All File Changes

v448_preview2 to v448_base (2023-05-08 to 2023-05-15) v448

• build/kent-core/makefile
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    e150b1260cc019af2f9e44ca412d8e83824c7eb2 Wed Apr 19 05:31:55 2023 -0700
    mistakenly committed the wrong file, restoring the previous file, refs #12785
• confs/asia.hg.conf
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    3e7d7440064d1bdea5f09654b926b2cbcb21e34f Sun May 14 01:11:26 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3e7d7440064d1bdea5f09654b926b2cbcb21e34f Sun May 14 01:11:26 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3e7d7440064d1bdea5f09654b926b2cbcb21e34f Sun May 14 01:11:26 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    3e7d7440064d1bdea5f09654b926b2cbcb21e34f Sun May 14 01:11:26 2023 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    3e7d7440064d1bdea5f09654b926b2cbcb21e34f Sun May 14 01:11:26 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/altSplice/altSplice/genePredToPsl.c
  • lines changed 1, context: html, text, full: html, text
    7708ad7ff3613a79d2baa018e02ebdafbbc1ab81 Thu May 11 22:48:05 2023 -0700
    fixed insert statistics for output of genePredToPsl
• src/hg/altSplice/altSplice/tests/expected/alt3Prime5PrimeCass.gold.agx
  • lines changed 1, context: html, text, full: html, text
    7708ad7ff3613a79d2baa018e02ebdafbbc1ab81 Thu May 11 22:48:05 2023 -0700
    fixed insert statistics for output of genePredToPsl
• src/hg/altSplice/altSplice/tests/expected/testLoci.psl
  • lines changed 1, context: html, text, full: html, text
    7708ad7ff3613a79d2baa018e02ebdafbbc1ab81 Thu May 11 22:48:05 2023 -0700
    fixed insert statistics for output of genePredToPsl
• src/hg/cgilib/cartJson.c
  • lines changed 2, context: html, text, full: html, text
    46d0cb2f5a90285bf6fc2de3ff9a3a3f542521ff Wed May 10 10:42:02 2023 -0700
    Fix for hgSearch not redirecting correctly when hgvs term is erroneous but a position can still be found. Fix hgSearch not handling errAborts and warns correctly when attempting to do a redirect, refs #31251
• src/hg/cgilib/pcrResult.c
  • lines changed 6, context: html, text, full: html, text
    410a7e213ee8129b4c1c8b44ac381c34cce9a0d5 Thu May 11 15:20:19 2023 -0700
    Fix gencode genes pcr links not working, refs #31248
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 11, context: html, text, full: html, text
    732a3a2888f039e163586d38688f1372aab04c78 Thu May 11 21:10:06 2023 -0700
    Fix html problems with hgHubConnect, fixes the alignment of columns to headers and also improves the alignment of the search details section. fixes #31250
• src/hg/hgSearch/hgSearch.c
  • lines changed 6, context: html, text, full: html, text
    46d0cb2f5a90285bf6fc2de3ff9a3a3f542521ff Wed May 10 10:42:02 2023 -0700
    Fix for hgSearch not redirecting correctly when hgvs term is erroneous but a position can still be found. Fix hgSearch not handling errAborts and warns correctly when attempting to do a redirect, refs #31251
  • lines changed 2, context: html, text, full: html, text
    465cbb88c7d13ef75dcafea5c6209bfbfe7218af Fri May 12 08:29:37 2023 -0700
    Fix searches that hit hub track names with special chars, refs #31234
• src/hg/hgSession/hgSession.c
  • lines changed 1, context: html, text, full: html, text
    4ed1b0b679e701fcb9f55f6b9ce1a57cc36210ae Fri May 12 15:00:37 2023 -0700
    cgiEncode the hubUrl's in the assumesHub statement
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 3, context: html, text, full: html, text
    50d5df2a88178ea49caa2fd1b41ce28af84f219f Mon May 8 12:36:08 2023 -0700
    support bigMaf for sequence logos
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    246448930e2c91af800f5a65e090182588517d2b Tue May 9 04:53:24 2023 -0700
    adding note about not-applied botDelay to measureTiming, and moving a few lines in botDelay where they belong, refs #14567
  • lines changed 4, context: html, text, full: html, text
    3fc35a6a1ae672294df62eeec6e0e153a39605f9 Thu May 11 15:05:52 2023 -0700
    correct target=_blank on chromSizes and chromAlias URLs on "sequence" page refs #31257
  • lines changed 5, context: html, text, full: html, text
    89cdb67d6b259acf5514e5bec9314126fa543486 Fri May 12 13:31:50 2023 -0700
    make sure curated hubs are using hgdownload for downloads
• src/hg/hgTracks/wigCommon.h
  • lines changed 3, context: html, text, full: html, text
    50d5df2a88178ea49caa2fd1b41ce28af84f219f Mon May 8 12:36:08 2023 -0700
    support bigMaf for sequence logos
• src/hg/hgTracks/wigTrack.c
  • lines changed 29, context: html, text, full: html, text
    50d5df2a88178ea49caa2fd1b41ce28af84f219f Mon May 8 12:36:08 2023 -0700
    support bigMaf for sequence logos
  • lines changed 27, context: html, text, full: html, text
    f4745cea41950290d1b583f7292996a4f1c09274 Fri May 12 16:25:44 2023 -0700
    some small tweaks to make sequence logo letters easier to read if zoomed way in, or the viewing range is restricted to a small range.
