All File Changes

v440_preview to v440_preview2 (2022-11-07 to 2022-11-14) v440

• confs/asia.hg.conf
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    2ec166626871846a759eeec5015569d74f6f641c Sun Nov 13 01:11:27 2022 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    2ec166626871846a759eeec5015569d74f6f641c Sun Nov 13 01:11:27 2022 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
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    2ec166626871846a759eeec5015569d74f6f641c Sun Nov 13 01:11:27 2022 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
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    2ec166626871846a759eeec5015569d74f6f641c Sun Nov 13 01:11:27 2022 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    588140729e49918f6f50cd3bc887a77f1c2bbd7a Mon Nov 7 16:08:10 2022 -0800
    Adding the public hub guidelines link to hgHubConnect, refs #30238
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    6341197a9466860f92232ddf81cc3df210159e68 Mon Nov 7 16:24:38 2022 -0800
    Cleaning up line limit, refs #30238
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 26, context: html, text, full: html, text
    d354f7c4ff9867b3a64ecaadba87ba2381371e27 Mon Nov 7 16:46:38 2022 -0800
    In Nextstrain view (JSON), show the Nextstrain clade and Pango lineage assigned by usher for uploaded samples. Make Pango lineage the default coloring, and add a filter to highlight uploaded samples so user immediately sees the uploaded samples' lineage(s) and placement in the subtree. Also, for uploaded names/IDs, don't truncate at first comma until we check whether line is a list of IDs / ID ranges.
• src/hg/hgPhyloPlace/phyloPlace.h
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    3b1a8fdcbd590a86ff2fe8a3256287708357419c Wed Nov 2 15:46:33 2022 -0700
    Raise the limit on how many sequences we'll show details for -- @corneliusroemer's request in #yatisht/usher/298.
  • lines changed 2, context: html, text, full: html, text
    d354f7c4ff9867b3a64ecaadba87ba2381371e27 Mon Nov 7 16:46:38 2022 -0800
    In Nextstrain view (JSON), show the Nextstrain clade and Pango lineage assigned by usher for uploaded samples. Make Pango lineage the default coloring, and add a filter to highlight uploaded samples so user immediately sees the uploaded samples' lineage(s) and placement in the subtree. Also, for uploaded names/IDs, don't truncate at first comma until we check whether line is a list of IDs / ID ranges.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 22, context: html, text, full: html, text
    d354f7c4ff9867b3a64ecaadba87ba2381371e27 Mon Nov 7 16:46:38 2022 -0800
    In Nextstrain view (JSON), show the Nextstrain clade and Pango lineage assigned by usher for uploaded samples. Make Pango lineage the default coloring, and add a filter to highlight uploaded samples so user immediately sees the uploaded samples' lineage(s) and placement in the subtree. Also, for uploaded names/IDs, don't truncate at first comma until we check whether line is a list of IDs / ID ranges.
  • lines changed 2, context: html, text, full: html, text
    11f81d207f0d0c4e66697e4df53f7cf2ed1f9a4d Tue Nov 8 13:08:17 2022 -0800
    Add node[branch_attrs][label][id] to JSON so links can be formed by node ID, HT @corneliusroemer in #yatisht/usher/#284.
• src/hg/hgTables/hgTables.c
  • lines changed 5, context: html, text, full: html, text
    ff1cf1f79afe9d6d19b4aa8e609b907868d2feed Tue Nov 8 16:38:58 2022 -0800
    don't assume there will be a current track in hgTables
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 1, context: html, text, full: html, text
    39f03efc4e38cefcf29a8456f52037a92363a89a Wed Nov 9 16:21:35 2022 -0800
    Typo fix from CR. Refs #30246
• src/hg/htdocs/staff.html
  • lines changed 20, context: html, text, full: html, text
    2a9fd3d0c5595449e78f5b0ebb9e757307ef4a31 Thu Nov 10 16:46:13 2022 -0800
    Updating staff page. No RM.
