All File Changes

v458_base to v459_preview (2023-12-11 to 2023-12-18) v459

• src/browserbox/root/updateBrowser.sh
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    bb03547b54fe7e5013d811c2f92c35a9ecdbfba4 Mon Dec 11 10:39:43 2023 -0800
    Fixing minor typo in GBiB update script for encRegTfbsClustered, no ticket
• src/hg/hgGeneGraph/hgGeneGraph
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    b29f234fdad274cd1355b6ccc019bc1bbbc12c2a Thu Dec 7 05:03:18 2023 -0800
    adapting comment, thanks to Chris, refs #32714
• src/hg/hgSearch/hgSearch.c
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    4b7650a3500f39cd9f58256d661f1f942372364c Mon Dec 11 14:40:26 2023 -0800
    Fix hgSearch redirect links when search results in a all_mrna track singlePos, refs Max email
• src/hg/hgTracks/decorator.c
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    d96ac78dc01133a55575481975194bfc1b8accc1 Tue Dec 12 13:11:04 2023 -0800
    Make glyph drawing code from decorators to being available to all of hgTracks. This is to allow for experimentation in using glyphs to draw SNPs. There is no functional changes, it just moves code around.
• src/hg/hgTracks/hgTracks.h
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    d96ac78dc01133a55575481975194bfc1b8accc1 Tue Dec 12 13:11:04 2023 -0800
    Make glyph drawing code from decorators to being available to all of hgTracks. This is to allow for experimentation in using glyphs to draw SNPs. There is no functional changes, it just moves code around.
• src/hg/hgTracks/simpleTracks.c
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    d96ac78dc01133a55575481975194bfc1b8accc1 Tue Dec 12 13:11:04 2023 -0800
    Make glyph drawing code from decorators to being available to all of hgTracks. This is to allow for experimentation in using glyphs to draw SNPs. There is no functional changes, it just moves code around.
• src/hg/htdocs/indexMeetings.html
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    590c1edb264663946c4fb5b38c2369fbc4276a58 Mon Dec 11 09:41:00 2023 -0800
    Removing CSHL and adding a new workshop b0b is doing.
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    09d72ab3f36626083fcd8989f0bc26747418f168 Mon Dec 11 10:27:45 2023 -0800
    Fixing order of meetings to be chronological.
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    fb7e24514cab6cc6dc4fe3140111821ffc8d0a67 Mon Dec 11 14:16:38 2023 -0800
    Adding virtual workshop in France.
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    8cb85c41a6510abb26d74d555016d9908ffc4991 Tue Dec 12 02:58:22 2023 -0800
    changing Sorbonne meeting a little, email with Lou
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    bce9673e4e67c4bfcd5d0fe4e1cea806c72428b8 Wed Dec 13 09:24:55 2023 -0800
    small change to meeting page after lou feedback, no redmine
• src/hg/inc/decoration.h
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    d96ac78dc01133a55575481975194bfc1b8accc1 Tue Dec 12 13:11:04 2023 -0800
    Make glyph drawing code from decorators to being available to all of hgTracks. This is to allow for experimentation in using glyphs to draw SNPs. There is no functional changes, it just moves code around.
• src/hg/js/hgSearch.js
  • lines changed 11, context: html, text, full: html, text
    0d4cd5a2b5b893b073cee6fdbcc740503497e20b Tue Dec 12 11:58:31 2023 -0800
    Fix hgSearch show/hide links to not remove event handlers when updating the text after click the link or icon, refs #31501
• src/hg/js/hgTracks.js
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    8dfbd1be0115e390a0d092183e972ffa160d3c32 Mon Dec 11 15:18:16 2023 -0800
    Make recommended track sets not lose it's dialog title, refs Max email
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    361b56f2d2108ebcf05ac0c6648acd0431c03e88 Tue Dec 12 04:59:01 2023 -0800
    making default highlight color darker, it.s currently very hard to see on a projector screenshare, suggested by Ana, no redmine
• src/hg/lib/customTrack.c
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    c289d133078f074b7c5d81912a47342413fbafab Mon Dec 11 09:22:31 2023 -0800
    polish up custom track error string
• src/hg/lib/decoration.c
  • lines changed 32, context: html, text, full: html, text
    d96ac78dc01133a55575481975194bfc1b8accc1 Tue Dec 12 13:11:04 2023 -0800
    Make glyph drawing code from decorators to being available to all of hgTracks. This is to allow for experimentation in using glyphs to draw SNPs. There is no functional changes, it just moves code around.
