All File Changes

v453_preview to v453_preview2 (2023-08-13 to 2023-08-21) v453

• build/kent-core/makeKentCore.rules
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    1940e5051adfdd71d35c9a329cd8e3bc407421a1 Wed Aug 16 05:22:45 2023 -0700
    fixing kent-core problem where a lot of tools were missing, refs #30812
• src/hg/hgPcr/hgPcr.c
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    4d7ad4d7fff4de41ae6ff3d1999df2cf640108db Tue Aug 15 07:53:17 2023 -0700
    docing primer3 formula that we use, refs #31950
• src/hg/hgTracks/hgTracks.c
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    f59ccdee6ad81274ffd827d1fed343cb6ba871a9 Mon Aug 14 14:54:58 2023 -0700
    don't open SQL connection is pcrResults unless it's using a target database (which isn't supported on hubs)
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    cae88d4a9f34c86d6a2af29b9a73c9957b237bdb Wed Aug 16 06:08:51 2023 -0700
    Revert "evert "adding timer to make sure that slow performance warning is shown even if page doesnt load, refs #31576"" This reverts commit 1876769e8169968bc53619c1b8a257ec76b2f74f.
• src/hg/htdocs/FAQ/FAQgenes.html
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    07c2860f23ceef6fd2952c5e0d10bd817dbe67f2 Tue Aug 15 10:24:28 2023 -0700
    Updating the FAQ on mitochondrial annotations for gene tracks, refs #19880
• src/hg/htdocs/cite.html
  • lines changed 93, context: html, text, full: html, text
    2742d9a7607a7e9f1862358779044a128b576fd4 Thu Aug 17 02:15:18 2023 -0700
    trying to improve cite.html a little, no redmine yet
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    e225d7f90a2efc41399a8739dac10b34ae5686c7 Thu Aug 17 04:58:55 2023 -0700
    few more changes to cite.html a little, no redmine
• src/hg/htdocs/goldenPath/help/publicHubGuidelines.html
  • lines changed 4, context: html, text, full: html, text
    f6e7622cea6e03b73d8c4a2347c14c386d40f99f Wed Aug 16 12:45:16 2023 -0700
    Tweaking the wording to make sure at least one track is turned on in public hubs as per our guidelines, refs #31767
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 44, context: html, text, full: html, text
    00edcd80bade80a533d5392af0106ab36daffd4f Thu Aug 17 17:15:41 2023 -0700
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #30837 #30838 #30839
• src/hg/htdocs/indexNews.html
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    00edcd80bade80a533d5392af0106ab36daffd4f Thu Aug 17 17:15:41 2023 -0700
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #30837 #30838 #30839
• src/hg/lib/chainArrange.as
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    cc15a08c33bde6a8bf15b0bf78548ef2b466a560 Sun Aug 13 12:29:29 2023 -0700
    correct the name for chainArrange
• src/hg/lib/hui.c
  • lines changed 4, context: html, text, full: html, text
    85b69d6ab5a3316fa2576a446cc5c55d86aa0d52 Fri Aug 18 17:02:02 2023 -0700
    all users to specify the label for the field that controls squishyPack
• src/hg/lib/instaPort.c
  • lines changed 2, context: html, text, full: html, text
    be4195f2c5ee017ac4ca603f7742bb70ed457e74 Mon Aug 14 14:23:51 2023 -0700
    take out a pesky printf that will become an optional dialog in the future
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    452c520b5692e08fa3977dc02d81d72d0116f69d Sun Aug 13 13:30:59 2023 -0700
    adding GCA_018873775.2_hg01243.v3.0 human (HG01243 John Hopkins 2021) for user interested in a different chrY/CM034974.1 refs #31844
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    ee2d91d9f91e87f02680184075bf8592b3a6ec93 Wed Aug 16 10:06:22 2023 -0700
    adding a number of primates discovered in a paper from the Illumina primate project refs #31528
• src/hg/makeDb/doc/hg19.txt
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    4adc5c603e035b607c14f9953f4196eeca3f93d1 Fri Aug 18 03:46:19 2023 -0700
    hgmd 2021 update, refs #14280
• src/hg/makeDb/doc/hg38/hgmd.txt
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    4adc5c603e035b607c14f9953f4196eeca3f93d1 Fri Aug 18 03:46:19 2023 -0700
    hgmd 2021 update, refs #14280
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    7c70450f4256398c6e502617f506d6c6585434b0 Fri Aug 18 04:03:34 2023 -0700
    hgmd 2021 update hg38, refs #14280
• src/hg/makeDb/doc/hg38/hprcReChain.txt
  • lines changed 108, context: html, text, full: html, text