• src/hg/hgc/hgc.c
  • lines changed 2, context: html, text, full: html, text
    a29f47ac15fc5b67afe74d68c763e14277731983 Tue May 9 02:20:49 2023 -0700
    allow longer labels in .as descriptions, separated with a | character, they appear in small font under the field label, came up in Clinvar discussion with Ana, Lou, Brian, Mar 7-14. Not used right now but the need has come up a few times. no redmine.
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    841ca7bd6e38614c2b323fe5f217c774f13ff55a Tue May 9 14:19:57 2023 -0700
    fixing dumb error that broke the build, thanks Lou
• src/hg/inc/botDelay.h
  • lines changed 4, context: html, text, full: html, text
    246448930e2c91af800f5a65e090182588517d2b Tue May 9 04:53:24 2023 -0700
    adding note about not-applied botDelay to measureTiming, and moving a few lines in botDelay where they belong, refs #14567
• src/hg/inc/cartJson.h
  • lines changed 6, context: html, text, full: html, text
    46d0cb2f5a90285bf6fc2de3ff9a3a3f542521ff Wed May 10 10:42:02 2023 -0700
    Fix for hgSearch not redirecting correctly when hgvs term is erroneous but a position can still be found. Fix hgSearch not handling errAborts and warns correctly when attempting to do a redirect, refs #31251
• src/hg/inc/hgMaf.h
  • lines changed 20, context: html, text, full: html, text
    50d5df2a88178ea49caa2fd1b41ce28af84f219f Mon May 8 12:36:08 2023 -0700
    support bigMaf for sequence logos
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    479ae8f44bd5005ad8737700bde652cbd971d913 Mon May 15 10:05:25 2023 -0700
    New version number v448
• src/hg/lib/botDelay.c
  • lines changed 24, context: html, text, full: html, text
    246448930e2c91af800f5a65e090182588517d2b Tue May 9 04:53:24 2023 -0700
    adding note about not-applied botDelay to measureTiming, and moving a few lines in botDelay where they belong, refs #14567
  • lines changed 1, context: html, text, full: html, text
    50a55a8ed6004c3c6634533d16cc1d1059a78821 Tue May 9 04:56:55 2023 -0700
    forgot to add file in previous commit, refs #14567
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    1eebf72e7ad8714a1e1747273feecad599bea8ec Tue May 9 06:55:25 2023 -0700
    improving error message when server cannot be connected to. refs #15324
• src/hg/lib/dupTrack.c
  • lines changed 4, context: html, text, full: html, text
    cb6306bf42be62003edb04945ab26f26c28afaa6 Tue May 9 01:12:38 2023 -0700
    changing copy to duplicate of cloned track, after long discussion of what a duplicate is and when to starting counting, refs #30911
  • lines changed 2, context: html, text, full: html, text
    b214d8509f814f46f6e99111015628362357388b Wed May 10 02:17:16 2023 -0700
    changing label back of duplicate track, refs #30911
• src/hg/lib/hgMaf.c
  • lines changed 78, context: html, text, full: html, text
    50d5df2a88178ea49caa2fd1b41ce28af84f219f Mon May 8 12:36:08 2023 -0700
    support bigMaf for sequence logos
• src/hg/lib/hubConnect.c
  • lines changed 8, context: html, text, full: html, text
    a31dd85d8e1322ae12d209aca3ce09504073493e Thu May 11 13:27:58 2023 -0700
    I really hate trying to read !isEmpty() when there is a prefectly good equivalent isNotEmpty() no redmine
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    fdf156b7fd0e45b245329dbf6c4e1fc286d61941 Sat May 13 09:36:50 2023 -0700
    make sure the cart has the right "db" when a curated hub has been selected from hgGateway
• src/hg/lib/trackHub.c
  • lines changed 21, context: html, text, full: html, text
    07180b149b187970f5cb3f272c607f5b24b57dee Thu May 11 14:32:50 2023 -0700
    correct hgdownload path for chromAlias and chrom.sizes file for "curated" hub refs #31257
  • lines changed 6, context: html, text, full: html, text
    092f837bff8a9b5951f18447d8a4314169d15e46 Thu May 11 14:42:22 2023 -0700
    use hDownloadsServer() to get the correct download URL refs #31257
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    75086be0f5ee3638664a7993b1a4510272bd1a55 Fri May 12 13:23:30 2023 -0700
    Revert "use hDownloadsServer() to get the correct download URL refs #31257" This reverts commit 092f837bff8a9b5951f18447d8a4314169d15e46.
