All File Changes

v447_preview2 to v447_base (2023-04-17 to 2023-04-24) v447

• build/kent-core/makefile
  • lines changed 223, context: html, text, full: html, text
    e88893818af35a8708ac59c4572e44272de8cedc Wed Apr 19 05:17:59 2023 -0700
    and even more changes requested by debian, refs #12785
• src/browserbox/root/fetchCramReference.sh
  • lines changed 2, context: html, text, full: html, text
    e61a23efaaa4baa0c8060e6a332f6b94f3b96bca Fri Apr 21 09:01:34 2023 -0700
    The -I and -n flags conflict; keeping the one we want. No ticket
• src/hg/cgilib/pcrResult.c
  • lines changed 6, context: html, text, full: html, text
    036e633e37ba018df11c2b2cb96c1dbd2eb46320 Thu Apr 20 12:12:09 2023 -0700
    Restore a blank item name in the pcr results track, but stuff the primer pair name (which is now in the psls qName) into the map item name so clicks into hgc can still show the right primer details, refs #30925
• src/hg/hgPcr/hgPcr.c
  • lines changed 20, context: html, text, full: html, text
    469c053163292224b75ee9ebb41117f694aed36b Tue Apr 18 16:12:07 2023 -0700
    Add a checkbox to enable/disable saving multiple hgPcr searches into the same track, refs #30925
• src/hg/hgSearch/hgSearch.c
  • lines changed 23, context: html, text, full: html, text
    7ce36f0c36f7d858a22186a84f621082ca6b17a1 Fri Apr 21 09:40:49 2023 -0700
    When doing a singplePos redirect I forgot to check for supertrack child settings and was missing the parent visibilities on the url, refs #31090
• src/hg/hgTracks/cds.c
  • lines changed 1, context: html, text, full: html, text
    036e633e37ba018df11c2b2cb96c1dbd2eb46320 Thu Apr 20 12:12:09 2023 -0700
    Restore a blank item name in the pcr results track, but stuff the primer pair name (which is now in the psls qName) into the map item name so clicks into hgc can still show the right primer details, refs #30925
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    cff41d740a8e5ee4bbc5a3f4385b7e939f42841f Tue Apr 18 15:54:01 2023 -0700
    Put the forward and reverse hgPcr primers into the qName of the psl so when we have multiple results, we are sure to show the primer pair for the right psl, refs #30925
  • lines changed 2, context: html, text, full: html, text
    3d79b89141253b72477ac9276f8acfc125efc7c6 Thu Apr 20 02:54:47 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix small tweaks to dumpToLog feature, refs #30591
  • lines changed 3, context: html, text, full: html, text
    036e633e37ba018df11c2b2cb96c1dbd2eb46320 Thu Apr 20 12:12:09 2023 -0700
    Restore a blank item name in the pcr results track, but stuff the primer pair name (which is now in the psls qName) into the map item name so clicks into hgc can still show the right primer details, refs #30925
• src/hg/hgc/hgc.c
  • lines changed 12, context: html, text, full: html, text
    cff41d740a8e5ee4bbc5a3f4385b7e939f42841f Tue Apr 18 15:54:01 2023 -0700
    Put the forward and reverse hgPcr primers into the qName of the psl so when we have multiple results, we are sure to show the primer pair for the right psl, refs #30925
  • lines changed 22, context: html, text, full: html, text
    a408f434abb09575b4735f71224cfca9cb8c90dc Wed Apr 19 05:09:47 2023 -0700
    allowing longer descriptions in .as field labels. Even if there are any pre-existing as files with | characters in them, they will still show up nicely, just on a new line. no redmine yet
  • lines changed 1, context: html, text, full: html, text
    89dba208305664efd8142a38805d84c858473d16 Thu Apr 20 13:09:56 2023 -0700
    Allow dgvMerged track to be a bigBed and do the standard bigBed details page, refs #30873
