All File Changes

v427_preview2 to v427_base (2022-02-14 to 2022-02-21) v427

• src/hg/cgilib/sessionThumbnail.c
  • lines changed 1, context: html, text, full: html, text
    0fe941a11146746fafbe81dffdd317074bd27ff4 Thu Feb 17 14:38:35 2022 -0800
    Fixing small logic error - when settings are used to force specific hgPublicSessions paths, the web path to a file should be based on the relevant setting, not the file path setting, no ticket
  • lines changed 2, context: html, text, full: html, text
    a30947b1ec3e1f14afc70537891759c32baf4154 Thu Feb 17 14:50:17 2022 -0800
    Fixing small logic error - determining if a string ends with a / should be calculated on the input, not on the output you haven't written yet. No ticket.
• src/hg/gar/gar.cgi.pl
  • lines changed 75, context: html, text, full: html, text
    fcc6dba75ad852dbc77d53999d574845c4c9f500 Wed Feb 16 20:20:59 2022 -0800
    the CGI receiver for the GenArk request page refs #28930
• src/hg/gar/garTable.pl
  • lines changed 1283, context: html, text, full: html, text
    6684918996cf61c1d1a7fb5ee3e6cb3a8a23f083 Fri Feb 18 09:27:46 2022 -0800
    version 0 before beginning modifications refs #28930
• src/hg/gar/garTable.sh
  • lines changed 103, context: html, text, full: html, text
    6684918996cf61c1d1a7fb5ee3e6cb3a8a23f083 Fri Feb 18 09:27:46 2022 -0800
    version 0 before beginning modifications refs #28930
• src/hg/gar/rebuild.sh
  • lines changed 32, context: html, text, full: html, text
    6684918996cf61c1d1a7fb5ee3e6cb3a8a23f083 Fri Feb 18 09:27:46 2022 -0800
    version 0 before beginning modifications refs #28930
• src/hg/gar/ucscEquiv.sh
  • lines changed 45, context: html, text, full: html, text
    6684918996cf61c1d1a7fb5ee3e6cb3a8a23f083 Fri Feb 18 09:27:46 2022 -0800
    version 0 before beginning modifications refs #28930
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    e4ed1facdb0060a449e8626b6574015d50881fe5 Wed Feb 16 15:54:09 2022 -0800
    Allowing vcg.gz custom track uploads again, refs #28915
  • lines changed 1, context: html, text, full: html, text
    380561300dc657184b93c33395263d3853e87e6c Thu Feb 17 16:26:35 2022 -0800
    Fixing fat finger mistake, refs #28915
• src/hg/hgTables/bam.c
  • lines changed 19, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/hg/hgTables/bigBed.c
  • lines changed 27, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/hg/hgTables/custom.c
  • lines changed 14, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/hg/hgTables/filterFields.c
  • lines changed 2, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/hg/hgTables/hgTables.c
  • lines changed 31, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/hg/hgTables/hgTables.h
  • lines changed 13, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/hg/hgTables/hic.c
  • lines changed 19, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/hg/hgTables/joining.c
  • lines changed 23, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/hg/hgTables/longRange.c
  • lines changed 17, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/hg/hgTables/maf.c
  • lines changed 1, context: html, text, full: html, text
    3daabd5c0256b5a9c02e071d09ec6172d56a7b3d Mon Feb 21 02:44:50 2022 -0800
    tiny code fix to address new gcc warning which is justified, no redmine
• src/hg/hgTables/mainPage.c
  • lines changed 42, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
  • lines changed 6, context: html, text, full: html, text
    677c0082f46dc7242db6b14ee3d79badc4bdf224 Thu Feb 17 10:00:14 2022 -0800
    Make note about adding .csv extension conditional on output type, refs #27623
• src/hg/hgTables/usage.c
  • lines changed 3, context: html, text, full: html, text
    0f718dba4d7acdde1a78c10e18d120cb49f54b96 Mon Feb 21 02:42:22 2022 -0800
    adding coord system note to hgTables, refs #28949
• src/hg/hgTracks/cds.c
  • lines changed 3, context: html, text, full: html, text
    73e706bbc55cb2eaa16c47e353f57103d3baaa8a Fri Feb 18 20:20:58 2022 -0800
    detected missing baseColorUseSequence rather tha SEGV
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    192f2d7825c9fab779962c9424c01e1f98876c92 Wed Feb 16 15:23:04 2022 -0800
    Revert "taking back accidental font size change, refs #28788" This reverts commit d6b685f5964b94f86db82ae4e02df4db410c32ec.
