 2, context: html, text, full: html, text
    aa7ec8a95c4054d4ce9501bed022fb510e50d94e Sat Jul 3 11:07:20 2021 -0700
    don't compile lowelab.c if LOWELAB isn't set
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 14, context: html, text, full: html, text
    7e0c9e2676d69bfb086eaa1fa8c8c02274fbf347 Fri Jul 2 06:40:08 2021 -0700
    changes after doc review by Jonathan, refs #27778
  • lines changed 1, context: html, text, full: html, text
    4137de18d409a3913bbbecfe5e1ab6f52a9715d1 Fri Jul 2 06:42:43 2021 -0700
    fixing small docs typo
  • lines changed 9, context: html, text, full: html, text
    310b7abb097f8f50d28eaca8149577b0f412e731 Fri Jul 2 06:46:42 2021 -0700
    more fixes for the genes faq page, refs #27778
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 1, context: html, text, full: html, text
    fb061c76bb820b2549203bcfe39bf0cd7f4d2854 Mon Jun 28 16:04:00 2021 -0700
    Doc'ing extra settings missing from the filter definition doc refs #27713. Also small changes forgot to commit from CR last week.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 1, context: html, text, full: html, text
    fb061c76bb820b2549203bcfe39bf0cd7f4d2854 Mon Jun 28 16:04:00 2021 -0700
    Doc'ing extra settings missing from the filter definition doc refs #27713. Also small changes forgot to commit from CR last week.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 1, context: html, text, full: html, text
    fb061c76bb820b2549203bcfe39bf0cd7f4d2854 Mon Jun 28 16:04:00 2021 -0700
    Doc'ing extra settings missing from the filter definition doc refs #27713. Also small changes forgot to commit from CR last week.
  • lines changed 1, context: html, text, full: html, text
    a8bd03e175b0527e4656e5528f9e88364a12cf7e Thu Jul 1 10:37:05 2021 -0700
    Moving visibility to required after Max comment in refs #27780
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 16, context: html, text, full: html, text
    fb061c76bb820b2549203bcfe39bf0cd7f4d2854 Mon Jun 28 16:04:00 2021 -0700
    Doc'ing extra settings missing from the filter definition doc refs #27713. Also small changes forgot to commit from CR last week.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 3, context: html, text, full: html, text
    7b6820b4e32bf5c1a9996acaae3547e236ccd15e Mon Jun 28 14:16:40 2021 -0700
    Trying to track down htmlCheck validate goldenPath/newsarch.html report of a missing </a> tag before announcing TrackDb Versioning.
  • lines changed 22, context: html, text, full: html, text
    162f6398bea8de3f5f1f17455aacc8a51f11d06c Mon Jun 28 14:54:15 2021 -0700
    Adding the announcement about v3 versioning of the trackDb doc refs #26598
  • lines changed 4, context: html, text, full: html, text
    d365ce310884503411d1fceff21ed997615e4d6d Mon Jun 28 15:01:16 2021 -0700
    Adding the index announcement about v3 versioning of the trackDb doc refs #26598
  • lines changed 3, context: html, text, full: html, text
    33b0e2745227c061b96dddcb215ee77c9fb6ad59 Mon Jun 28 15:06:19 2021 -0700
    Wordsmithing trackDb announcement refs #26598
  • lines changed 5, context: html, text, full: html, text
    8d9c032cec6621134038a076a40d8a687ea62cff Tue Jun 29 11:20:39 2021 -0700
    tiny tweaks for consistency
  • lines changed 3, context: html, text, full: html, text
    4d5f3cd7c83132956e5d279f268fac6e235f1e41 Tue Jun 29 11:23:07 2021 -0700
    Minor edits for CR refs #27772
  • lines changed 19, context: html, text, full: html, text
    dd5a47ece8fac7228760f769b57e1ab62408a3e2 Fri Jul 2 12:16:22 2021 -0700
    Announcing dbSnp Archive #26712
• src/hg/htdocs/images/dbSnp.Archive.png
  • lines changed 0, context: html, text, full: html, text
    dd5a47ece8fac7228760f769b57e1ab62408a3e2 Fri Jul 2 12:16:22 2021 -0700
    Announcing dbSnp Archive #26712
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    d365ce310884503411d1fceff21ed997615e4d6d Mon Jun 28 15:01:16 2021 -0700
    Adding the index announcement about v3 versioning of the trackDb doc refs #26598
  • lines changed 12, context: html, text, full: html, text
    dd5a47ece8fac7228760f769b57e1ab62408a3e2 Fri Jul 2 12:16:22 2021 -0700
    Announcing dbSnp Archive #26712
• src/hg/htdocs/license/index.html
  • lines changed 16, context: html, text, full: html, text
    039fa92ec80287b514c60a4c7dbffac0b4c6b8fc Wed Jun 30 08:20:08 2021 -0700
    clarifying API is free, refs #27781
