All File Changes

v455_preview to v455_preview2 (2023-09-25 to 2023-10-02) v455

• confs/rr.hg.conf
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    4f7d1b78fd8a46850f64417108189eabccf2b2d5 Sun Oct 1 01:11:25 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgTables/schema.c
  • lines changed 4, context: html, text, full: html, text
    dadd1fb9e595faeff35a1c5f4a8f9f89ece397c8 Thu Sep 28 11:46:16 2023 -0700
    table browser should point to bigBed file for knownGene track, refs #32295
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 14, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/hgTracks/bedTrack.c
  • lines changed 2, context: html, text, full: html, text
    4c18b3b304307799d2875220deff659b2ee0f292 Sun Oct 1 21:36:37 2023 -0700
    Missed a few pathways for creating tracks; the generic label and map functions need to be available for all the tracks they were already a part of. refs #32303, #30237
• src/hg/hgTracks/decorator.c
  • lines changed 1387, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/hgTracks/decorator.h
  • lines changed 163, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    aa476446c38237cc1917bbdccf554d89effae119 Mon Sep 25 13:51:10 2023 -0700
    include the preDraw times in the draw times for measureTiming
  • lines changed 95, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/hgTracks/hgTracks.h
  • lines changed 16, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
  • lines changed 14, context: html, text, full: html, text
    4c18b3b304307799d2875220deff659b2ee0f292 Sun Oct 1 21:36:37 2023 -0700
    Missed a few pathways for creating tracks; the generic label and map functions need to be available for all the tracks they were already a part of. refs #32303, #30237
• src/hg/hgTracks/makefile
  • lines changed 3, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/hgTracks/mouseOver.c
  • lines changed 60, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/hgTracks/mouseOver.h
  • lines changed 21, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/hgTracks/simpleTracks.c
  • lines changed 194, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
  • lines changed 1, context: html, text, full: html, text
    94cb3a8fc27c6d25c975aaaba7d49ce4ca129270 Thu Sep 28 11:32:34 2023 -0700
    Revert "increase maxItemsInFullTrack to 10,000 from 1,000" This reverts commit 003ab3805f814b34afad5ef601beb2caa984d0ca.
  • lines changed 9, context: html, text, full: html, text
    4c18b3b304307799d2875220deff659b2ee0f292 Sun Oct 1 21:36:37 2023 -0700
    Missed a few pathways for creating tracks; the generic label and map functions need to be available for all the tracks they were already a part of. refs #32303, #30237
• src/hg/hgTracks/wigTrack.c
  • lines changed 1, context: html, text, full: html, text
    789ad69b3d2a5c937ff33843283ae3ed2a902e12 Mon Sep 25 13:57:16 2023 -0700
    make sure we don't do any prep for drawing sequence logos if we're not at codon level
• src/hg/htdocs/goldenPath/help/decorator.html
  • lines changed 157, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 5, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 11, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 39, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 11, context: html, text, full: html, text
    42483d750b87803ff9d93efac2090595ba16ea55 Mon Oct 2 10:06:31 2023 -0700
    Adding Hirams Genark paper to the Selected Publications html page, refs #32304
• src/hg/htdocs/images/decoration_example.png
  • lines changed 0, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/htdocs/images/phylo/hg38_447way.png
  • lines changed 0, context: html, text, full: html, text
    c0d666ca90ab648fbc256dec31ebef793795c54a Sun Oct 1 21:52:56 2023 -0700
    correctly named 447-way png image one fourth of the species refs #31528
• src/hg/htdocs/images/phylo/hg38_477way.png
  • lines changed 0, context: html, text, full: html, text
    e1aef9187e9d71e1798a071232bf86c1f684f772 Sun Oct 1 21:53:19 2023 -0700
    correctly named 447-way png image one fourth of the species refs #31528
• src/hg/inc/decoration.h