    7f114623aa512095de2a6a83cab942ca3829ea60 Tue Aug 15 10:18:17 2023 -0700
    reChain the chains refs #31561
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
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    7c70450f4256398c6e502617f506d6c6585434b0 Fri Aug 18 04:03:34 2023 -0700
    hgmd 2021 update hg38, refs #14280
• src/hg/makeDb/doc/hs1/t2t-supplied.txt
  • lines changed 14, context: html, text, full: html, text
    83907f5791ff62eaef130ea0b0ded3f437ff7ad6 Tue Aug 15 14:58:47 2023 -0700
    t2t-chm13 file fix
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    3545ad4bc93b9a36a73ad9f2f9005ddcdb87bd47 Tue Aug 15 16:42:41 2023 -0700
    fixed doc to match accidental rename in directory
• src/hg/makeDb/doc/macFas5/lastzRuns.txt
  • lines changed 95, context: html, text, full: html, text
    6997c15d6e5bba74c31803ae79cd1be779688f7a Sun Aug 13 14:28:50 2023 -0700
    crab-eating macaque (GCA_011100615.1) vs. macFas5, lastz/chain/net run for user, refs #31769
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    452c520b5692e08fa3977dc02d81d72d0116f69d Sun Aug 13 13:30:59 2023 -0700
    adding GCA_018873775.2_hg01243.v3.0 human (HG01243 John Hopkins 2021) for user interested in a different chrY/CM034974.1 refs #31844
  • lines changed 36, context: html, text, full: html, text
    ee2d91d9f91e87f02680184075bf8592b3a6ec93 Wed Aug 16 10:06:22 2023 -0700
    adding a number of primates discovered in a paper from the Illumina primate project refs #31528
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    00edcd80bade80a533d5392af0106ab36daffd4f Thu Aug 17 17:15:41 2023 -0700
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #30837 #30838 #30839
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
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    bae4d7622280c17149e475da24502ee29de69920 Mon Aug 14 17:05:15 2023 -0700
    Fixing gnomAD filters which had incorrect ranges causing all items to be hidden by default, refs #31962
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV43lift37.ra
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    883535e45177d62d6495ebefbc13682e33b00033 Thu Aug 17 11:27:48 2023 -0700
    Staging 3 All GENCODE tracks, refs #30837 #30839 #30838
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV44lift37.ra
  • lines changed 1, context: html, text, full: html, text
    883535e45177d62d6495ebefbc13682e33b00033 Thu Aug 17 11:27:48 2023 -0700
    Staging 3 All GENCODE tracks, refs #30837 #30839 #30838
• src/hg/makeDb/trackDb/human/hg38/chainsReHprc.ra
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    de24277b1786c47fa9ba420c0858f56bb648f981 Tue Aug 15 11:50:57 2023 -0700
    add the re-chain HPRC alignments refs #31561
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    baf353f458d71234e27d15f6c1a3ef8cf703625a Thu Aug 17 19:24:18 2023 -0700
    now ordered by population then subpopulation and with longer subpopulation labels refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
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    8e3a8202a0a0503451ab3a466683448b704c956d Sun Aug 13 12:42:04 2023 -0700
    add HPRC rearrangement summary tracks to hg38
• src/hg/makeDb/trackDb/human/hg38/hprcArrV1.html
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    e0ca9650735ee5e9dd92811e127e15b74e1ac060 Mon Aug 14 14:03:40 2023 -0700
    add a tiny bit of method doc to hprc rearrangement summary tracks
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    3299cac6d6b5348138c1517187311a7a914cb030 Fri Aug 18 17:26:49 2023 -0700
    add squishyPackLabel to hg38 knownGene
• src/hg/makeDb/trackDb/human/hg38/knownGeneV43.html
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    84e74564b378c3f4da31aea1c5e62c67a395575c Thu Aug 17 11:07:22 2023 -0700
    Adding an anchor to the squishy pank transcript explanation so we can link to it, refs #31834
• src/hg/makeDb/trackDb/human/hg38/netsReHprc.ra
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    e77b7fbee5c6e7693e1ebb796a0af57cccd6fcfe Thu Aug 17 11:49:42 2023 -0700
    add the re-net HPRC alignments refs #31561
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    8f584e5787939093cc317e78db7f5ceb2927bc1f Thu Aug 17 19:04:22 2023 -0700
    longer labels on the subpopulations refs #31561
