All File Changes

v425_preview to v425_preview2 (2021-12-13 to 2021-12-20) v425

• confs/asia.hg.conf
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    baf8067d5cc4e1586eff43333f360ba3731eb1b7 Sun Dec 19 01:11:57 2021 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 8, context: html, text, full: html, text
    baf8067d5cc4e1586eff43333f360ba3731eb1b7 Sun Dec 19 01:11:57 2021 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 10, context: html, text, full: html, text
    baf8067d5cc4e1586eff43333f360ba3731eb1b7 Sun Dec 19 01:11:57 2021 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 8, context: html, text, full: html, text
    baf8067d5cc4e1586eff43333f360ba3731eb1b7 Sun Dec 19 01:11:57 2021 -0800
    Installing updated hg.conf files from UCSC servers
• src/browserbox/usr/local/apache/cgi-bin/hg.conf
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    2c3992191c69ef9090c2807d5ad538a172bc5a97 Tue Dec 14 16:04:24 2021 -0800
    Adding genark prefixes to github, refs #28522
• src/hg/cgilib/makefile
  • lines changed 1, context: html, text, full: html, text
    312002c4b4015a4e5acedd47dad9e5d6b8d3c1b1 Mon Nov 22 18:38:59 2021 -0800
    move rmskAlign and rmskJoined to lib so it they can be used by programs
• src/hg/cgilib/rmskAlign.c
  • lines changed 212, context: html, text, full: html, text
    312002c4b4015a4e5acedd47dad9e5d6b8d3c1b1 Mon Nov 22 18:38:59 2021 -0800
    move rmskAlign and rmskJoined to lib so it they can be used by programs
• src/hg/cgilib/rmskJoined.c
  • lines changed 215, context: html, text, full: html, text
    312002c4b4015a4e5acedd47dad9e5d6b8d3c1b1 Mon Nov 22 18:38:59 2021 -0800
    move rmskAlign and rmskJoined to lib so it they can be used by programs
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    33d00cb65d2f44cce214f6de74d01184874d1292 Thu Dec 16 11:11:12 2021 -0800
    Updating links to have target=”_blank” to be consistent with the hgCustom page, refs #28638
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    651392e779790538b17faea2a79ffce9b6f01487 Tue Dec 14 16:19:17 2021 -0800
    Updating the hubCheck message to reflect it can take up to 20 minutes, refs #28646
• src/hg/hgTracks/barChartTrack.c
  • lines changed 74, context: html, text, full: html, text
    d3f9b9ecf2a6d30bd8f97566f72e5650982c308d Mon Dec 13 15:22:03 2021 -0800
    Adding hgTracks display of merged bar charts.
  • lines changed 3, context: html, text, full: html, text
    f9d03e79d5565c0d9a28d57c0c67986a085a40c4 Tue Dec 14 21:09:37 2021 -0800
    Fixing a three little bugs. Adding some #defines to avoid magic numbers. Fixing differences in sorting between expression values and labels.
  • lines changed 22, context: html, text, full: html, text
    dc8c6d138d71dfc4c0be0224de14c2106b9ae61e Wed Dec 15 09:21:32 2021 -0800
    Making it handle zoomed out views with many bars in the chart better. Stop making map-boxes for mouse-overs when they are a pixel or less, which sped up the page a lot. Also expanded sub-pixel scaling with more cases.
  • lines changed 22, context: html, text, full: html, text
    3c50590d0e6574120daeec33c5b5b4e90ba782da Fri Dec 17 16:52:06 2021 -0800
    Making scaling work better on graphs with a larger number of bars. Improving mouse-over messages.
• src/hg/hgTracks/searchTracks.c
  • lines changed 22, context: html, text, full: html, text
    f183ef95b2e4a00177a3e21a47b6272da746ce4c Mon Dec 13 15:21:15 2021 -0800
    hgTracks track search on hubs: Angie noticed that calling pthread_join will wait for a still running thread to finish, which nullifies the point of having a timeout, while also discovering that if we have fewer threads than hubs to work through, we will never work through some hubs at all because of a missing loop in addUnconnectedHubSearchResults(). This commit rectifies both problems
• src/hg/hgc/barChartClick.c
  • lines changed 4, context: html, text, full: html, text
    d3f9b9ecf2a6d30bd8f97566f72e5650982c308d Mon Dec 13 15:22:03 2021 -0800
    Adding hgTracks display of merged bar charts.
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 3, context: html, text, full: html, text
    e550e8c40e6139e4570787293063d11c7c40430d Mon Dec 20 10:55:55 2021 -0800
    Fixing broken link No Rm
• src/hg/htdocs/goldenPath/help/cram.html
  • lines changed 1, context: html, text, full: html, text
    b1d88f6e2c5626249bc8c34d2a36c224ee65c871 Wed Dec 15 09:21:16 2021 -0800
    Updating link found by monthly static page checker.