• src/hg/lib/featureBits.c
  • lines changed 3, context: html, text, full: html, text
    f1256eb735a0f31e9495e0f9d5dc3ec95fdf7eda Tue Nov 8 16:02:49 2022 -0800
    Fix negative strand exon number output in Table Browser, refs #30232
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 3, context: html, text, full: html, text
    4d648b0bb9722abbaacd781994254f1ac0b998de Fri Nov 11 10:28:10 2022 -0800
    adding a couple of assemblies per user requests refs#29545
• src/hg/makeDb/doc/assemblyEquivalence/update.2022-10-18.txt
  • lines changed 446, context: html, text, full: html, text
    5909d2770c119549fd088df7eb210679e6b93b27 Wed Nov 9 15:11:08 2022 -0800
    update to Ensembl v107 plus rapidRelease no redmine
• src/hg/makeDb/doc/hg38/ucscToEnsembl.txt
  • lines changed 276, context: html, text, full: html, text
    6ab4773bd8416a2c4442b6e2cbc96af077033383 Wed Nov 9 13:44:43 2022 -0800
    update for patch 14, turns out to be the same as before refs #29964
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    4d648b0bb9722abbaacd781994254f1ac0b998de Fri Nov 11 10:28:10 2022 -0800
    adding a couple of assemblies per user requests refs#29545
• src/hg/makeDb/trackDb/drosophila/dm6/reMap.ra
  • lines changed 1, context: html, text, full: html, text
    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/genCC.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg19/reMap.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV26lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV27lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV28lift37.ra
  • lines changed 1, context: html, text, full: html, text
    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV29lift37.ra
  • lines changed 1, context: html, text, full: html, text
    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV30lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV31lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV32lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV33lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV34lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV35lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV36lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV37lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV38lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV39lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV40lift37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.new.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.release2.new.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/dbSnpArchiveHg38.new.ra
  • lines changed 227, context: html, text, full: html, text
    866b02c9c682445729bd49417427e54a0c402fa7 Thu Nov 10 15:15:02 2022 -0800
    Making new.ra file for hg38 dbSnpArchive changes/updates, refs #30252
• src/hg/makeDb/trackDb/human/hg38/gerp.ra
  • lines changed 10, context: html, text, full: html, text
    897b8de3bc98cba637b52be332636ba35041ab2a Mon Nov 14 08:09:30 2022 -0800
    gerp for hg38, refs #30265
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1_1.html
  • lines changed 3, context: html, text, full: html, text
    4578730f96ad6711d1d614fb1994d66a5b86facf Wed Nov 9 13:58:38 2022 -0800
    Tweaking desc page from author feedback. No RM.
  • lines changed 1, context: html, text, full: html, text
    b4827c1da05cdd77a8faa1c92185a9f5edc232fe Wed Nov 9 14:21:27 2022 -0800
    Fixing small typo.
• src/hg/makeDb/trackDb/human/hg38/gtexEqtlHighConf.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/reMap.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/singleCellMerged.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/tabulaSapiens.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
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    897b8de3bc98cba637b52be332636ba35041ab2a Mon Nov 14 08:09:30 2022 -0800
    gerp for hg38, refs #30265
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV23.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV24.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV25.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV27.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV28.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV29.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV30.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV31.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV32.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV33.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV34.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV35.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV36.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV37.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV38.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV39.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV40.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.new.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/human/trackDb.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/mouse/mm10/reMap.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM11.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM14.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM15.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM17.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM18.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM19.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM20.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM21.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM22.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM23.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm10/wgEncodeGencodeVM24.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/mouse/mm39/reMap.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM26.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM27.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM28.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM29.ra
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    f6a1ffbc8acdedbd8b4ce11f1fb73aef70b18bdb Sat Nov 12 16:13:43 2022 -0800
    change older all gencode tracks to be hidden by default
• src/hg/makeDb/trackDb/trackDb.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/galaxyEna.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/pond.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
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    68bef8efb4e94146828cbdcda01a1abe508a86a9 Wed Nov 9 10:29:41 2022 -0800
    Sqwashing stale pennantIcons, no RM.