• src/hg/lib/hdb.c
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    72e4774cd62b49fe88984f0ae6eba75ee5f02843 Wed Dec 13 12:54:16 2023 -0800
    add hg.conf variable (trustTrackDb) to force the CGI's to validate trackDb instead of just trusting it
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    db46ecd0260c15597cef130a001946c39dfafa70 Fri Dec 15 12:24:15 2023 -0800
    correct error message, remove obsolete reference to hFindTableInfoDb refs #32779
• src/hg/lib/jksql.c
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    4aeb7ec91d0af424b00b2a5aa5bb205a2afa03e6 Tue Dec 12 00:46:09 2023 -0800
    improving jksql error message when no ~/.hg.conf file was found, refs #32741, also improving error message when the hgcentral server is not working and the CGI is running on the RR, email with browser-staff on Oct 23 and group meeting about what to do when hgcentral is down, no redmine
• src/hg/makeDb/doc/asmHubs/master.run.list
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    fa98e446f407fea17bba34275f57d5d68cf766dd Fri Dec 15 11:10:45 2023 -0800
    update VGP assemblies adding 20 refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
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    fa98e446f407fea17bba34275f57d5d68cf766dd Fri Dec 15 11:10:45 2023 -0800
    update VGP assemblies adding 20 refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
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    fa98e446f407fea17bba34275f57d5d68cf766dd Fri Dec 15 11:10:45 2023 -0800
    update VGP assemblies adding 20 refs #29545
• src/hg/makeDb/doc/hg38/lastzRuns.txt
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    bc46f17c49d80193157e45e9916ff3032598a245 Tue Dec 12 07:45:44 2023 -0800
    lastz chain net hg38 to hs1 refs #31977
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
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    fa98e446f407fea17bba34275f57d5d68cf766dd Fri Dec 15 11:10:45 2023 -0800
    update VGP assemblies adding 20 refs #29545
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    8c37804ff583775097b85db4018cbbcfa3c65597 Fri Dec 15 12:20:39 2023 -0800
    missing definition for GCA_020745735.1_sHemOce1.pat.X.cur. refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
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    fa98e446f407fea17bba34275f57d5d68cf766dd Fri Dec 15 11:10:45 2023 -0800
    update VGP assemblies adding 20 refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
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    fa98e446f407fea17bba34275f57d5d68cf766dd Fri Dec 15 11:10:45 2023 -0800
    update VGP assemblies adding 20 refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
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    fa98e446f407fea17bba34275f57d5d68cf766dd Fri Dec 15 11:10:45 2023 -0800
    update VGP assemblies adding 20 refs #29545
• src/hg/makeDb/trackDb/human/clinvar.alpha.ra
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    68edf2faf95319175aafd4769d1b084cd6377664 Thu Dec 14 05:23:13 2023 -0800
    fixing up clinvar alpha track for dev, no redmine
• src/hg/makeDb/trackDb/human/hg38/mane.ra
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    4bc8b854dfa86abb0960553d09be0bbb42333043 Fri Dec 8 04:19:01 2023 -0800
    adapt mane longLabel, based on Anna feedback, no redmine
• src/hg/makeDb/trackDb/human/trackDb.ra
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    68edf2faf95319175aafd4769d1b084cd6377664 Thu Dec 14 05:23:13 2023 -0800
    fixing up clinvar alpha track for dev, no redmine
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    f3af8e86c4b50d09e00ba5fdfba7f5600e0ac2fc Thu Dec 14 10:20:16 2023 -0800
    Fixing up the trackDb since Max added clinvar alpha but other track also had alpha release tag, no RM.
