All File Changes

v418_base to v419_preview (2021-07-26 to 2021-08-02) v419

• src/hg/hgConvert/hgConvert.c
  • lines changed 2, context: html, text, full: html, text
    7a4641fb6869e372e88498be6c33c3fc7462ab86 Fri Jul 30 14:22:16 2021 -0700
    Kate forgot to fix these when changing the name of the virtual chrom from "virt" to "multi". fixes #27920
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 2, context: html, text, full: html, text
    7a4641fb6869e372e88498be6c33c3fc7462ab86 Fri Jul 30 14:22:16 2021 -0700
    Kate forgot to fix these when changing the name of the virtual chrom from "virt" to "multi". fixes #27920
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 17, context: html, text, full: html, text
    d903a7409978ea81cc0f2e6e34687319f7d9d222 Wed Jul 28 15:50:24 2021 -0700
    When extracting samples from the tree with matUtils, add the new --usher-clades-txt option and create empty placementInfo's to hold the results of parsing clades.txt so we can show clades/lineages according to the tree in the result summary table.
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    7a4641fb6869e372e88498be6c33c3fc7462ab86 Fri Jul 30 14:22:16 2021 -0700
    Kate forgot to fix these when changing the name of the virtual chrom from "virt" to "multi". fixes #27920
  • lines changed 12, context: html, text, full: html, text
    ae751438b669c74fd5809bfed90f725037f60417 Fri Jul 30 16:18:11 2021 -0700
    add support for second page of help results to hgTables and hgVai. Move "no results" printf to library. Change comment in hgTables/identifiers.c to make more sense.
• src/hg/hgTables/identifiers.c
  • lines changed 2, context: html, text, full: html, text
    ae751438b669c74fd5809bfed90f725037f60417 Fri Jul 30 16:18:11 2021 -0700
    add support for second page of help results to hgTables and hgVai. Move "no results" printf to library. Change comment in hgTables/identifiers.c to make more sense.
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    607ae9e8ce482f440b1378f3ff750b715b7a759c Mon Jul 26 10:29:48 2021 -0700
    remove debug cruft
  • lines changed 1, context: html, text, full: html, text
    a1a5a001f0074b0683e602c91be1f8299be2bd54 Mon Jul 26 10:49:02 2021 -0700
    more debug cruft
  • lines changed 11, context: html, text, full: html, text
    ae751438b669c74fd5809bfed90f725037f60417 Fri Jul 30 16:18:11 2021 -0700
    add support for second page of help results to hgTables and hgVai. Move "no results" printf to library. Change comment in hgTables/identifiers.c to make more sense.
• src/hg/hgVai/hgVai.c
  • lines changed 2, context: html, text, full: html, text
    7a4641fb6869e372e88498be6c33c3fc7462ab86 Fri Jul 30 14:22:16 2021 -0700
    Kate forgot to fix these when changing the name of the virtual chrom from "virt" to "multi". fixes #27920
  • lines changed 11, context: html, text, full: html, text
    ae751438b669c74fd5809bfed90f725037f60417 Fri Jul 30 16:18:11 2021 -0700
    add support for second page of help results to hgTables and hgVai. Move "no results" printf to library. Change comment in hgTables/identifiers.c to make more sense.
• src/hg/inc/hgHgvs.h
  • lines changed 3, context: html, text, full: html, text
    3e70e7601a08e28667531d5abe3fe8b04ee95ded Fri Jul 16 11:23:58 2021 -0700
    Return multiple transcripts for pseudo hgvs search, refs #15554
• src/hg/js/hgTracks.js
  • lines changed 12, context: html, text, full: html, text
    2d820c127e278ecf3e4162048ddef02544a2b5ff Wed Jul 28 11:27:17 2021 -0700
    Make hgTrackUi pop-up control on hgTracks inner data scrollable, which prevents the pop-up window from extending past the bottom of the screen, in turn fixing the always would have been hidden submit buttons, refs #20242
• src/hg/lib/defaultKnown.as
  • lines changed 5, context: html, text, full: html, text
    156285591ea89b04acaf0f97c123e67f481c521e Thu Jul 29 11:45:20 2021 -0700
    some AS files to support knownGene in a separate database
• src/hg/lib/defaultKnown.sql
  • lines changed 11, context: html, text, full: html, text
    156285591ea89b04acaf0f97c123e67f481c521e Thu Jul 29 11:45:20 2021 -0700
    some AS files to support knownGene in a separate database
• src/hg/lib/hgFind.c
  • lines changed 30, context: html, text, full: html, text
    3e70e7601a08e28667531d5abe3fe8b04ee95ded Fri Jul 16 11:23:58 2021 -0700
    Return multiple transcripts for pseudo hgvs search, refs #15554
  • lines changed 11, context: html, text, full: html, text
    9a6328c45c6b94efdceaebd999984eefc43dd857 Tue Jul 27 12:22:05 2021 -0700
    Forgot to check for successful mapping of hgvs when allowing multiple transcripts, refs #15554
  • lines changed 51, context: html, text, full: html, text
    a05e08a84139434ed78426823738269d12cc323e Tue Jul 27 17:13:48 2021 -0700
    When an hgvs search results in multiple transcripts at that map to the same location, only give the user the list of unique positions, or just go straight to the position if there is only one unique position, refs #15554
  • lines changed 14, context: html, text, full: html, text
    ae751438b669c74fd5809bfed90f725037f60417 Fri Jul 30 16:18:11 2021 -0700
    add support for second page of help results to hgTables and hgVai. Move "no results" printf to library. Change comment in hgTables/identifiers.c to make more sense.
