All File Changes

v438_preview to v438_preview2 (2022-09-26 to 2022-10-03) v438

• confs/asia.hg.conf
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    10b6e49ee9a7d70d295e9bc66ba46a1040e6f900 Sun Oct 2 01:11:25 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    10b6e49ee9a7d70d295e9bc66ba46a1040e6f900 Sun Oct 2 01:11:25 2022 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 2, context: html, text, full: html, text
    10b6e49ee9a7d70d295e9bc66ba46a1040e6f900 Sun Oct 2 01:11:25 2022 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 14, context: html, text, full: html, text
    5a8586105ed720ed3fb1038c61db8fcfcc7f3ef6 Fri Sep 30 21:13:57 2022 -0700
    Some final cleanup for sqlSafef V2. fixes cdwMakeFileTags. no redmine.
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 1, context: html, text, full: html, text
    669de3ad32094c5c0a9272caa60d081cc7222141 Mon Sep 26 13:40:56 2022 -0700
    recognize the things that are type bigGenePred may have extra words tacked onto the end
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    1b064d465adce57c7f8b07e61d38e04ec385e0c9 Tue Sep 27 13:30:21 2022 -0700
    don't parallel load bigInteract
• src/hg/hgTracks/interactTrack.c
  • lines changed 1, context: html, text, full: html, text
    7eb7071e960db1722c1597e2d2f7b113868efbb2 Mon Sep 26 14:37:45 2022 -0700
    in intersection graphs in pack mode, don't descedn into the linkFeatures draw code if there are no items because thar be dragons
  • lines changed 1, context: html, text, full: html, text
    dc1ded825fcd848daa61680b21bcc01893a0075f Tue Sep 27 13:10:33 2022 -0700
    Revert "in intersection graphs in pack mode, don't descedn into the linkFeatures" This reverts commit 7eb7071e960db1722c1597e2d2f7b113868efbb2.
• src/hg/hgc/barChartClick.c
  • lines changed 27, context: html, text, full: html, text
    093cdb88859d6e144f97c121b9175f9e7ac98f07 Tue Sep 27 09:22:47 2022 -0700
    Get $<fieldName> substitution supported in bigBarChart url link outs, refs #29954
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    2e892c47ff9a4682a4f9868e52706f6e46b5b47b Tue Sep 27 13:22:09 2022 -0700
    Make urlLabel setting support variable substitutions to allow for custom labels, useful when '336104' is not in the url, refs #29954
• src/hg/inc/chromInfo.h
  • lines changed 9, context: html, text, full: html, text
    ea09f3a92d57f23c6a26118009a34a18ec7f46fb Fri Sep 30 15:27:54 2022 -0700
    some functions had not been declared here refs #29819
• src/hg/inc/jksql.h
  • lines changed 2, context: html, text, full: html, text
    5a8586105ed720ed3fb1038c61db8fcfcc7f3ef6 Fri Sep 30 21:13:57 2022 -0700
    Some final cleanup for sqlSafef V2. fixes cdwMakeFileTags. no redmine.
• src/hg/lib/cart.c
  • lines changed 6, context: html, text, full: html, text
    5ba6d13d8817b098b3594afe5704b3e6a52c3d61 Thu Sep 29 12:50:25 2022 -0700
    increase the size of the buffer to hold the default cart contents to be arbitrarily large
• src/hg/lib/chromInfo.c
  • lines changed 6, context: html, text, full: html, text
    c8ca88c9c4552b413376e7cf2a5b84100793b88b Fri Sep 30 15:26:43 2022 -0700
    allow chromInfo to read from URL refs #29819
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    5a8586105ed720ed3fb1038c61db8fcfcc7f3ef6 Fri Sep 30 21:13:57 2022 -0700
    Some final cleanup for sqlSafef V2. fixes cdwMakeFileTags. no redmine.