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    bc3bb05dc921ff5bfca856abaf519bb2eab9134e Thu Aug 17 19:27:19 2023 -0700
    with correct priorities refs #31561
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
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    6d71edab2f5be83d635411c1cd3de8e343c26115 Sun Aug 20 15:10:13 2023 -0700
    now with phyloP track refs #31528
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    00edcd80bade80a533d5392af0106ab36daffd4f Thu Aug 17 17:15:41 2023 -0700
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #30837 #30838 #30839
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    4cf25e53e77ad1de56b7bd119e8a473f58c9fd32 Sun Aug 13 12:58:25 2023 -0700
    add hprcArr.ra to hg38/trackDb.ra
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    de24277b1786c47fa9ba420c0858f56bb648f981 Tue Aug 15 11:50:57 2023 -0700
    add the re-chain HPRC alignments refs #31561
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    e77b7fbee5c6e7693e1ebb796a0af57cccd6fcfe Thu Aug 17 11:49:42 2023 -0700
    add the re-net HPRC alignments refs #31561
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV43.ra
  • lines changed 1, context: html, text, full: html, text
    883535e45177d62d6495ebefbc13682e33b00033 Thu Aug 17 11:27:48 2023 -0700
    Staging 3 All GENCODE tracks, refs #30837 #30839 #30838
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV44.ra
  • lines changed 1, context: html, text, full: html, text
    883535e45177d62d6495ebefbc13682e33b00033 Thu Aug 17 11:27:48 2023 -0700
    Staging 3 All GENCODE tracks, refs #30837 #30839 #30838
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
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    b671ee33a104a5b4e1a93e23271db96455381898 Mon Aug 21 03:28:55 2023 -0700
    removing submission ID field from clinvar tracks hgc page, refs #31970
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.alpha.ra
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    379796bee0c8cb25c143f10836e1b8b6209eac37 Thu Aug 17 11:18:02 2023 -0700
    VM33 knownGene trackDb
• src/hg/makeDb/trackDb/mouse/mm39/knownGeneVM33.html
  • lines changed 143, context: html, text, full: html, text
    379796bee0c8cb25c143f10836e1b8b6209eac37 Thu Aug 17 11:18:02 2023 -0700
    VM33 knownGene trackDb
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    00edcd80bade80a533d5392af0106ab36daffd4f Thu Aug 17 17:15:41 2023 -0700
    Announcing the release of All GENCODE for hg38, hg19, and mm39. refs #30837 #30838 #30839
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    379796bee0c8cb25c143f10836e1b8b6209eac37 Thu Aug 17 11:18:02 2023 -0700
    VM33 knownGene trackDb
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM32.ra
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    883535e45177d62d6495ebefbc13682e33b00033 Thu Aug 17 11:27:48 2023 -0700
    Staging 3 All GENCODE tracks, refs #30837 #30839 #30838
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM33.ra
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    883535e45177d62d6495ebefbc13682e33b00033 Thu Aug 17 11:27:48 2023 -0700
    Staging 3 All GENCODE tracks, refs #30837 #30839 #30838
• src/hg/makeDb/trackDb/tagTypes.tab
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    98d908ff5f395fb6dc954d46cd330b5f6d509ae0 Fri Aug 18 17:30:10 2023 -0700
    oops... need to update tagTypes.tab
• src/hg/makefile
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    1940e5051adfdd71d35c9a329cd8e3bc407421a1 Wed Aug 16 05:22:45 2023 -0700
    fixing kent-core problem where a lot of tools were missing, refs #30812
• src/hg/mouseStuff/makefile
  • lines changed 5, context: html, text, full: html, text
    1940e5051adfdd71d35c9a329cd8e3bc407421a1 Wed Aug 16 05:22:45 2023 -0700
    fixing kent-core problem where a lot of tools were missing, refs #30812
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 9, context: html, text, full: html, text
    2ce0876f4171ec948fb7705a9f42047e0f059eea Wed Aug 16 09:24:11 2023 -0700
    get the ebiGene and ensGene tests correct and protect against missing liftOver file in a blat directory refs #31844
• src/hg/utils/automation/doAssemblyHub.pl
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    167a944687bd484f0dc6c8821749c08053a2a0a5 Sun Aug 13 18:47:43 2023 -0700