  • lines changed 21, context: html, text, full: html, text
    21dc568ad9fe4e77547cb5f018fe6d3dab713430 Fri May 12 13:23:41 2023 -0700
    Revert "correct hgdownload path for chromAlias and chrom.sizes file for "curated" hub refs #31257" This reverts commit 07180b149b187970f5cb3f272c607f5b24b57dee.
• src/hg/lib/web.c
  • lines changed 4, context: html, text, full: html, text
    a6aae1e394e6092f1f44897ea954ea44af3c63ec Wed May 3 06:32:44 2023 -0700
    changes after code review, refs #31069
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    1f6cee9b82def5df03e6e4ebdfbff3059b3484da Fri May 12 10:29:07 2023 -0700
    adding one per user request GCA_018150745.1_ASM1815074v1 Drosophila_sucinea refs #29545
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    e4f8c5da0ae09be898aa97068847f92f1f54042f Fri May 12 22:38:14 2023 -0700
    adding three Dengue virus per user request refs #29545
• src/hg/makeDb/doc/hg38/problematic.txt
  • lines changed 26, context: html, text, full: html, text
    9e0c4de768fdd79c8c5332814c2b13db5a84fe12 Wed May 10 16:09:20 2023 -0700
    Add highly reproducible regions track, refs #31122
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    1f6cee9b82def5df03e6e4ebdfbff3059b3484da Fri May 12 10:29:07 2023 -0700
    adding one per user request GCA_018150745.1_ASM1815074v1 Drosophila_sucinea refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    c4c7301f19ec3f7996d7f1e94e8b165e3969640a Tue May 9 13:22:39 2023 -0700
    adding a gorilla assembly from the T2T Primates project refs #29545
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    7af467d22562fa9fefb7e25165ff41068e9d73ae Mon May 8 16:52:05 2023 -0700
    mistaken duplication of GCF_903992535.2_mArvAmp1.2 no redmine
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    e4f8c5da0ae09be898aa97068847f92f1f54042f Fri May 12 22:38:14 2023 -0700
    adding three Dengue virus per user request refs #29545
• src/hg/makeDb/trackDb/human/chainNetHuman.ra
  • lines changed 881, context: html, text, full: html, text
    47c696264270bef1361aa36b12f3eb89e7dec4e2 Wed May 10 15:39:54 2023 -0700
    adding in the HPRC computed chain tracks #refs 20508
• src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra
  • lines changed 1, context: html, text, full: html, text
    9a0480e3c7b2e366be92b348dce5333d7a13ef9f Mon May 8 17:13:29 2023 -0700
    Adding logoMaf to all the model conservation tracks. The logo display will now be shown by default when you zoom closely in the phyloP track. Refs #31060
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    9a0480e3c7b2e366be92b348dce5333d7a13ef9f Mon May 8 17:13:29 2023 -0700
    Adding logoMaf to all the model conservation tracks. The logo display will now be shown by default when you zoom closely in the phyloP track. Refs #31060
• src/hg/makeDb/trackDb/human/hg38/problematic.ra
  • lines changed 149, context: html, text, full: html, text
    9e0c4de768fdd79c8c5332814c2b13db5a84fe12 Wed May 10 16:09:20 2023 -0700
    Add highly reproducible regions track, refs #31122
  • lines changed 16, context: html, text, full: html, text
    13cc978531f3bf8a9304b593d55a60e133a49fd3 Mon May 15 09:45:36 2023 -0700
    Fix missing release tags in subtracks of highly reproducible regions track, refs build email
• src/hg/makeDb/trackDb/human/hg38/trackDb.30way.ra
  • lines changed 1, context: html, text, full: html, text
    9a0480e3c7b2e366be92b348dce5333d7a13ef9f Mon May 8 17:13:29 2023 -0700
    Adding logoMaf to all the model conservation tracks. The logo display will now be shown by default when you zoom closely in the phyloP track. Refs #31060
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
  • lines changed 1, context: html, text, full: html, text
    dd5f85728132bc8354dd2afff00d4d6ae31fe183 Mon May 8 12:42:35 2023 -0700
    turn on sequence logo for 470 way
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.60way.ra
  • lines changed 4, context: html, text, full: html, text
    9a0480e3c7b2e366be92b348dce5333d7a13ef9f Mon May 8 17:13:29 2023 -0700
    Adding logoMaf to all the model conservation tracks. The logo display will now be shown by default when you zoom closely in the phyloP track. Refs #31060
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.35way.ra