• src/hg/lib/wiggleCart.c
  • lines changed 1, context: html, text, full: html, text
    c6869c14d3ed3376970313ee12eed696ddc864ee Fri Sep 30 16:26:18 2022 -0700
    don't allow tracks that aren't composite children to set autoScale to group
• src/hg/makeDb/autoSql/viralzone.as
  • lines changed 14, context: html, text, full: html, text
    f3b0f36ba4671a8315afc12ec2eacf5e4c6b75c3 Fri Sep 30 03:13:20 2022 -0700
    adding monkeypox transcriptomic stage track, refs #30074
• src/hg/makeDb/doc/hg38/ukbDepletion.txt
  • lines changed 13, context: html, text, full: html, text
    80def04a3a6e24537a0669ecc0d61b189457bd62 Thu Sep 29 05:29:54 2022 -0700
    adding UK Biobank depletion rank score track, refs #30070
• src/hg/makeDb/doc/mpxvRivers/dynamicBlat.txt
  • lines changed 28, context: html, text, full: html, text
    1f903fb4d0e10487d6bb9305d74adf57fa3f3f52 Fri Sep 30 11:39:16 2022 -0700
    add files to dynamic blat server refs #29811
• src/hg/makeDb/doc/mpxvRivers/pcrAmplicon.txt
  • lines changed 3, context: html, text, full: html, text
    914384264d6d019d05db34ceec0e0ce8ddc9d8e3 Fri Sep 30 02:09:13 2022 -0700
    fixing monkeyprimer primer 102 manually, arg, refs #30010
• src/hg/makeDb/doc/mpxvRivers/viralzoneGenes.txt
  • lines changed 5, context: html, text, full: html, text
    f3b0f36ba4671a8315afc12ec2eacf5e4c6b75c3 Fri Sep 30 03:13:20 2022 -0700
    adding monkeypox transcriptomic stage track, refs #30074
• src/hg/makeDb/doc/wuhCor1/recomb.txt
  • lines changed 6, context: html, text, full: html, text
    bf8c83cb36f5e791e4c0fc9eeefe715cc06b1c80 Fri Sep 30 02:42:13 2022 -0700
    adding recombination track to SARS-CoV-2, refs #30074
• src/hg/makeDb/hgLoadOut/hgLoadOut.c
  • lines changed 15, context: html, text, full: html, text
    dc4322ce21733176ef6b04f060f15c6a3c7c773a Thu Sep 29 12:09:25 2022 -0700
    moving the reading of rmsk .out files into library function refs #29819
  • lines changed 3, context: html, text, full: html, text
    3dce48f138f6d1e533c85911b29c19d1f719ac85 Fri Sep 30 13:55:10 2022 -0700
    indicate input file options in the usage message refs #29819
• src/hg/makeDb/hgLoadOut/tests/GCA_001708105.1.expected.tab.gz
  • lines changed 0, context: html, text, full: html, text
    39b563455274f8e71dce53a9f8d9f8f5ad7d7832 Fri Sep 30 10:37:37 2022 -0700
    testing the URL input option refs #29819
• src/hg/makeDb/hgLoadOut/tests/chrCp.expected.tab
  • lines changed 198, context: html, text, full: html, text
    f84f4de709143cb83d1478762b1556de255e157c Thu Sep 29 12:05:39 2022 -0700
    preparing to use reading of rmsk.out file into a library function refs #29819
• src/hg/makeDb/hgLoadOut/tests/chrCp.fa.out.gz
  • lines changed 0, context: html, text, full: html, text
    f84f4de709143cb83d1478762b1556de255e157c Thu Sep 29 12:05:39 2022 -0700
    preparing to use reading of rmsk.out file into a library function refs #29819
• src/hg/makeDb/hgLoadOut/tests/makefile
  • lines changed 10, context: html, text, full: html, text
    f84f4de709143cb83d1478762b1556de255e157c Thu Sep 29 12:05:39 2022 -0700
    preparing to use reading of rmsk.out file into a library function refs #29819
  • lines changed 21, context: html, text, full: html, text
    39b563455274f8e71dce53a9f8d9f8f5ad7d7832 Fri Sep 30 10:37:37 2022 -0700
    testing the URL input option refs #29819
  • lines changed 4, context: html, text, full: html, text
    ff4077c982e6b7fc46830e9899120983065438d2 Fri Sep 30 10:38:37 2022 -0700