  • lines changed 112, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/inc/decoratorUi.h
  • lines changed 41, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/js/utils.js
  • lines changed 114, context: html, text, full: html, text
    ef0895aab6133bd856473607aa3716f13ccb9860 Thu Sep 28 18:09:29 2023 -0700
    Fix new mouseover code to better handle the case of moving between close items and moving to the popup. I was using a second timer correctly but not setting the flags correctly for the control of showing/hiding the popup. Also did some refactoring to make the flag setting possible, refs Jonathan email, refs #31365
  • lines changed 17, context: html, text, full: html, text
    278567b33248ccea53eb047f876897a87d470d1e Fri Sep 29 14:51:16 2023 -0700
    Add a javascript function for converting two html nodes to be pop ups, the first node is the hoverable element and the second node is the pop up text/html, refs #32011
• src/hg/lib/decoration.as
  • lines changed 20, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/lib/decoration.c
  • lines changed 375, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/lib/decoration.sql
  • lines changed 26, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/lib/decoratorUi.c
  • lines changed 161, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    4140b3fc69c92c3331daca4f7bf35fafc81a5b1f Thu Sep 28 16:05:26 2023 -0700
    don't check for data accessibility, just trust trackDb Refs #32299
  • lines changed 11, context: html, text, full: html, text
    20613b1aeff2c61eb73a78d741db49f543c92114 Mon Oct 2 07:52:20 2023 -0700
    avoiding fstat calls in hReplaceGbdb, refs #32299
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/makeDb/doc/asmHubs/hubIndex.pl
  • lines changed 5, context: html, text, full: html, text
    f59854748caf4d0e6e30adfb21a7b8081a6adde2 Mon Oct 2 10:22:16 2023 -0700
    adding the CCGP project
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 6, context: html, text, full: html, text
    dc8a08fcc82b341a89fc2fdc58754f7c0a29ea31 Thu Sep 28 12:09:36 2023 -0700
    update five assemblies refs #29545
  • lines changed 2, context: html, text, full: html, text
    be4a74e4c1b83140220404396b6e9f945edd8fb2 Thu Sep 28 21:05:25 2023 -0700
    adding two per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    18ffabcfa64766bfdd5ba5bfc5d91a6a8b759c74 Thu Sep 28 22:07:37 2023 -0700
    adding a primate per user request refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    dc8a08fcc82b341a89fc2fdc58754f7c0a29ea31 Thu Sep 28 12:09:36 2023 -0700
    update five assemblies refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    dc8a08fcc82b341a89fc2fdc58754f7c0a29ea31 Thu Sep 28 12:09:36 2023 -0700
    update five assemblies refs #29545
• src/hg/makeDb/doc/hg19.txt
  • lines changed 26, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
  • lines changed 5, context: html, text, full: html, text
    1dedbd46c366091fd9d93d961b4b7b91d83ad743 Mon Oct 2 07:50:55 2023 -0700
    adding polygenic risk scores track, refs #31546
• src/hg/makeDb/doc/hg38/vistaEnhancers.txt
  • lines changed 14, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 6, context: html, text, full: html, text
    dc8a08fcc82b341a89fc2fdc58754f7c0a29ea31 Thu Sep 28 12:09:36 2023 -0700
    update five assemblies refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    dc8a08fcc82b341a89fc2fdc58754f7c0a29ea31 Thu Sep 28 12:09:36 2023 -0700
    update five assemblies refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    dc8a08fcc82b341a89fc2fdc58754f7c0a29ea31 Thu Sep 28 12:09:36 2023 -0700
    update five assemblies refs #29545
• src/hg/makeDb/doc/mm10.txt
  • lines changed 13, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
• src/hg/makeDb/doc/mm39/vistaEnhancers.txt
  • lines changed 13, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
• src/hg/makeDb/doc/mm9.txt
  • lines changed 26, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    be4a74e4c1b83140220404396b6e9f945edd8fb2 Thu Sep 28 21:05:25 2023 -0700
    adding two per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    18ffabcfa64766bfdd5ba5bfc5d91a6a8b759c74 Thu Sep 28 22:07:37 2023 -0700