• src/hg/hgc/hgc.h
  • lines changed 5, context: html, text, full: html, text
    937028df8583dc20713b1343522ddd038ad5375e Wed Apr 19 05:13:52 2023 -0700
    forgot to commit file in previous commit, no redmine
• src/hg/hgc/interactClick.c
  • lines changed 5, context: html, text, full: html, text
    46abf3fb921e63487aff04b1305c75adf26f67cf Mon Apr 17 20:41:00 2023 -0700
    When hgc makes a multiregion view file for interact tracks, it should make sure to account for the track using chromosome aliases, refs #31056
• src/hg/htdocs/FAQ/FAQgenes.html
  • lines changed 14, context: html, text, full: html, text
    62911c15d391ddc8b1ae94d2ccbfef7519fa67c9 Fri Apr 21 03:26:19 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix adding another genes FAQ for the specific question on duplicates in refGene, hopefully people will find this in google, refs #31077
  • lines changed 2, context: html, text, full: html, text
    6218aa92f1135a9cae1423439ddf13dddd65655e Fri Apr 21 03:27:45 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix fix typos in last commit
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 1, context: html, text, full: html, text
    90c7c79830fcf633543d0fdb16fdbc21f1ae6e6f Fri Apr 21 02:42:26 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix various doc fixes related to bigDataIndex, no redmine, email and galaxy ticket with Jennifer Jackson, see https://help.galaxyproject.org/t/send-files-from-galaxy-to-ucscs-eu-mirror/9921/3
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 8, context: html, text, full: html, text
    7bac7ad656d887ac590f13743461a5e676dbb89f Fri Apr 21 02:43:57 2023 -0700
    doc fixes around bigDataIndex, no redmine, galaxy ticket with Jennifer Jackson, see https://help.galaxyproject.org/t/send-files-from-galaxy-to-ucscs-eu-mirror/9921/3
• src/hg/htdocs/goldenPath/help/cram.html
  • lines changed 2, context: html, text, full: html, text
    90c7c79830fcf633543d0fdb16fdbc21f1ae6e6f Fri Apr 21 02:42:26 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix various doc fixes related to bigDataIndex, no redmine, email and galaxy ticket with Jennifer Jackson, see https://help.galaxyproject.org/t/send-files-from-galaxy-to-ucscs-eu-mirror/9921/3
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 8, context: html, text, full: html, text
    90c7c79830fcf633543d0fdb16fdbc21f1ae6e6f Fri Apr 21 02:42:26 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix various doc fixes related to bigDataIndex, no redmine, email and galaxy ticket with Jennifer Jackson, see https://help.galaxyproject.org/t/send-files-from-galaxy-to-ucscs-eu-mirror/9921/3
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 9, context: html, text, full: html, text
    7bac7ad656d887ac590f13743461a5e676dbb89f Fri Apr 21 02:43:57 2023 -0700
    doc fixes around bigDataIndex, no redmine, galaxy ticket with Jennifer Jackson, see https://help.galaxyproject.org/t/send-files-from-galaxy-to-ucscs-eu-mirror/9921/3
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 19, context: html, text, full: html, text
    7bac7ad656d887ac590f13743461a5e676dbb89f Fri Apr 21 02:43:57 2023 -0700
    doc fixes around bigDataIndex, no redmine, galaxy ticket with Jennifer Jackson, see https://help.galaxyproject.org/t/send-files-from-galaxy-to-ucscs-eu-mirror/9921/3
• src/hg/inc/cStraw.h
  • lines changed 3, context: html, text, full: html, text
    023255de913dda73eeceee882e1b5f824c94f34f Tue Apr 18 10:52:42 2023 -0700
    Need to catch errors on opening a hic file with Straw, because the magic string check can also generate an exception. refs #31071
• src/hg/inc/pcrResult.h