• src/hg/utils/automation/aliasTextToBed.pl
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    26d45e650717542b662ab602aa4d9a37dda67885 Wed Nov 9 19:14:57 2022 -0800
    generate error if a chromsome in first column of chromAlias is not in chromSizes instead of spew perl warnings
• src/hg/utils/automation/asmHubGatewayPage.pl
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    135828f0756c11a8c125d1bbef9d4839a51b44b7 Thu Nov 10 11:51:30 2022 -0800
    remove note about case sensitive gene name searchs, not necessary no redmin
• src/hg/utils/automation/asmHubTrackDb.sh
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    e54f20a28dc5dbe09d90abb37b633be3797eb66d Fri Nov 11 10:46:27 2022 -0800
    correct label field on ncbiRefSeqOther refs #29545
• src/hg/utils/automation/asmHubXenoRefGene.pl
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    811dd66056e8ee6ceca4b67ea0551a0540ded944 Thu Nov 10 11:15:09 2022 -0800
    eliminate the bit about name searching no redmine
• src/hg/utils/automation/xenoRefGeneIx.pl
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    60cbd8384a71282078c4651971c1c8857aa3be23 Thu Nov 10 11:25:22 2022 -0800
    not necessary to include both Case and non case strings ix is all lower case no redmine
• src/hg/utils/overlapSelect/chromAnn.c
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    2c43bbe76a2350dfd358bbb5047237243dcb984e Tue Nov 8 23:09:32 2022 -0800
    added a test case and improved debug and clarified code. However it was pointless, because there was not accutally a bug, just a confused user
• src/hg/utils/overlapSelect/selectTable.c
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    2c43bbe76a2350dfd358bbb5047237243dcb984e Tue Nov 8 23:09:32 2022 -0800
    added a test case and improved debug and clarified code. However it was pointless, because there was not accutally a bug, just a confused user
• src/hg/utils/overlapSelect/tests/expected/cdsOverlapGpBed12.bed
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    2c43bbe76a2350dfd358bbb5047237243dcb984e Tue Nov 8 23:09:32 2022 -0800
    added a test case and improved debug and clarified code. However it was pointless, because there was not accutally a bug, just a confused user
• src/hg/utils/overlapSelect/tests/input/cds-overlap.gencode.gp
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    2c43bbe76a2350dfd358bbb5047237243dcb984e Tue Nov 8 23:09:32 2022 -0800
    added a test case and improved debug and clarified code. However it was pointless, because there was not accutally a bug, just a confused user
• src/hg/utils/overlapSelect/tests/input/cds-overlap.rmsk.bed
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    2c43bbe76a2350dfd358bbb5047237243dcb984e Tue Nov 8 23:09:32 2022 -0800
    added a test case and improved debug and clarified code. However it was pointless, because there was not accutally a bug, just a confused user
• src/hg/utils/overlapSelect/tests/makefile
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    2c43bbe76a2350dfd358bbb5047237243dcb984e Tue Nov 8 23:09:32 2022 -0800
    added a test case and improved debug and clarified code. However it was pointless, because there was not accutally a bug, just a confused user
• src/inc/common.mk
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    0771e75d0cf20a731479d0231db8e3fd2357712a Fri Nov 11 13:00:53 2022 -0800
    new location for libmysqlclient on Mac OSX 12.6.1 Monterey arm64 arch no redmine
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    379ce66045730c6b05a996312622b9696cfdb78b Fri Nov 11 15:52:55 2022 -0800
    more libraries for kent source build on Mac OSX Monterey arm64 machine no redmine
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    7dbf62b3ebac4ec5f0ce9fd8c4dd8821f9c22c2c Sun Nov 13 18:39:41 2022 -0800
    closer to a legal compile on Mac OSX Monterey for arm64 architecture no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    02793f36716f0a88e3147ff02169fa99f3c6a5c9 Mon Nov 14 10:28:21 2022 -0800
    v440 preview2, refs #30233

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