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    3183269829f070c9976373c808cfcfebaf4a25d2 Mon Jul 5 10:16:25 2021 -0700
    New version number v417
• src/hg/lib/cartRewrite.c
  • lines changed 6, context: html, text, full: html, text
    055623004394631452df0ee15fab1d00f0c3d57e Thu Jul 1 10:50:41 2021 -0700
    add some copyright and explanatory text at the top of cartRewrite.c
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
  • lines changed 6, context: html, text, full: html, text
    9755f05c30ccecf47565cf5e7b2796cd42fc635b Mon Jun 28 14:18:49 2021 -0700
    rsync dynamic blat files to the dynablat-01 machine and add rules to test dynamic blat refs #27556
• src/hg/makeDb/doc/asmHubs/rtp1.ace2.faa.gz
  • lines changed 0, context: html, text, full: html, text
    18ca361b254102fc711e421c2056771598d6fc34 Mon Jun 28 14:18:36 2021 -0700
    rsync dynamic blat files to the dynablat-01 machine and add rules to test dynamic blat refs #27556
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
  • lines changed 14, context: html, text, full: html, text
    9755f05c30ccecf47565cf5e7b2796cd42fc635b Mon Jun 28 14:18:49 2021 -0700
    rsync dynamic blat files to the dynablat-01 machine and add rules to test dynamic blat refs #27556
• src/hg/makeDb/doc/asmHubs/testDynBlat.sh
  • lines changed 64, context: html, text, full: html, text
    18ca361b254102fc711e421c2056771598d6fc34 Mon Jun 28 14:18:36 2021 -0700
    rsync dynamic blat files to the dynablat-01 machine and add rules to test dynamic blat refs #27556
  • lines changed 34, context: html, text, full: html, text
    27268fcd94123d7c1fe0cd4f30c3520978fcd46e Mon Jun 28 14:20:57 2021 -0700
    eliminate test junk refs #27556
  • lines changed 6, context: html, text, full: html, text
    9e3ba7e02f241e806c6a656329ea8aee730d000b Mon Jun 28 15:09:07 2021 -0700
    indicate error when dynamic blat does not respond refs #27556
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    d7397434548b97dca7543c9fc2f46b5901d2c6e4 Wed Jun 30 12:29:01 2021 -0700
    adding GCF_000009045.1_ASM904v1 Bacillus subtilis strain 168 per user request refs #27790
• src/hg/makeDb/doc/gorGor5/initialBuild.txt
  • lines changed 92, context: html, text, full: html, text
    1b810c39a0876696d70ef6787bb0a3e029f2ca57 Mon Jul 5 07:57:33 2021 -0700
    adding chromAlias table and chromAlias.txt file no redmine
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 50, context: html, text, full: html, text
    703e07e1d02ee1e346d5dcf6c0610a3d4d5f4069 Tue Jun 29 17:12:38 2021 -0700
    import of GENCODE V38lift37
• src/hg/makeDb/doc/hg19.txt
  • lines changed 20, context: html, text, full: html, text
    2fdcabb36f9906a0bbb8e6c2c2fbe43e32543946 Tue Jun 29 11:14:10 2021 -0700
    ncbiRefSeq update refs #27552
  • lines changed 79, context: html, text, full: html, text
    40a49b0eb0c44d5a5fd20fb43468405b12d0390c Tue Jun 29 16:21:53 2021 -0700
    lastz chainNet per user request hg19 gorGor6, refs #27757
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 6, context: html, text, full: html, text
    f42dddff0ade4e265463411f9526491ec4e4c84a Tue Jun 29 15:06:30 2021 -0700
    replace gencode V38 pre-release with final
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 64, context: html, text, full: html, text
    6d039ce16bfa7c8c38372807bf21155c86819dc2 Tue Jun 29 09:41:09 2021 -0700
    Commiting script and makedoc for gnomAD v3.1.1 track
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 41, context: html, text, full: html, text
    b52d9c0661e61818af15e7ceb544e0790c94e2ab Mon Jun 28 14:24:03 2021 -0700
    adding the mouse strains to the GenArk refs #27754
• src/hg/makeDb/doc/mm10.patchUpdate.6.txt
  • lines changed 1, context: html, text, full: html, text
    ab2397a17e14b1ba1c9deb7481eadfc08d58b966 Fri Jul 2 11:32:20 2021 -0700
    mm10.2bit and tables on RR, update GRCIncident db
  • lines changed 23, context: html, text, full: html, text
    1cb08c59e884b67fbfcbf79f9dc416574e5c6239 Fri Jul 2 11:55:28 2021 -0700
    Added a note about extra mouse strains appearing in the mm10 patch6
  • lines changed 22, context: html, text, full: html, text
    dac1d9e2d193f587f633dcfb619103d8dd86d47c Fri Jul 2 13:05:28 2021 -0700
    adding text to mm10 description.html about the inclusion of alternate scaffolds on other mouse strains, part of the NCBI mm38 release.