    testing the URL input option refs #29819
  • lines changed 10, context: html, text, full: html, text
    02b89750add031d61f9781126b261e412ef493da Fri Sep 30 10:47:20 2022 -0700
    use local copy of test when present refs #29819
• src/hg/makeDb/hgLoadOut/tests/triCas2.expected.md5sum
  • lines changed 1, context: html, text, full: html, text
    39b563455274f8e71dce53a9f8d9f8f5ad7d7832 Fri Sep 30 10:37:37 2022 -0700
    testing the URL input option refs #29819
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeGxfParser.py
  • lines changed 1, context: html, text, full: html, text
    6ce91b1d42d007a689c4444374f0f76a9b26e9ee Fri Sep 30 19:51:34 2022 -0700
    fix invalid variable name in error message
• src/hg/makeDb/outside/gencode/lib/gencode/gencodeGxfRec.py
  • lines changed 2, context: html, text, full: html, text
    1a436eaf846822c48298fbab5ac009889fe72f48 Fri Sep 30 19:51:56 2022 -0700
    added hgnc_id to standzrd GxF attributes that are parsed
  • lines changed 3, context: html, text, full: html, text
    6d307e25ee11d40aa0c65ff4d0971baec22f9356 Sat Oct 1 12:19:21 2022 -0700
    fix field name in toy GFF3 parser for GENCODE loads
• src/hg/makeDb/trackDb/ebola/eboVir3/spUniprot.html
  • lines changed 2, context: html, text, full: html, text
    ecc936e1b2c4bf8fbd37e1dc6bbc616b947c369e Tue Sep 27 07:29:58 2022 -0700
    fixing small typo in spUniprot track, no redmine, just saw this
• src/hg/makeDb/trackDb/human/constraintSuper.html
  • lines changed 41, context: html, text, full: html, text
    80def04a3a6e24537a0669ecc0d61b189457bd62 Thu Sep 29 05:29:54 2022 -0700
    adding UK Biobank depletion rank score track, refs #30070
• src/hg/makeDb/trackDb/human/constraintSuper.ra
  • lines changed 2, context: html, text, full: html, text
    80def04a3a6e24537a0669ecc0d61b189457bd62 Thu Sep 29 05:29:54 2022 -0700
    adding UK Biobank depletion rank score track, refs #30070
• src/hg/makeDb/trackDb/human/hg19/panelAppTracks.html
  • lines changed 12, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/makeDb/trackDb/human/hg38/gtexSingleCell.ra
  • lines changed 1, context: html, text, full: html, text
    093cdb88859d6e144f97c121b9175f9e7ac98f07 Tue Sep 27 09:22:47 2022 -0700
    Get $<fieldName> substitution supported in bigBarChart url link outs, refs #29954
  • lines changed 1, context: html, text, full: html, text
    2e892c47ff9a4682a4f9868e52706f6e46b5b47b Tue Sep 27 13:22:09 2022 -0700
    Make urlLabel setting support variable substitutions to allow for custom labels, useful when '336104' is not in the url, refs #29954
• src/hg/makeDb/trackDb/human/hg38/panelAppTracks.html
  • lines changed 18, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 57, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/makeDb/trackDb/human/hmc.ra
  • lines changed 1, context: html, text, full: html, text
    baa7c0f9f1c8d08da187dc9ce180e448d802bd39 Thu Sep 29 05:32:10 2022 -0700
    cleaning up UK Biobank depletion rank score trackdb, and removing HMC pennant icon, refs #30070
• src/hg/makeDb/trackDb/human/panelApp.html
  • lines changed 43, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/makeDb/trackDb/human/panelApp.ra
  • lines changed 52, context: html, text, full: html, text
    b699b06e04864f35702fbb42cbd20fdf9e67420c Fri Sep 30 08:42:24 2022 -0700
    panelApp trackDb file, refs #25568
  • lines changed 1, context: html, text, full: html, text