    adding a primate per user request refs #29545
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV44.sh
  • lines changed 21, context: html, text, full: html, text
    a3fa5699e76f0ca4a07e3b6c4bf4c7f8de356c85 Fri Sep 29 09:15:52 2023 -0700
    Forgot to check in makedocs for knownGeneV44 on hg38/m39, refs #30840, #30841
• src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM33.sh
  • lines changed 2, context: html, text, full: html, text
    a3fa5699e76f0ca4a07e3b6c4bf4c7f8de356c85 Fri Sep 29 09:15:52 2023 -0700
    Forgot to check in makedocs for knownGeneV44 on hg38/m39, refs #30840, #30841
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    dc8a08fcc82b341a89fc2fdc58754f7c0a29ea31 Thu Sep 28 12:09:36 2023 -0700
    update five assemblies refs #29545
• src/hg/makeDb/doc/wuhCor1/variantMuts.txt
  • lines changed 409, context: html, text, full: html, text
    7191463e0a7926fba66d307049370d179a37cfd6 Mon Sep 25 16:59:28 2023 -0700
    Updating SARS-CoV-2 Variants of Concern track with more recent Omicron lineages.
• src/hg/makeDb/scripts/prsEmerge/prs2bed.py
  • lines changed 38, context: html, text, full: html, text
    1dedbd46c366091fd9d93d961b4b7b91d83ad743 Mon Oct 2 07:50:55 2023 -0700
    adding polygenic risk scores track, refs #31546
• src/hg/makeDb/scripts/prsEmerge/prs2bigBed.sh
  • lines changed 17, context: html, text, full: html, text
    1dedbd46c366091fd9d93d961b4b7b91d83ad743 Mon Oct 2 07:50:55 2023 -0700
    adding polygenic risk scores track, refs #31546
• src/hg/makeDb/trackDb/human/hg19/prs.html
  • lines changed 52, context: html, text, full: html, text
    1dedbd46c366091fd9d93d961b4b7b91d83ad743 Mon Oct 2 07:50:55 2023 -0700
    adding polygenic risk scores track, refs #31546
• src/hg/makeDb/trackDb/human/hg19/prs.ra
  • lines changed 1, context: html, text, full: html, text
    1dedbd46c366091fd9d93d961b4b7b91d83ad743 Mon Oct 2 07:50:55 2023 -0700
    adding polygenic risk scores track, refs #31546
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
• src/hg/makeDb/trackDb/human/hg38/cactus447way.html
  • lines changed 8, context: html, text, full: html, text
    89f815d5f53c0abcad1d2245f2a854cf0fe6e85c Sun Oct 1 13:25:34 2023 -0700
    name changes from Lukas refs #31528
• src/hg/makeDb/trackDb/human/hg38/hprcVCF.ra
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    144a87fa85e631b576be62763fb366648f0de72d Tue Sep 26 15:07:49 2023 -0700
    more VCF files refs #31561
• src/hg/makeDb/trackDb/human/hg38/trackDb.447way.ra
  • lines changed 1, context: html, text, full: html, text
    7f3f704f1c57409f82b6a3a13846c562a51be3f0 Sat Sep 30 15:18:22 2023 -0700
    some name updates from Lukas refs #31528
  • lines changed 1, context: html, text, full: html, text
    677db624689ffdfb64899cff55850b1b784b9187 Sun Oct 1 12:44:00 2023 -0700
    including the appropriate html description page refs #31528
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    865832763d2228e9a65125606d9d254bd89d9e8a Sun Oct 1 13:04:21 2023 -0700
    get the corrected names next to their counterpart in order refs #31528
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    cf1ed103bd83b128211aea75b66efa34364a7285 Sun Oct 1 20:55:07 2023 -0700
    coordinate the common name with Lukas recent spreadsheet refs #31528
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    f8c6ef44d4ed2ccc9639bfe47f9183df15b4a929 Sun Oct 1 22:03:20 2023 -0700
    remove version comment from phyloFit longLabels refs #31528
• src/hg/makeDb/trackDb/human/hg38/trackDb.470way.ra
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    cddca785f74601253994630b201079246da12acf Wed Sep 27 16:45:19 2023 -0700
    correct phastCons.bw now in gbdb refs @29898
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
• src/hg/makeDb/trackDb/tagTypes.tab
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    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.html
  • lines changed 166, context: html, text, full: html, text
    7191463e0a7926fba66d307049370d179a37cfd6 Mon Sep 25 16:59:28 2023 -0700
    Updating SARS-CoV-2 Variants of Concern track with more recent Omicron lineages.