• src/hg/hgUserSuggestion/hgUserSuggestion.c
  • lines changed 8, context: html, text, full: html, text
    e3ffe3658c2a385ab0d628b0783864465e26f7c3 Fri Feb 18 14:41:11 2022 -0800
    code cleanup on hgSuggestion
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    6a634821ca3d72356dc52fc816c3b4651c471e3c Tue Feb 15 16:48:29 2022 -0800
    make a bigBed version of the TOGA track
• src/hg/hgc/togaClick.c
  • lines changed 200, context: html, text, full: html, text
    6a634821ca3d72356dc52fc816c3b4651c471e3c Tue Feb 15 16:48:29 2022 -0800
    make a bigBed version of the TOGA track
• src/hg/hgc/togaClick.h
  • lines changed 1, context: html, text, full: html, text
    6a634821ca3d72356dc52fc816c3b4651c471e3c Tue Feb 15 16:48:29 2022 -0800
    make a bigBed version of the TOGA track
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 12, context: html, text, full: html, text
    00057db86302a9c69088b6f89ee6884b428754d1 Mon Feb 14 10:59:56 2022 -0800
    Fixing incorrect ordering and titles suggested by refs #28912
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 56, context: html, text, full: html, text
    3093b11e9c0b496cbe59c362a6d64a0efd0001ca Thu Feb 17 14:53:22 2022 -0800
    Adding a new announcement about the Track Sets paper by Ana and b0b
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 9, context: html, text, full: html, text
    e216b3afb532ce1f353080ea960a58f010844440 Thu Feb 17 11:24:58 2022 -0800
    Adding Ana and b0b's paper now it has PMID
• src/hg/htdocs/googledcab671c1d5c7242.html
  • lines changed 1, context: html, text, full: html, text
    71d3bad369da23634a507ba7577005ec73ab6e5e Fri Feb 18 16:51:20 2022 -0800
    Google verification for Search console rm #28945
• src/hg/htdocs/images/newsArchImages/track_sets1.png
  • lines changed 0, context: html, text, full: html, text
    5e59c3033dbd0deed853de56dcfc3ff0381e6777 Thu Feb 17 14:35:24 2022 -0800
    Adding images for track sets paper announcement
• src/hg/htdocs/images/newsArchImages/track_sets2.png
  • lines changed 0, context: html, text, full: html, text
    5e59c3033dbd0deed853de56dcfc3ff0381e6777 Thu Feb 17 14:35:24 2022 -0800
    Adding images for track sets paper announcement
• src/hg/htdocs/inc/garModal.html
  • lines changed 28, context: html, text, full: html, text
    fffe3d880ef524fd079479587f11ea08ec3f4d2c Wed Feb 16 20:16:45 2022 -0800
    modal pop up page for GenArk request submission refs #28930
• src/hg/htdocs/inc/gbFooter.html
  • lines changed 1, context: html, text, full: html, text
    c2af722dc1de19ba7d02e3546204f9808c0649f2 Wed Feb 16 12:48:15 2022 -0800
    Updating copyright info to 2022. Refs #28923
• src/hg/htdocs/inc/gbFooterHardcoded.html
  • lines changed 1, context: html, text, full: html, text
    c2af722dc1de19ba7d02e3546204f9808c0649f2 Wed Feb 16 12:48:15 2022 -0800
    Updating copyright info to 2022. Refs #28923
• src/hg/htdocs/inc/gbsFooter.html
  • lines changed 1, context: html, text, full: html, text
    c2af722dc1de19ba7d02e3546204f9808c0649f2 Wed Feb 16 12:48:15 2022 -0800
    Updating copyright info to 2022. Refs #28923
• src/hg/htdocs/inc/jWestFooter.html
  • lines changed 1, context: html, text, full: html, text
    c2af722dc1de19ba7d02e3546204f9808c0649f2 Wed Feb 16 12:48:15 2022 -0800
    Updating copyright info to 2022. Refs #28923
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    3093b11e9c0b496cbe59c362a6d64a0efd0001ca Thu Feb 17 14:53:22 2022 -0800
    Adding a new announcement about the Track Sets paper by Ana and b0b
• src/hg/htdocs/robots.rr.txt
  • lines changed 1, context: html, text, full: html, text
    b33337fce474304b575c8167bcf33b709288660d Thu Feb 17 16:08:04 2022 -0800