    6f12bc42ce58df255b9bb28320ab29b0956b12c2 Mon Oct 3 04:24:27 2022 -0700
    adding publications field to panelapp, refs #25568
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/makeDb/trackDb/human/ukbDepletion.ra
  • lines changed 18, context: html, text, full: html, text
    80def04a3a6e24537a0669ecc0d61b189457bd62 Thu Sep 29 05:29:54 2022 -0700
    adding UK Biobank depletion rank score track, refs #30070
  • lines changed 8, context: html, text, full: html, text
    baa7c0f9f1c8d08da187dc9ce180e448d802bd39 Thu Sep 29 05:32:10 2022 -0700
    cleaning up UK Biobank depletion rank score trackdb, and removing HMC pennant icon, refs #30070
  • lines changed 2, context: html, text, full: html, text
    30121498c6fa71d6fe94a21d48c63130dd370572 Thu Sep 29 06:39:51 2022 -0700
    last author suggests to add deCODE to uk biobank score, refs #30070
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    70e06f150344d64bfd5cb16e70b9f65e68289c69 Mon Oct 3 09:23:46 2022 -0700
    add mpxvRivers to normal trackDb build
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    37720f2ddc791da76c5f08fd33bc0a81dba783cb Fri Sep 30 06:10:49 2022 -0700
    adding doWiggle to tagTypes, no idea how that was missing... apparently we have no single track that uses it, no redmine
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 97, context: html, text, full: html, text
    16db4fab0d0beacea2a743bde43856408a1847d1 Wed Sep 28 12:05:06 2022 -0700
    adding definitions for chainNetHs1 refs #29819
  • lines changed 14, context: html, text, full: html, text
    af7fd9fe9619c76334b32d4598ea54bb31d98d4b Wed Sep 28 16:33:16 2022 -0700
    better short long lables for hs1 refs #29819
• src/hg/makeDb/trackDb/virus/mpxvRivers/pcrAmplicon.html
  • lines changed 2, context: html, text, full: html, text
    914384264d6d019d05db34ceec0e0ce8ddc9d8e3 Fri Sep 30 02:09:13 2022 -0700
    fixing monkeyprimer primer 102 manually, arg, refs #30010
• src/hg/makeDb/trackDb/virus/mpxvRivers/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f3b0f36ba4671a8315afc12ec2eacf5e4c6b75c3 Fri Sep 30 03:13:20 2022 -0700
    adding monkeypox transcriptomic stage track, refs #30074
  • lines changed 1, context: html, text, full: html, text
    633b963290422cb3bbfbe3c7970f1e960473292e Fri Sep 30 08:31:55 2022 -0700
    small changes to the monkeypox browser trackDb, no redmine
• src/hg/makeDb/trackDb/virus/mpxvRivers/viralzone.html
  • lines changed 70, context: html, text, full: html, text
    f3b0f36ba4671a8315afc12ec2eacf5e4c6b75c3 Fri Sep 30 03:13:20 2022 -0700
    adding monkeypox transcriptomic stage track, refs #30074
• src/hg/makeDb/trackDb/virus/mpxvRivers/viralzone.ra
  • lines changed 18, context: html, text, full: html, text
    f3b0f36ba4671a8315afc12ec2eacf5e4c6b75c3 Fri Sep 30 03:13:20 2022 -0700
    adding monkeypox transcriptomic stage track, refs #30074
  • lines changed 8, context: html, text, full: html, text
    633b963290422cb3bbfbe3c7970f1e960473292e Fri Sep 30 08:31:55 2022 -0700
    small changes to the monkeypox browser trackDb, no redmine
• src/hg/makeDb/trackDb/virus/wuhCor1/recomb.html
  • lines changed 35, context: html, text, full: html, text
    bf8c83cb36f5e791e4c0fc9eeefe715cc06b1c80 Fri Sep 30 02:42:13 2022 -0700
    adding recombination track to SARS-CoV-2, refs #30074
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    bf8c83cb36f5e791e4c0fc9eeefe715cc06b1c80 Fri Sep 30 02:42:13 2022 -0700