• src/hg/makeDb/trackDb/virus/wuhCor1/variantMuts.ra
  • lines changed 270, context: html, text, full: html, text
    7191463e0a7926fba66d307049370d179a37cfd6 Mon Sep 25 16:59:28 2023 -0700
    Updating SARS-CoV-2 Variants of Concern track with more recent Omicron lineages.
• src/hg/makeDb/trackDb/vistaEnhancersBb.html
  • lines changed 85, context: html, text, full: html, text
    2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 Wed Sep 27 13:56:11 2023 -0700
    Making VISTA Enhancers into native track, refs #16044
• src/inc/htmshell.h
  • lines changed 4, context: html, text, full: html, text
    cffb8fcb4dff1693ded92803c47c317f8ed02e1b Wed Sep 27 10:07:22 2023 -0700
    switching off translation bar for DNA output, refs #32275
• src/inc/memgfx.h
  • lines changed 20, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/lib/bbiWrite.c
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    5c9078c4286bdfec0fa9d39de2802151a5ac69a8 Thu Sep 28 09:07:58 2023 -0700
    when calculating zoom levels, don't seek on the input if it's already at the beginning of the file. Refs #32293
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    dd6685988d7600e805dcf71b943d806dd10289cf Sat Sep 30 17:05:23 2023 -0700
    relax the constraint on sorting for bedToBigBed and bedGraphToBigWig.
• src/lib/htmshell.c
  • lines changed 18, context: html, text, full: html, text
    cffb8fcb4dff1693ded92803c47c317f8ed02e1b Wed Sep 27 10:07:22 2023 -0700
    switching off translation bar for DNA output, refs #32275
• src/lib/memgfx.c
  • lines changed 1, context: html, text, full: html, text
    b038f3dafce99493b0ca00305538c6a3dd6f041a Tue Sep 26 15:58:44 2023 -0700
    Initial commit of track decorators, refs #30237
• src/lib/pslTransMap.c
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    e813f6c7cfd2f8f110266c0824062964322d62a3 Wed Sep 20 00:01:21 2023 -0700
    fixed problems handling overlapping PSL blocks caused by protein to NA alignemtns. Now handles internal coversions create overlapoing blocks
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    0b79c15eb1f296cb7bb64ab6e7e1d3adf0eb0599 Wed Sep 20 12:56:24 2023 -0700
    fixed unsiged underflow
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    dd6685988d7600e805dcf71b943d806dd10289cf Sat Sep 30 17:05:23 2023 -0700
    relax the constraint on sorting for bedToBigBed and bedGraphToBigWig.
• src/utils/bedToBigBed/bedToBigBed.c
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    ef80854d868978e0da8e60f4ec0aad06b10f8a82 Thu Sep 28 09:42:31 2023 -0700
    allow bedToBigBed to use compressed input
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    dd6685988d7600e805dcf71b943d806dd10289cf Sat Sep 30 17:05:23 2023 -0700
    relax the constraint on sorting for bedToBigBed and bedGraphToBigWig.