• src/hg/lib/hgHgvs.c
  • lines changed 23, context: html, text, full: html, text
    3e70e7601a08e28667531d5abe3fe8b04ee95ded Fri Jul 16 11:23:58 2021 -0700
    Return multiple transcripts for pseudo hgvs search, refs #15554
• src/hg/lib/masterGeneTrack.as
  • lines changed 5, context: html, text, full: html, text
    156285591ea89b04acaf0f97c123e67f481c521e Thu Jul 29 11:45:20 2021 -0700
    some AS files to support knownGene in a separate database
• src/hg/lib/masterGeneTrack.sql
  • lines changed 11, context: html, text, full: html, text
    156285591ea89b04acaf0f97c123e67f481c521e Thu Jul 29 11:45:20 2021 -0700
    some AS files to support knownGene in a separate database
• src/hg/lib/tests/expected/hgvs/validTerms.txt
  • lines changed 14, context: html, text, full: html, text
    3e70e7601a08e28667531d5abe3fe8b04ee95ded Fri Jul 16 11:23:58 2021 -0700
    Return multiple transcripts for pseudo hgvs search, refs #15554
• src/hg/lib/tests/hgvsTester.c
  • lines changed 24, context: html, text, full: html, text
    3e70e7601a08e28667531d5abe3fe8b04ee95ded Fri Jul 16 11:23:58 2021 -0700
    Return multiple transcripts for pseudo hgvs search, refs #15554
• src/hg/makeDb/trackDb/human/hg19/dbSnpArchiveHg19.ra
  • lines changed 48, context: html, text, full: html, text
    f02333eac281a5d6ad5fe023f0d70db2c20f09a4 Tue Jul 27 11:50:23 2021 -0700
    Fixing supertrack syntax to recommended guidelines for dbSnpArchive, previous working and tested working refs #27877 and #26719
• src/hg/makeDb/trackDb/human/hg38/bloodHao.html
  • lines changed 82, context: html, text, full: html, text
    4ca20f1795e3d4cf3f0687889cf1c9e670abf35b Mon Aug 2 08:05:41 2021 -0700
    New details page.
• src/hg/makeDb/trackDb/human/hg38/colonWang.html
  • lines changed 24, context: html, text, full: html, text
    51650e7bd89d9df0ca95de94b766381163b9c18b Mon Aug 2 08:06:47 2021 -0700
    New draft with edits from previous code reviews.
• src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.html
  • lines changed 14, context: html, text, full: html, text
    51650e7bd89d9df0ca95de94b766381163b9c18b Mon Aug 2 08:06:47 2021 -0700
    New draft with edits from previous code reviews.
• src/hg/makeDb/trackDb/human/hg38/dbSnpArchiveHg38.ra
  • lines changed 31, context: html, text, full: html, text
    f02333eac281a5d6ad5fe023f0d70db2c20f09a4 Tue Jul 27 11:50:23 2021 -0700
    Fixing supertrack syntax to recommended guidelines for dbSnpArchive, previous working and tested working refs #27877 and #26719
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.html
  • lines changed 23, context: html, text, full: html, text
    51650e7bd89d9df0ca95de94b766381163b9c18b Mon Aug 2 08:06:47 2021 -0700
    New draft with edits from previous code reviews.
• src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.html
  • lines changed 92, context: html, text, full: html, text
    4ca20f1795e3d4cf3f0687889cf1c9e670abf35b Mon Aug 2 08:05:41 2021 -0700
    New details page.
• src/hg/makeDb/trackDb/human/hg38/ileumWang.html
  • lines changed 28, context: html, text, full: html, text
    51650e7bd89d9df0ca95de94b766381163b9c18b Mon Aug 2 08:06:47 2021 -0700
    New draft with edits from previous code reviews.
• src/hg/makeDb/trackDb/human/hg38/kidneyStewart.html
  • lines changed 79, context: html, text, full: html, text
    da13ad58f6199a876c748a7d873843b4307b3d73 Mon Aug 2 09:04:21 2021 -0700
    New details page.
• src/hg/makeDb/trackDb/human/hg38/liverMacParland.html
  • lines changed 11, context: html, text, full: html, text
    51650e7bd89d9df0ca95de94b766381163b9c18b Mon Aug 2 08:06:47 2021 -0700
    New draft with edits from previous code reviews.
• src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.html
  • lines changed 85, context: html, text, full: html, text
    4ca20f1795e3d4cf3f0687889cf1c9e670abf35b Mon Aug 2 08:05:41 2021 -0700
    New details page.