  • lines changed 1, context: html, text, full: html, text
    036e633e37ba018df11c2b2cb96c1dbd2eb46320 Thu Apr 20 12:12:09 2023 -0700
    Restore a blank item name in the pcr results track, but stuff the primer pair name (which is now in the psls qName) into the map item name so clicks into hgc can still show the right primer details, refs #30925
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    a04e280e8401aa9f7c02abf1c038b9aa6b253ab1 Mon Apr 24 10:18:34 2023 -0700
    New version number v447
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    671f8e4fac56f9dcd5497c1e45e7cda89d98cceb Wed Apr 19 14:45:03 2023 -0700
    Adding an asynchronous logging function for the javascript
  • lines changed 9, context: html, text, full: html, text
    3d79b89141253b72477ac9276f8acfc125efc7c6 Thu Apr 20 02:54:47 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix small tweaks to dumpToLog feature, refs #30591
• src/hg/js/utils.js
  • lines changed 24, context: html, text, full: html, text
    671f8e4fac56f9dcd5497c1e45e7cda89d98cceb Wed Apr 19 14:45:03 2023 -0700
    Adding an asynchronous logging function for the javascript
  • lines changed 1, context: html, text, full: html, text
    3d79b89141253b72477ac9276f8acfc125efc7c6 Thu Apr 20 02:54:47 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix small tweaks to dumpToLog feature, refs #30591
• src/hg/lib/cart.c
  • lines changed 25, context: html, text, full: html, text
    671f8e4fac56f9dcd5497c1e45e7cda89d98cceb Wed Apr 19 14:45:03 2023 -0700
    Adding an asynchronous logging function for the javascript
  • lines changed 1, context: html, text, full: html, text
    3d79b89141253b72477ac9276f8acfc125efc7c6 Thu Apr 20 02:54:47 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix small tweaks to dumpToLog feature, refs #30591
• src/hg/lib/hic.c
  • lines changed 5, context: html, text, full: html, text
    023255de913dda73eeceee882e1b5f824c94f34f Tue Apr 18 10:52:42 2023 -0700
    Need to catch errors on opening a hic file with Straw, because the magic string check can also generate an exception. refs #31071
• src/hg/lib/straw/cStraw.cpp
  • lines changed 14, context: html, text, full: html, text
    023255de913dda73eeceee882e1b5f824c94f34f Tue Apr 18 10:52:42 2023 -0700
    Need to catch errors on opening a hic file with Straw, because the magic string check can also generate an exception. refs #31071
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 67, context: html, text, full: html, text
    e5af81a97f124a83f19628ccf80c9c870403f752 Fri Apr 21 14:12:24 2023 -0700
    continuing adding CCGP genome browsers refs #30912
• src/hg/makeDb/doc/ccgpAsmHub/ccgp.orderList.tsv
  • lines changed 66, context: html, text, full: html, text
    fc52fd7f9debee0b2779f8dc340a03b2feaabcd1 Fri Apr 21 14:47:28 2023 -0700
    adding 66 more assemblies refs #30912
• src/hg/makeDb/doc/ccgpAsmHub/ccgp.taxId.asmId.class.txt
  • lines changed 66, context: html, text, full: html, text
    f7ecd61b761d9cfb0616c050471d1291ab7a7d12 Fri Apr 21 14:42:39 2023 -0700
    adding 66 more assemblies refs #30912
• src/hg/makeDb/doc/hprcAsmHub/assembly.hprcName.asmId.txt
  • lines changed 94, context: html, text, full: html, text
    6bf27cd221e1528b06c422696d0229e1f98fb2b2 Fri Apr 21 15:09:28 2023 -0700
    list to relate the NCBI names with the names used by HPRC refs #30508
• src/hg/makeDb/trackDb/human/hg19/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    e80df61390e3d7b9969163d58d386fcb9fcc418d Fri Apr 21 13:34:59 2023 -0700
    Adding the mouseOver to hg19 as well as hg38. Refs #30908
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 6, context: html, text, full: html, text