• src/utils/bedToBigBed/tests/input/itemRgb.bed.gz
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    ef80854d868978e0da8e60f4ec0aad06b10f8a82 Thu Sep 28 09:42:31 2023 -0700
    allow bedToBigBed to use compressed input
• src/utils/bedToBigBed/tests/makefile
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    ef80854d868978e0da8e60f4ec0aad06b10f8a82 Thu Sep 28 09:42:31 2023 -0700
    allow bedToBigBed to use compressed input
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    dd6685988d7600e805dcf71b943d806dd10289cf Sat Sep 30 17:05:23 2023 -0700
    relax the constraint on sorting for bedToBigBed and bedGraphToBigWig.
• src/utils/pslMap/tests/expected/testProtNa_NaNa.psl
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    e813f6c7cfd2f8f110266c0824062964322d62a3 Wed Sep 20 00:01:21 2023 -0700
    fixed problems handling overlapping PSL blocks caused by protein to NA alignemtns. Now handles internal coversions create overlapoing blocks
• src/utils/pslMap/tests/expected/testProtTrans.psl
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    e813f6c7cfd2f8f110266c0824062964322d62a3 Wed Sep 20 00:01:21 2023 -0700
    fixed problems handling overlapping PSL blocks caused by protein to NA alignemtns. Now handles internal coversions create overlapoing blocks
• src/utils/pslMap/tests/input/README
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    e813f6c7cfd2f8f110266c0824062964322d62a3 Wed Sep 20 00:01:21 2023 -0700
    fixed problems handling overlapping PSL blocks caused by protein to NA alignemtns. Now handles internal coversions create overlapoing blocks
• src/utils/pslMap/tests/input/annotProt.psl
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    e813f6c7cfd2f8f110266c0824062964322d62a3 Wed Sep 20 00:01:21 2023 -0700
    fixed problems handling overlapping PSL blocks caused by protein to NA alignemtns. Now handles internal coversions create overlapoing blocks
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    0b79c15eb1f296cb7bb64ab6e7e1d3adf0eb0599 Wed Sep 20 12:56:24 2023 -0700
    fixed unsiged underflow
• src/utils/pslMap/tests/input/protGencode.psl
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    e813f6c7cfd2f8f110266c0824062964322d62a3 Wed Sep 20 00:01:21 2023 -0700
    fixed problems handling overlapping PSL blocks caused by protein to NA alignemtns. Now handles internal coversions create overlapoing blocks
• src/utils/pslMap/tests/makefile
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    e813f6c7cfd2f8f110266c0824062964322d62a3 Wed Sep 20 00:01:21 2023 -0700
    fixed problems handling overlapping PSL blocks caused by protein to NA alignemtns. Now handles internal coversions create overlapoing blocks
• src/utils/qa/filterCartDumps.sh
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    08df4a9ab30ba68cdc62960a47ce65ddb5570574 Sun Oct 1 13:10:27 2023 -0700
    Adding a script that filters long session cart dumps by region size limit and appends the first 10 slowest and 20 random sessions to a file, refs #31585
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    add042a1608bb6bd29b7690875c889f6bc0fbc6e Sun Oct 1 21:59:53 2023 -0700
    Adding an output message for cron, refs #31585
• src/utils/qa/hubCheckPublicHubs.sh
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    6b286d22a77aecb95c842c8b9416153b4007d64d Fri Sep 29 13:47:16 2023 -0700
    Suppressing https timeout expired output from the cron, refs #29319
• src/utils/qa/makefile
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    add042a1608bb6bd29b7690875c889f6bc0fbc6e Sun Oct 1 21:59:53 2023 -0700
    Adding an output message for cron, refs #31585
• src/utils/qa/weeklybld/buildEnv.csh
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    6d325ddb85bbf66a1e726c73c156d45128788177 Mon Oct 2 10:26:21 2023 -0700
    v455 preview2

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