  • lines changed 1, context: html, text, full: html, text
    9a0480e3c7b2e366be92b348dce5333d7a13ef9f Mon May 8 17:13:29 2023 -0700
    Adding logoMaf to all the model conservation tracks. The logo display will now be shown by default when you zoom closely in the phyloP track. Refs #31060
• src/inc/net.h
  • lines changed 2, context: html, text, full: html, text
    1eebf72e7ad8714a1e1747273feecad599bea8ec Tue May 9 06:55:25 2023 -0700
    improving error message when server cannot be connected to. refs #15324
• src/inc/srcVersion.h
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    479ae8f44bd5005ad8737700bde652cbd971d913 Mon May 15 10:05:25 2023 -0700
    New version number v448
• src/lib/https.c
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    3d1b05a678e23bfe074bf3d615b8f62c01160d21 Mon May 15 00:08:13 2023 -0700
    This should be the final time adding to the whitelist, as I plan to turn on hg.conf setting to activate domain checking after the next release v448 goes in a week.
• src/lib/net.c
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    1eebf72e7ad8714a1e1747273feecad599bea8ec Tue May 9 06:55:25 2023 -0700
    improving error message when server cannot be connected to. refs #15324
• src/lib/pslTransMap.c
  • lines changed 137, context: html, text, full: html, text
    442e76e6f50e9c79f3dde2964d6f754511908e44 Sun May 14 17:32:02 2023 -0700
    trim overlapping blocks as can happen when mapping protein to DNA alignments
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    fd802431971bf493181727133d48e13beea7d74e Sun May 14 19:28:01 2023 -0700
    as long as hood is up, make pslTransMap function thread-safe
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    591cbd0e7a73bf20acc96b89b165bedb79206892 Sun May 14 19:33:37 2023 -0700
    fixed incorrectly terminates string (how did this ever work?)
• src/lib/udc.c
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    604560a8f78d593e0cc998b26efd4c060fe34a40 Tue May 9 04:54:16 2023 -0700
    tiny bit more UDC debugging output, no redmine
• src/makefile
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    970aa24b23d625782b7bfb9031ddecd4148f6a1d Thu May 11 13:19:42 2023 -0700
    eliminate the userApps source hierarchy from tags-all to prevent the duplicate useless matches no redmine
• src/utils/pslMap/tests/expected/testSpGencode.mapinfo
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    442e76e6f50e9c79f3dde2964d6f754511908e44 Sun May 14 17:32:02 2023 -0700
    trim overlapping blocks as can happen when mapping protein to DNA alignments
• src/utils/pslMap/tests/expected/testSpGencode.psl
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    442e76e6f50e9c79f3dde2964d6f754511908e44 Sun May 14 17:32:02 2023 -0700
    trim overlapping blocks as can happen when mapping protein to DNA alignments
• src/utils/pslMap/tests/input/spAnnotIso.psl
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    442e76e6f50e9c79f3dde2964d6f754511908e44 Sun May 14 17:32:02 2023 -0700
    trim overlapping blocks as can happen when mapping protein to DNA alignments
• src/utils/pslMap/tests/input/spGencode.psl
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    442e76e6f50e9c79f3dde2964d6f754511908e44 Sun May 14 17:32:02 2023 -0700
    trim overlapping blocks as can happen when mapping protein to DNA alignments
• src/utils/pslMap/tests/makefile
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    b0fa397cc96b7cb098c1c8fb03456216053d5045 Sun May 14 15:32:14 2023 -0700
    re-enable test that were disabled furing CVS to git conversion
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    442e76e6f50e9c79f3dde2964d6f754511908e44 Sun May 14 17:32:02 2023 -0700
    trim overlapping blocks as can happen when mapping protein to DNA alignments
• src/utils/qa/searchedTermsCron.py
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    260be3a6cb98c5f933001b83f21674a8fbb97748 Mon May 8 10:38:47 2023 -0700
    Added indexing by position then concatenating terms after a
• src/utils/qa/weeklybld/buildEnv.csh
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    5fba02a9a477bbdf3a5613a43325b73c2bd7e069 Mon May 15 10:04:11 2023 -0700
    v448 final build, refs #31125

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• files changed: 74