    Adding a rule to stop robots from crawling custom track links, refs #28929
• src/hg/htdocs/style/gar.css
  • lines changed 499, context: html, text, full: html, text
    ad451c18f90f9da8836d5f72aaf49e56194ddb26 Wed Feb 16 20:17:49 2022 -0800
    css rules for for GenArk request page refs #28930
• src/hg/inc/rmskAlign.h
  • lines changed 1, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    87a799fab9e776e6d437edb5e0e7503d30541f46 Mon Feb 21 10:12:48 2022 -0800
    New version number v427
• src/hg/js/gar.js
  • lines changed 634, context: html, text, full: html, text
    fb6e28585e71195df1fecbe0b83aa80f5cd39a6d Wed Feb 16 16:25:51 2022 -0800
    working code refs #28930
  • lines changed 2, context: html, text, full: html, text
    0e4f88897ef3a4bb310a5d9cf85ddcc7b9ac4bc9 Wed Feb 16 20:15:17 2022 -0800
    modal page variable names need to be id unique refs #28930
• src/hg/lib/togaData.as
  • lines changed 36, context: html, text, full: html, text
    6a634821ca3d72356dc52fc816c3b4651c471e3c Tue Feb 15 16:48:29 2022 -0800
    make a bigBed version of the TOGA track
• src/hg/lib/togaInactMut.as
  • lines changed 15, context: html, text, full: html, text
    6a634821ca3d72356dc52fc816c3b4651c471e3c Tue Feb 15 16:48:29 2022 -0800
    make a bigBed version of the TOGA track
• src/hg/lib/togaNucl.as
  • lines changed 18, context: html, text, full: html, text
    6a634821ca3d72356dc52fc816c3b4651c471e3c Tue Feb 15 16:48:29 2022 -0800
    make a bigBed version of the TOGA track
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    596139b5338c6dbe305e35b37a4c5a4f284f7d6e Mon Jan 24 15:02:43 2022 -0800
    setting gnomAD hg38 to squish since it is so big refs #28666
• src/hg/makeDb/trackDb/uniprotAlpha.html
  • lines changed 21, context: html, text, full: html, text
    1ce5b46ce00a99dd7a61a0e68c67651bb75c0d55 Tue Feb 15 09:49:45 2022 -0800
    Updating and fixing some of Max additions to the UniProt track description page, refs #28560
• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
  • lines changed 8, context: html, text, full: html, text
    2c992eaad50f54b7480aef148a8cbbbbc2bc168d Mon Feb 21 01:30:07 2022 -0800
    adding links to bv-brc and niaid, refs #28949
  • lines changed 3, context: html, text, full: html, text
    f321aa30b499dd1dad183ecf5e63d9e3f1eeea72 Mon Feb 21 01:44:46 2022 -0800
    moving up BV-BRC link in wuhCor1 desc page, refs #28949
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    2c992eaad50f54b7480aef148a8cbbbbc2bc168d Mon Feb 21 01:30:07 2022 -0800
    adding links to bv-brc and niaid, refs #28949
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.html
  • lines changed 229, context: html, text, full: html, text
    2c992eaad50f54b7480aef148a8cbbbbc2bc168d Mon Feb 21 01:30:07 2022 -0800
    adding links to bv-brc and niaid, refs #28949
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
  • lines changed 216, context: html, text, full: html, text
    2c992eaad50f54b7480aef148a8cbbbbc2bc168d Mon Feb 21 01:30:07 2022 -0800
    adding links to bv-brc and niaid, refs #28949
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMutsV2.html
  • lines changed 8, context: html, text, full: html, text
    69e99ce86c9fc721ebbb0ece96887f4c0feefe57 Tue Feb 15 10:28:03 2022 -0800
    Adding fasta link refs #28914
  • lines changed 357, context: html, text, full: html, text
    2c992eaad50f54b7480aef148a8cbbbbc2bc168d Mon Feb 21 01:30:07 2022 -0800
    adding links to bv-brc and niaid, refs #28949
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMutsV2.ra
  • lines changed 267, context: html, text, full: html, text
    2c992eaad50f54b7480aef148a8cbbbbc2bc168d Mon Feb 21 01:30:07 2022 -0800
    adding links to bv-brc and niaid, refs #28949