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 7, context: html, text, full: html, text
    2e85d518a6bc169b901b3c0b57e24b45694296fc Tue Jun 29 16:05:38 2021 -0700
    update GENCODE VM27 from pre-release from final
• src/hg/makeDb/gnomad/gnomadVcfBedToBigBed
  • lines changed 282, context: html, text, full: html, text
    6d039ce16bfa7c8c38372807bf21155c86819dc2 Tue Jun 29 09:41:09 2021 -0700
    Commiting script and makedoc for gnomAD v3.1.1 track
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 4, context: html, text, full: html, text
    f42dddff0ade4e265463411f9526491ec4e4c84a Tue Jun 29 15:06:30 2021 -0700
    replace gencode V38 pre-release with final
  • lines changed 2, context: html, text, full: html, text
    2e85d518a6bc169b901b3c0b57e24b45694296fc Tue Jun 29 16:05:38 2021 -0700
    update GENCODE VM27 from pre-release from final
  • lines changed 4, context: html, text, full: html, text
    703e07e1d02ee1e346d5dcf6c0610a3d4d5f4069 Tue Jun 29 17:12:38 2021 -0700
    import of GENCODE V38lift37
• src/hg/makeDb/schema/all.joiner
  • lines changed 157, context: html, text, full: html, text
    703e07e1d02ee1e346d5dcf6c0610a3d4d5f4069 Tue Jun 29 17:12:38 2021 -0700
    import of GENCODE V38lift37
  • lines changed 102, context: html, text, full: html, text
    de64c79aa1f9e02854d88d6d53a442b8eb5c8474 Tue Jun 29 19:02:31 2021 -0700
    removed dead-end scheme change checks
• src/hg/makeDb/trackDb/dbSnpArchive.html
  • lines changed 471, context: html, text, full: html, text
    d487014430745c01bad1f9e96a0907185e4d2147 Fri Jul 2 12:19:23 2021 -0700
    Committing tdb changes for dbSnp Archive #26712
• src/hg/makeDb/trackDb/ensGene.html
  • lines changed 1, context: html, text, full: html, text
    fb061c76bb820b2549203bcfe39bf0cd7f4d2854 Mon Jun 28 16:04:00 2021 -0700
    Doc'ing extra settings missing from the filter definition doc refs #27713. Also small changes forgot to commit from CR last week.