    adding recombination track to SARS-CoV-2, refs #30074
  • lines changed 19, context: html, text, full: html, text
    09caafffbfa1ca9b04f613b6db5223aede591180 Fri Sep 30 02:51:14 2022 -0700
    trying to move to bottom of browser image, refs #30074
  • lines changed 1, context: html, text, full: html, text
    c92f7b90d84743f704b29b131f7bf4e33aefb2f5 Fri Sep 30 02:53:36 2022 -0700
    making recomb in wuCor1 a bit smaller, refs #30074
• src/hg/mouseStuff/netClass/netClass.c
  • lines changed 30, context: html, text, full: html, text
    aa6447741ae61479b43cbd2b02182aa405487dab Fri Sep 30 15:19:00 2022 -0700
    can now read qSizes from file or URL refs #29819
• src/hg/mouseStuff/netClass/tests/dm6.apiMel4.expected.net.gz
  • lines changed 0, context: html, text, full: html, text
    1759ea445907a44278042b057685fa448325c845 Fri Sep 30 11:44:18 2022 -0700
    preparing to alter netClass to work with assembly hubs refs #29819
• src/hg/mouseStuff/netClass/tests/dm6.apiMel4.noClass.net.gz
  • lines changed 0, context: html, text, full: html, text
    1759ea445907a44278042b057685fa448325c845 Fri Sep 30 11:44:18 2022 -0700
    preparing to alter netClass to work with assembly hubs refs #29819
• src/hg/mouseStuff/netClass/tests/makefile
  • lines changed 13, context: html, text, full: html, text
    1759ea445907a44278042b057685fa448325c845 Fri Sep 30 11:44:18 2022 -0700
    preparing to alter netClass to work with assembly hubs refs #29819
  • lines changed 12, context: html, text, full: html, text
    aa6447741ae61479b43cbd2b02182aa405487dab Fri Sep 30 15:19:00 2022 -0700
    can now read qSizes from file or URL refs #29819
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    6b2cab8abbdd64d0bf86e1d4cdbe35b41e717d59 Fri Sep 30 15:25:14 2022 -0700
    need to have bash pipefail to make it exit on a command error refs #29819
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    8b94d24f7e61509d03bde9f91472a6d20651c3da Fri Sep 30 21:36:09 2022 -0700
    fixing broken make clean for mouseStuff/netClass
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 16, context: html, text, full: html, text
    75892bebe2505e10302cb56e9e1050bd811351d9 Tue Sep 27 09:03:45 2022 -0700
    accomodate promoted hubs with db but no chromInfo refs #29819
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 17, context: html, text, full: html, text
    75892bebe2505e10302cb56e9e1050bd811351d9 Tue Sep 27 09:03:45 2022 -0700
    accomodate promoted hubs with db but no chromInfo refs #29819
  • lines changed 12, context: html, text, full: html, text
    b0b850bdc2557fed7f69594bc8fe013d478dbe85 Wed Sep 28 10:19:12 2022 -0700
    fixups for hs1 to database assemblies refs #29819
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    587c0ae924cde64738db226abbf1b0ef4ba86ff9 Wed Sep 28 11:12:52 2022 -0700
    fixups for hs1 to database assemblies refs #29819
• src/hg/utils/automation/doRecipBest.pl
  • lines changed 11, context: html, text, full: html, text
    75892bebe2505e10302cb56e9e1050bd811351d9 Tue Sep 27 09:03:45 2022 -0700
    accomodate promoted hubs with db but no chromInfo refs #29819
  • lines changed 6, context: html, text, full: html, text
    b0b850bdc2557fed7f69594bc8fe013d478dbe85 Wed Sep 28 10:19:12 2022 -0700
    fixups for hs1 to database assemblies refs #29819
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 1, context: html, text, full: html, text
    2bf1e00740d90f2c6879c12f6b502222fc2393da Fri Sep 30 21:15:53 2022 -0700
