File Changes for max

v471_base to v472_preview (2024-09-16 to 2024-09-23) v472

• src/browserbox/root/updateBrowser.sh
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    acfa1cf389ae85ab23161a84bc0dacad0945d1a6 Tue Sep 17 13:12:18 2024 -0700
    fixing mysql tables before trying to access them, refs #34469
• src/hg/cartReset/cartReset.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/hgMenubar/hgMenubar.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/hgMirror/hgMirror
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/hgTables/galaxy.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/hgTracks/hgTracks.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
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    8d70c954c12f93446dbb76b06a99297a8ce06647 Mon Sep 23 04:49:55 2024 -0700
    fixing amino acid display is always on, even for very large regions, if the user has set the option to always show them, refs #34481
• src/hg/hgTracks/simpleTracks.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/hgc/hgc.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/htdocs/goldenPath/credits.html
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/htdocs/inc/gbPageStartHardcoded.html
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    68bb818d4487c5ed0f0e7faa720f2b4890a657d9 Tue Sep 17 13:17:14 2024 -0700
    skipping local storage on cart reset, to make the static pages menu identical to the hgTracks menu, no redmine
• src/hg/htdocs/index.html
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/inc/interactUi.h
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/inc/jksql.h
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/js/hgTracks.js
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/js/subCfg.js
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/lib/encode/encodePeak.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/lib/hgFind.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/liftOver/liftOver.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/makeDb/cadd/caddToWig.py
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/makeDb/revel/revelToWig-hg38.py
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/makeDb/scripts/prsEmerge/prs2bigBed.sh
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/makeDb/trackDb/buildTrix
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/makeDb/trackDb/human/clinvar.ra
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/makeDb/trackDb/virus/mpxvRivers/mask.ra
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/hg/utils/otto/clinvar/clinvar.as
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    917176d5ba361d19ec6c34d37c770bfa6550337d Wed Sep 18 13:39:23 2024 -0700
    adding clinvar.as forgotten in the recent clinvar changes
• src/inc/psGfx.h
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/lib/cheapcgi.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/lib/psGfx.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/utils/bigWigToWig/bigWigToWig.c
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/utils/hubMake/hubMake
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/utils/hubMake/makefile
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/utils/hubtools/hubtools
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    f6c44a86607233aaf1755321277340fade45f2b2 Wed Sep 18 07:55:41 2024 -0700
    adding a .ra to .tsv converter to hubtools, motivated by MarcP
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    fea4e31015340a94c10cec9261bfaaefc733b52f Thu Sep 19 09:34:17 2024 -0700
    adding features to hubtools: yaml support, reorder composites by meta, order tracks by meta, allow both baseNames or actual trackNames in the meta for both this and all other meta data lookups
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.
• src/utils/hubtools/makefile
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    05e67c59a20a5d00b810a981aef3b00c5bef82e1 Fri Sep 20 06:03:18 2024 -0700
    more features to hubtools: search in both parent and subdirs, better docs
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    0f3ca3eaf5792df01b7c600a5428d2d0b2809fcd Fri Sep 20 13:18:01 2024 -0700
    Revert "more features to hubtools: search in both parent and subdirs, better docs" This reverts commit 05e67c59a20a5d00b810a981aef3b00c5bef82e1.