• src/hg/makeDb/trackDb/human/hg19/dbSnpArchiveHg19.ra
  • lines changed 1, context: html, text, full: html, text
    d487014430745c01bad1f9e96a0907185e4d2147 Fri Jul 2 12:19:23 2021 -0700
    Committing tdb changes for dbSnp Archive #26712
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    eb58511478b5cff91b41234e38327c4cdb3c8a3a Tue Jun 29 18:52:21 2021 -0700
    forgot to enable V38lift37
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    d487014430745c01bad1f9e96a0907185e4d2147 Fri Jul 2 12:19:23 2021 -0700
    Committing tdb changes for dbSnp Archive #26712
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 8, context: html, text, full: html, text
    eb58511478b5cff91b41234e38327c4cdb3c8a3a Tue Jun 29 18:52:21 2021 -0700
    forgot to enable V38lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV38lift37.html
  • lines changed 32, context: html, text, full: html, text
    703e07e1d02ee1e346d5dcf6c0610a3d4d5f4069 Tue Jun 29 17:12:38 2021 -0700
    import of GENCODE V38lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV38lift37.ra
  • lines changed 224, context: html, text, full: html, text
    703e07e1d02ee1e346d5dcf6c0610a3d4d5f4069 Tue Jun 29 17:12:38 2021 -0700
    import of GENCODE V38lift37
• src/hg/makeDb/trackDb/human/hg38/dbSnpArchiveHg38.ra
  • lines changed 2, context: html, text, full: html, text
    d487014430745c01bad1f9e96a0907185e4d2147 Fri Jul 2 12:19:23 2021 -0700
    Committing tdb changes for dbSnp Archive #26712
• src/hg/makeDb/trackDb/human/hg38/gnomad.alpha.ra
  • lines changed 5, context: html, text, full: html, text
    fdf3d9a3a4d5e9b02fb0b5d4ce1256f55fea0bfc Tue Jun 29 14:22:24 2021 -0700
    Fix up searching on gnomad v3.1.1 track, refs #27256
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 4, context: html, text, full: html, text
    fdf3d9a3a4d5e9b02fb0b5d4ce1256f55fea0bfc Tue Jun 29 14:22:24 2021 -0700
    Fix up searching on gnomad v3.1.1 track, refs #27256
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    d487014430745c01bad1f9e96a0907185e4d2147 Fri Jul 2 12:19:23 2021 -0700
    Committing tdb changes for dbSnp Archive #26712
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    f42dddff0ade4e265463411f9526491ec4e4c84a Tue Jun 29 15:06:30 2021 -0700
    replace gencode V38 pre-release with final
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV38.html
  • lines changed 1, context: html, text, full: html, text
    f42dddff0ade4e265463411f9526491ec4e4c84a Tue Jun 29 15:06:30 2021 -0700
    replace gencode V38 pre-release with final
• src/hg/makeDb/trackDb/makefile
  • lines changed 4, context: html, text, full: html, text
    1eef01b7a5ae3f24d3c69328c6d7581d91feceb9 Thu Jul 1 08:23:43 2021 -0700
    add cartVersion information to public trackDb build
• src/hg/makeDb/trackDb/mouse/mm10/dbSnpArchiveMm10.ra
  • lines changed 1, context: html, text, full: html, text
    d487014430745c01bad1f9e96a0907185e4d2147 Fri Jul 2 12:19:23 2021 -0700
    Committing tdb changes for dbSnp Archive #26712
• src/hg/makeDb/trackDb/mouse/mm10/description.html
  • lines changed 39, context: html, text, full: html, text
    dac1d9e2d193f587f633dcfb619103d8dd86d47c Fri Jul 2 13:05:28 2021 -0700
    adding text to mm10 description.html about the inclusion of alternate scaffolds on other mouse strains, part of the NCBI mm38 release.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    d487014430745c01bad1f9e96a0907185e4d2147 Fri Jul 2 12:19:23 2021 -0700
    Committing tdb changes for dbSnp Archive #26712
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    2e85d518a6bc169b901b3c0b57e24b45694296fc Tue Jun 29 16:05:38 2021 -0700
    update GENCODE VM27 from pre-release from final
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM27.html
  • lines changed 1, context: html, text, full: html, text
    2e85d518a6bc169b901b3c0b57e24b45694296fc Tue Jun 29 16:05:38 2021 -0700
    update GENCODE VM27 from pre-release from final
• src/hg/utils/automation/chromAliasToTxt.pl
  • lines changed 39, context: html, text, full: html, text
    9578d5ecb6f52b870b436a05ba64844e801b1853 Fri Jul 2 15:33:47 2021 -0700
    to convert chromAlias table to text version for download directory no redmine
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 5, context: html, text, full: html, text
    2c4255b30f6c2aa11ce8c86396eaed8975d52a36 Thu Jul 1 10:55:43 2021 -0700
    Don't run nextclade when there are no new sequences; it will fail & cause script to halt.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    3183269829f070c9976373c808cfcfebaf4a25d2 Mon Jul 5 10:16:25 2021 -0700
    New version number v417
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    5b5ae4250160d3aac2c23cad97139907abc0956c Mon Jul 5 10:15:25 2021 -0700
    v417 final build, refs #27752

• lines changed: 2134
• files changed: 78