• src/hg/mouseStuff/chainCleaner/chainCleaner.c
  • lines changed 15, context: html, text, full: html, text
    27747b7e78fb65a5fc35388b39a381a9937c0724 Wed Feb 16 15:23:21 2022 -0800
    a small chainCleaner change from Michael Hiller
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/utils/otto/omim/checkOmimUpload.sh
  • lines changed 1, context: html, text, full: html, text
    490598d3b0bd8599908253ece43d519d5772b5e9 Mon Feb 14 15:21:42 2022 -0800
    Adding change between otto running script in hive vs tree, refs Jonathan
  • lines changed 1, context: html, text, full: html, text
    cc76e234959d26c4be6274ccc857c293ddf1e4c4 Fri Feb 18 12:49:21 2022 -0800
    Disabling the no new table echo, no RM
• src/hg/utils/rmskAlignToPsl/makefile
  • lines changed 3, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/utils/rmskAlignToPsl/rmskAlignToPsl.c
  • lines changed 586, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/utils/rmskAlignToPsl/tests/expected/hg38Test.psl
  • lines changed 60, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/utils/rmskAlignToPsl/tests/expected/mm39ProbTest.err
  • lines changed 4, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/utils/rmskAlignToPsl/tests/expected/mm39ProbTest.psl
  • lines changed 10, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/utils/rmskAlignToPsl/tests/expected/mm39Test.psl
  • lines changed 4, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/utils/rmskAlignToPsl/tests/input/hg38.align.tsv
  • lines changed 81, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/utils/rmskAlignToPsl/tests/input/mm39.align.tsv
  • lines changed 6, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/utils/rmskAlignToPsl/tests/input/mm39.prob.align.tsv
  • lines changed 26, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/hg/utils/rmskAlignToPsl/tests/makefile
  • lines changed 30, context: html, text, full: html, text
    d7ff43fdbd408928d1d0b66a1f791e4635032c47 Sun Feb 20 08:44:04 2022 -0800
    add program to take repeat masker .align.tsv files and convert to PSL for use with pslMap
• src/inc/cheapcgi.h
  • lines changed 3, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    87a799fab9e776e6d437edb5e0e7503d30541f46 Mon Feb 21 10:12:48 2022 -0800
    New version number v427
• src/lib/cheapcgi.c
  • lines changed 6, context: html, text, full: html, text
    5e8e0ed53c05f2ef9b51ce897440bae308367f47 Wed Feb 9 14:45:54 2022 -0800
    Add csv output option to table browser to support opening files in Excel, refs #27623. Also change the output filename message to hint that Excel can auto-recognize .csv extensions and behave appropriately. Lastly, fix output dropdown selection to properly warn on update when using GTF output option or a snp table.
• src/lib/common.c
  • lines changed 2, context: html, text, full: html, text
    5613df12040240ef2a0779bccd3e0916e7e0700a Fri Feb 18 12:01:15 2022 -0800
    Fixing MacOS issue with readFd where single read call cannot ask for more than 2GB. fixes #28946
• src/lib/https.c
  • lines changed 2, context: html, text, full: html, text
    1d98fd724d46352fed719317c72d3e276ba56696 Sun Feb 20 23:46:21 2022 -0800
    Removing some domains from the https whitelist no longer needed since they updated their certs.
  • lines changed 32, context: html, text, full: html, text
    c2562408988670c1db95ef862f011097bbf54fec Mon Feb 21 00:45:33 2022 -0800
    Undoing a change made in 2016 since it is not compatible with MacOS. fixes #28948
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    d538526966dee5685ca9458ecdf64066135f820c Mon Feb 21 10:11:55 2022 -0800
    v427 final build, refs #28882

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• files changed: 80