• src/hg/utils/fixTrackDb/fixTrackDb.c
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    2a3ad7819d330c0b7cde7bd748c379685533630b Tue Dec 12 12:16:13 2023 -0800
    add schema to delete command.
• src/hg/utils/otto/clinvar/clinVarToBed
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    61dccdb3f1405aeee1c397b5247e673cab010911 Thu Dec 14 05:02:54 2023 -0800
    adding version.txt files to clinvar. Also starting work on the --alpha switch, but not tested yet
• src/hg/utils/otto/clinvar/clinvarSubLolly
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    61dccdb3f1405aeee1c397b5247e673cab010911 Thu Dec 14 05:02:54 2023 -0800
    adding version.txt files to clinvar. Also starting work on the --alpha switch, but not tested yet
• src/hg/utils/otto/clinvar/doUpdate.sh
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    61dccdb3f1405aeee1c397b5247e673cab010911 Thu Dec 14 05:02:54 2023 -0800
    adding version.txt files to clinvar. Also starting work on the --alpha switch, but not tested yet
• src/inc/psl.h
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    5711ac6c2bcaeda814ae1049a0661f499775885e Wed Dec 13 00:36:12 2023 -0800
    change pslProtToRnaCoords to use common code with pslMap to convert protein/NA to CDS-coordinate/NA alignments. This will correctly remove overlapping blocks after conversion
• src/inc/pslTransMap.h
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    5711ac6c2bcaeda814ae1049a0661f499775885e Wed Dec 13 00:36:12 2023 -0800
    change pslProtToRnaCoords to use common code with pslMap to convert protein/NA to CDS-coordinate/NA alignments. This will correctly remove overlapping blocks after conversion
• src/lib/psl.c
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    5711ac6c2bcaeda814ae1049a0661f499775885e Wed Dec 13 00:36:12 2023 -0800
    change pslProtToRnaCoords to use common code with pslMap to convert protein/NA to CDS-coordinate/NA alignments. This will correctly remove overlapping blocks after conversion
• src/lib/pslTransMap.c
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    5711ac6c2bcaeda814ae1049a0661f499775885e Wed Dec 13 00:36:12 2023 -0800
    change pslProtToRnaCoords to use common code with pslMap to convert protein/NA to CDS-coordinate/NA alignments. This will correctly remove overlapping blocks after conversion
• src/utils/pslProtToRnaCoords/pslProtToRnaCoords.c
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    5711ac6c2bcaeda814ae1049a0661f499775885e Wed Dec 13 00:36:12 2023 -0800
    change pslProtToRnaCoords to use common code with pslMap to convert protein/NA to CDS-coordinate/NA alignments. This will correctly remove overlapping blocks after conversion
• src/utils/pslProtToRnaCoords/tests/expected/kgProtTest.psl
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    5711ac6c2bcaeda814ae1049a0661f499775885e Wed Dec 13 00:36:12 2023 -0800
    change pslProtToRnaCoords to use common code with pslMap to convert protein/NA to CDS-coordinate/NA alignments. This will correctly remove overlapping blocks after conversion
• src/utils/pslProtToRnaCoords/tests/expected/spGencodeTest.psl
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    5711ac6c2bcaeda814ae1049a0661f499775885e Wed Dec 13 00:36:12 2023 -0800
    change pslProtToRnaCoords to use common code with pslMap to convert protein/NA to CDS-coordinate/NA alignments. This will correctly remove overlapping blocks after conversion
• src/utils/qa/weeklybld/buildEnv.csh
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    fee731740b846fabc20051bacc8b44003c5a0b4f Mon Dec 18 11:31:45 2023 -0800
    v459 preview1, refs #32676

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• files changed: 45