• src/hg/makeDb/trackDb/human/hg38/lungTravaglini2020.ra
  • lines changed 19, context: html, text, full: html, text
    8d4db7736e1e433be1359bf9c3002bf996c1cd4a Mon Jul 19 08:45:47 2021 -0700
    Added html setting to child stanzas. refs #27725
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.html
  • lines changed 13, context: html, text, full: html, text
    51650e7bd89d9df0ca95de94b766381163b9c18b Mon Aug 2 08:06:47 2021 -0700
    New draft with edits from previous code reviews.
• src/hg/makeDb/trackDb/human/hg38/pancreasBaron.html
  • lines changed 90, context: html, text, full: html, text
    4ca20f1795e3d4cf3f0687889cf1c9e670abf35b Mon Aug 2 08:05:41 2021 -0700
    New details page.
• src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.html
  • lines changed 87, context: html, text, full: html, text
    b55f7531286e4d654f0aa1899f60fc8255f0f8f2 Mon Aug 2 09:37:47 2021 -0700
    New details page.
• src/hg/makeDb/trackDb/human/hg38/rectumWang.html
  • lines changed 21, context: html, text, full: html, text
    51650e7bd89d9df0ca95de94b766381163b9c18b Mon Aug 2 08:06:47 2021 -0700
    New draft with edits from previous code reviews.
• src/hg/makeDb/trackDb/human/hg38/skinSoleBoldo.html
  • lines changed 88, context: html, text, full: html, text
    7976ac486f4c1fce03c3f6754e82bfacbc9fe543 Mon Aug 2 09:54:39 2021 -0700
    New details page.
• src/hg/makeDb/trackDb/mouse/mm10/dbSnpArchiveMm10.ra
  • lines changed 8, context: html, text, full: html, text
    f02333eac281a5d6ad5fe023f0d70db2c20f09a4 Tue Jul 27 11:50:23 2021 -0700
    Fixing supertrack syntax to recommended guidelines for dbSnpArchive, previous working and tested working refs #27877 and #26719
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
  • lines changed 22, context: html, text, full: html, text
    adf9e0ab72b7333b256857ad28c4be05676f9356 Wed Jul 28 13:00:49 2021 -0700
    add knownGene VM27
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f02333eac281a5d6ad5fe023f0d70db2c20f09a4 Tue Jul 27 11:50:23 2021 -0700
    Fixing supertrack syntax to recommended guidelines for dbSnpArchive, previous working and tested working refs #27877 and #26719
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.html
  • lines changed 17, context: html, text, full: html, text
    8a59d4f5c187773fb73c69298a032b6f3f403d55 Thu Jul 29 16:24:25 2021 -0700
    added Greek-letter names for variants. Added examples for nomenclature descriptions
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
  • lines changed 1, context: html, text, full: html, text
    e618b0d0a61a3c50464250108a5ead4446e35777 Thu Jul 29 17:09:39 2021 -0700
    Removing stale pennantIcon, no RM
• src/hg/utils/otto/knownGene/buildCore.sh
  • lines changed 112, context: html, text, full: html, text
    86190fe42f04ba7f10072f73b02dfc609ba0b587 Wed Jul 28 10:59:52 2021 -0700
    first cut at the script to build the core knownGene tables and files.
  • lines changed 56, context: html, text, full: html, text
    695f027f92b391a4309f52c446d2825ed20c788d Thu Jul 29 11:43:06 2021 -0700
    ongoing work on buildCore.sh
• src/hg/utils/otto/otto.crontab
  • lines changed 45, context: html, text, full: html, text
    970443639c19a0b93218f0a9ee13d8743f62dd5a Tue Jul 27 14:27:28 2021 -0700
    Adding the otto crontab to the kent tree, no RM
• src/hg/utils/otto/sarscov2phylo/extractPublicTree.sh
  • lines changed 103, context: html, text, full: html, text
    3feec259f20a7cc03affb9fae613492486bdd91a Wed Jul 28 15:41:37 2021 -0700
    Move out the extraction of the public-sequences-only tree from the combined tree into a separate script for ease of manually continuing runs when there's a failure (most often matUtils annotate -P failing due to a changed path in the tree).
• src/hg/utils/otto/sarscov2phylo/gisaidNameToCountry.pl
  • lines changed 2, context: html, text, full: html, text
    632628f9f28b14ca87d07d4baff47822579a5eb1 Wed Jul 28 15:40:58 2021 -0700
    Clean up stripping of trailing \r\n - code review, thx Jonathan.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 79, context: html, text, full: html, text
    3feec259f20a7cc03affb9fae613492486bdd91a Wed Jul 28 15:41:37 2021 -0700
    Move out the extraction of the public-sequences-only tree from the combined tree into a separate script for ease of manually continuing runs when there's a failure (most often matUtils annotate -P failing due to a changed path in the tree).
• src/lib/htmlPage.c
  • lines changed 2, context: html, text, full: html, text
    0b55999baeab139445bde4517e8346f6dea4514b Tue Jul 27 13:46:28 2021 -0700
    Adding COLOR to the list of recognized HTML input types, refs #27917
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    04401e668e9e0d50341dbb67e14616e4a085d42b Mon Aug 2 10:15:03 2021 -0700
    v419 preview1, refs #27854

• lines changed: 1563
• files changed: 54