    c283cc94fbb268d9d9ec0989acace6308a25a665 Mon Apr 17 21:11:53 2023 -0700
    next version of Ensembl genes for HPRC genomes refs #30508
• src/hg/utils/otto/sarscov2phylo/getCncb.sh
  • lines changed 131, context: html, text, full: html, text
    f2aee59866d6bdd224a7183323f72390a861b328 Sat Apr 22 18:17:02 2023 -0700
    Auto-download new GenBase sequences from China National Center for Bioinformation.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 8, context: html, text, full: html, text
    2df325b2cfee5a71d16157bf3aaa62c3e6734ec3 Sat Apr 22 18:23:06 2023 -0700
    Guard against truncated download file which can happen despite successful return from datasets command.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
  • lines changed 225, context: html, text, full: html, text
    8ec3c55d2932bb09df06ae9bd9be0b0dd37c2ea9 Sat Apr 22 18:21:48 2023 -0700
    Overhaul detection of duplicates in previous day's protobuf vs. today's ID-mapping, and get latest sequence names from metadata, by first converting previous day's names to accessions only. Add in detection of new CNCB sequences.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 3, context: html, text, full: html, text
    7a92e3aa307573ab74f5f17cba55934b9a18ab15 Thu Apr 6 11:13:22 2023 -0700
    Corrections to XBB.1.2, XBB.2.3 and XBB.2.3.2: mask bases that aren't essential to the lineage definition. Order of mutations changed quite a bit for XBB.2.3[.2]. HT @corneliusroemer
  • lines changed 35, context: html, text, full: html, text
    d2edb9c3250f1d05950235c55998d9e00a450016 Sat Apr 22 18:24:17 2023 -0700
    New lineages and a few missed pango-maskings (C193T to C193N) from earlier.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
  • lines changed 5, context: html, text, full: html, text
    d091ea9bacb0841f1aa4b17b5f1e8a5219b43929 Sat Apr 22 18:25:31 2023 -0700
    Get new sequences from CNCB.
• src/hg/utils/otto/sarscov2phylo/util.sh
  • lines changed 5, context: html, text, full: html, text
    fa9ed9b7c17b901dd736a36049879099d23badd2 Sat Apr 22 18:26:59 2023 -0700
    Strip out more fluff from sequence names.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    a04e280e8401aa9f7c02abf1c038b9aa6b253ab1 Mon Apr 24 10:18:34 2023 -0700
    New version number v447
• src/jkOwnLib/gfPcrLib.c
  • lines changed 6, context: html, text, full: html, text
    cff41d740a8e5ee4bbc5a3f4385b7e939f42841f Tue Apr 18 15:54:01 2023 -0700
    Put the forward and reverse hgPcr primers into the qName of the psl so when we have multiple results, we are sure to show the primer pair for the right psl, refs #30925
• src/makefile
  • lines changed 2, context: html, text, full: html, text
    e88893818af35a8708ac59c4572e44272de8cedc Wed Apr 19 05:17:59 2023 -0700
    and even more changes requested by debian, refs #12785
• src/product/installer/browserSetup.sh
  • lines changed 11, context: html, text, full: html, text
    a1c69079b7b57db91458371d8367d55b7b016c79 Fri Apr 21 07:12:04 2023 -0700
    #Preview2 week - bugs introduced now will need a build patch to fix fixing mysql tables after gbic run, reported by Lon, no redmine
• src/product/scripts/fetchCramReference.sh
  • lines changed 2, context: html, text, full: html, text
    e61a23efaaa4baa0c8060e6a332f6b94f3b96bca Fri Apr 21 09:01:34 2023 -0700
    The -I and -n flags conflict; keeping the one we want. No ticket
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    c73979566e6734d112581b6982b31c07f6b8644c Mon Apr 24 10:17:23 2023 -0700
    v447 final build, refs #31044

• lines changed: 1211
• files changed: 52