    add -ram argument to doAugustus to allow smaller ram size on the paraRun, this should be an argument to the paraRun setup no redmine
• src/hg/utils/automation/doAugustus.pl
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    167a944687bd484f0dc6c8821749c08053a2a0a5 Sun Aug 13 18:47:43 2023 -0700
    add -ram argument to doAugustus to allow smaller ram size on the paraRun, this should be an argument to the paraRun setup no redmine
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
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    416dec4bcf1854bcc0cf18e6521379dd601a7231 Sun Aug 13 18:37:33 2023 -0700
    allow -ram=Ng argument to get through to the para make command no redmine
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    5b4e0ab9dcf0345d588a88049923a619515ed211 Sun Aug 13 18:38:47 2023 -0700
    allow -ram=Ng argument to get through to the para make command no redmine
• src/hg/utils/chainArrange/chainArrange.c
  • lines changed 158, context: html, text, full: html, text
    474877488f16b5c6888313e4d25dc4b89c7a6896 Thu Aug 17 15:44:18 2023 -0700
    a utility to find inversions and duplications in a set of chains
• src/hg/utils/chainArrange/makefile
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    474877488f16b5c6888313e4d25dc4b89c7a6896 Thu Aug 17 15:44:18 2023 -0700
    a utility to find inversions and duplications in a set of chains
• src/hg/utils/makefile
  • lines changed 5, context: html, text, full: html, text
    1940e5051adfdd71d35c9a329cd8e3bc407421a1 Wed Aug 16 05:22:45 2023 -0700
    fixing kent-core problem where a lot of tools were missing, refs #30812
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    2f282ed299262340a89ced0cf024acd7a8378ce2 Wed Aug 16 12:57:38 2023 -0700
    fixing stupid typo found by Angie, refs #30812
• src/hg/utils/otto/clinvar/clinVarToBed
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    c0a8cbabcde0c34dd630b98c16c603d8ff8feb90 Mon Aug 14 08:53:39 2023 -0700
    adding VCV id to clinvar hgc page, refs #31966
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.py
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    0b6529d0ca040778605cb0e1537813bbce276493 Thu Aug 17 20:18:32 2023 -0700
    Fix format string, check __name__ before calling main so this can be used as a module.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    6765acb3e5e0fe4dec0403f7803ca170c080f19c Thu Aug 17 20:19:09 2023 -0700
    Update representative for XBB.1.5 to accommodate shuffling of branches.
• src/hg/utils/otto/sarscov2phylo/branchSpecificMaskStats.py
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    74115dfde3f8c981f8f9119875d8bb014cce7b50 Thu Aug 17 20:23:19 2023 -0700
    Script to identify most specific branch and total number of sites masked for each sample, for https://github.com/iqbal-lab/improve-sc2-phylo-paper/issues/1
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
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    462e893f28fe026bc87f7ffdc9c88dbabfe13193 Mon Aug 14 13:06:40 2023 -0700
    Updated Omicron labels for Nexstrain clades and added new clades.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    0d6e7229499aa6fdfc9a77433f5bd2fc4fe60047 Mon Aug 14 13:08:30 2023 -0700
    Added B.1.1.7_dropout label and made B.1.1.7 more complete in terms of expected mutations - refs https://github.com/andersen-lab/Freyja/issues/151 . Added new lineages.
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    0380553f88742abdadd8d99301b9209fd5140249 Thu Aug 17 20:14:56 2023 -0700
    More new lineages for pango-designation v1.22. Replaced some Ns with expected alleles. Added XBB.1.5_17124 because base XBB.1.5 moved to a different flip-flop branch.
• src/lib/spaceSaver.c
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    333a62a6e44ae1fe7696231a1a83d4daa89d92d2 Tue Aug 15 14:17:02 2023 -0700
    Fix for typo - should be setting height=height, not range=height. refs #31800
• src/makefile
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    70234ec76d6e06d040ff04a0cc50bb4283bb0f80 Wed Aug 16 05:30:12 2023 -0700
    forgot to commit file in last commit, refs #30812
• src/utils/qa/weeklybld/buildEnv.csh
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    5318c8ae43d41a9860876e1989c481b8b2f098ae Mon Aug 21 10:51:03 2023 -0700
    v453 preview2, refs #31976

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• files changed: 74