    fix for makeGenomeDb.pl from hg38 patch14
• src/hg/utils/otto/panelApp/cnv.as
  • lines changed 37, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/utils/otto/panelApp/cnv.py
  • lines changed 200, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/utils/otto/panelApp/genes.as
  • lines changed 41, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/utils/otto/panelApp/genes.py
  • lines changed 425, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
  • lines changed 52, context: html, text, full: html, text
    88d86eb7a11bad9d37c6908d3ab5e5c2e1fc1273 Mon Oct 3 03:39:03 2022 -0700
    updating panelApp otto, refs #25568
• src/hg/utils/otto/panelApp/makefile
  • lines changed 6, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/utils/otto/panelApp/tandRep.as
  • lines changed 44, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/utils/otto/panelApp/tandRep.py
  • lines changed 223, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/utils/otto/panelApp/test.py
  • lines changed 447, context: html, text, full: html, text
    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
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    c4e4f05177a63a6d7a4e42c87c54d676f2d54b73 Fri Sep 30 08:41:25 2022 -0700
    removing test file committed by mistake, no redmine
• src/hg/utils/otto/panelApp/updatePanelApp
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    f94190412d16ea558ace1ec9ea175db39aaa104b Fri Sep 30 08:40:43 2022 -0700
    panelApp otto job, refs #25568
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
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    ed83da4edfadf6a6952d43aee9853a69a7d3ca06 Tue Sep 27 10:57:09 2022 -0700
    Accumulated changes over the past month: Change BA.2 representative sequence after pruning a bunch of basal incomplete sequences. Expand masking of 28362-28370 deletion in BA.2 branch to 28361-28371. Mask 21765-21770 and 686-694 deletions in BA.4. Mask homoplasic 28877+28878 in BA.2 branch. Mask a bunch of 5' UTR sites that were causing a lot of messes in BA.2 branch. Mask a bunch of reversion sites in BA.2.75 and BA.5.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    612e090ae2bd69331bf2b612961eaeb834e5c19c Mon Sep 26 13:07:49 2022 -0700
    Added a ridiculous number of new lineages: BLs, BMs, BN-CA, BA.4s, BA.5s, XAW-XBC. Also old lineages B.1.631 and XB, and proposed1006. Removed BA.5.1.13 (withdrawn). Tweaked some paths and removed BF.3.1_revs after adding branch-specific masking on BA.2.75 and BA.5.
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    9cd6960c3ab7292990b5c8a9c29085e30266c890 Tue Sep 27 10:48:21 2022 -0700
    Resolve some unnecessary Ns to expected values in sublineages of BA.2 and BA.5.
• src/inc/repMask.h
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    dc4322ce21733176ef6b04f060f15c6a3c7c773a Thu Sep 29 12:09:25 2022 -0700
    moving the reading of rmsk .out files into library function refs #29819
• src/lib/repMask.c
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    dc4322ce21733176ef6b04f060f15c6a3c7c773a Thu Sep 29 12:09:25 2022 -0700
    moving the reading of rmsk .out files into library function refs #29819
• src/utils/qa/weeklybld/buildEnv.csh
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    6924047ef25d880a8257603c4e3cbb94de75d2e2 Mon Oct 3 10:06:35 2022 -0700
    v438 preview2, refs #30058

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• files changed: 96