• src/hg/htdocs/goldenPath/help/customTrackLoad.html
  • lines changed 1, context: html, text, full: html, text
    33d00cb65d2f44cce214f6de74d01184874d1292 Thu Dec 16 11:11:12 2021 -0800
    Updating links to have target=”_blank” to be consistent with the hgCustom page, refs #28638
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 51, context: html, text, full: html, text
    4ca3c3018d2b74d1a51a0bc79d5ad50f944a7e38 Thu Dec 16 15:45:56 2021 -0800
    Adding a news announcement about trackDb settings specific to filters page, with intro paragraph about Track Hubs as mentioned in refs #27879
  • lines changed 2, context: html, text, full: html, text
    0da9dc1900ad12eacce12c8228e279d6d525834a Thu Dec 16 15:53:22 2021 -0800
    Adjusting 2nd image size for when viewing on large screens refs #27879
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    4ca3c3018d2b74d1a51a0bc79d5ad50f944a7e38 Thu Dec 16 15:45:56 2021 -0800
    Adding a news announcement about trackDb settings specific to filters page, with intro paragraph about Track Hubs as mentioned in refs #27879
• src/hg/htdocs/training/index.html
  • lines changed 32, context: html, text, full: html, text
    80e881d8370217e252d36d0d068faf6e0677057b Mon Dec 13 15:06:14 2021 -0800
    remving completed workshops japan and asilomar. moving later workshops into place
• src/hg/inc/barChartUi.h
  • lines changed 13, context: html, text, full: html, text
    d3f9b9ecf2a6d30bd8f97566f72e5650982c308d Mon Dec 13 15:22:03 2021 -0800
    Adding hgTracks display of merged bar charts.
• src/hg/inc/facetedTable.h
  • lines changed 27, context: html, text, full: html, text
    d3f9b9ecf2a6d30bd8f97566f72e5650982c308d Mon Dec 13 15:22:03 2021 -0800
    Adding hgTracks display of merged bar charts.
  • lines changed 2, context: html, text, full: html, text
    f9d03e79d5565c0d9a28d57c0c67986a085a40c4 Tue Dec 14 21:09:37 2021 -0800
    Fixing a three little bugs. Adding some #defines to avoid magic numbers. Fixing differences in sorting between expression values and labels.
• src/hg/lib/barChartUi.c
  • lines changed 31, context: html, text, full: html, text
    d3f9b9ecf2a6d30bd8f97566f72e5650982c308d Mon Dec 13 15:22:03 2021 -0800
    Adding hgTracks display of merged bar charts.
• src/hg/lib/cart.c
  • lines changed 4, context: html, text, full: html, text
    fa56a49c43067fd2f3d0fbec1864bf26b1cda0d3 Mon Dec 20 05:50:53 2021 -0800
    taking back accidental commit of cart.c found in code review, refs #28637
• src/hg/lib/facetField.c
  • lines changed 1, context: html, text, full: html, text
    d3f9b9ecf2a6d30bd8f97566f72e5650982c308d Mon Dec 13 15:22:03 2021 -0800
    Adding hgTracks display of merged bar charts.
• src/hg/lib/facetedTable.c
  • lines changed 202, context: html, text, full: html, text
    d3f9b9ecf2a6d30bd8f97566f72e5650982c308d Mon Dec 13 15:22:03 2021 -0800
    Adding hgTracks display of merged bar charts.
  • lines changed 1, context: html, text, full: html, text
    44e41d5c98ea28f0e52d04527cafda9a2024d7a0 Mon Dec 13 18:28:48 2021 -0800
    Changing separater in generated key from space to /
  • lines changed 76, context: html, text, full: html, text
    f9d03e79d5565c0d9a28d57c0c67986a085a40c4 Tue Dec 14 21:09:37 2021 -0800
    Fixing a three little bugs. Adding some #defines to avoid magic numbers. Fixing differences in sorting between expression values and labels.
  • lines changed 11, context: html, text, full: html, text
    23b9c239a6c92dc82a54294f9c99aa4b47292b79 Wed Dec 15 08:29:05 2021 -0800
    Making merged bars respect individual field selection too on genome browser.
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    af8d21ecd875295fe5c1c75f786a60896042c8ac Tue Dec 14 14:33:25 2021 -0800
    Slight wording change to container mouseover refs #28558
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    312002c4b4015a4e5acedd47dad9e5d6b8d3c1b1 Mon Nov 22 18:38:59 2021 -0800
    move rmskAlign and rmskJoined to lib so it they can be used by programs
• src/hg/lib/rmskAlign.c
  • lines changed 212, context: html, text, full: html, text
    312002c4b4015a4e5acedd47dad9e5d6b8d3c1b1 Mon Nov 22 18:38:59 2021 -0800
    move rmskAlign and rmskJoined to lib so it they can be used by programs
• src/hg/lib/rmskJoined.c
  • lines changed 215, context: html, text, full: html, text
    312002c4b4015a4e5acedd47dad9e5d6b8d3c1b1 Mon Nov 22 18:38:59 2021 -0800
    move rmskAlign and rmskJoined to lib so it they can be used by programs
• src/hg/lib/tablesTables.c
  • lines changed 23, context: html, text, full: html, text
    a9b3f2ba629176ff781c64587544b78ddfa1557b Mon Dec 13 18:30:59 2021 -0800
    Making merge/unmerge buttons jump page on return to where they are rather than to top of page. Saves scrolling when merging/unmerging a lot of things.
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 188, context: html, text, full: html, text
    83cf9e0118ba4fe127774251cc914ddd764037a0 Sun Dec 19 19:06:13 2021 -0800
    adding 188 assemblies to catch up all Zoonomia 241 xx minus 2 broken sources xx no redming
• src/hg/makeDb/doc/asmHubs/mkSendList.pl
  • lines changed 34, context: html, text, full: html, text
    a34a4a7e02d098251a61edf3c85d629ad2174667 Wed Dec 15 11:40:57 2021 -0800
    catch up outstanding file no redmine
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    f44d5b894cf549947ac06bf2203670b6c56b3c31 Fri Dec 17 09:21:39 2021 -0800
    adding exome probesets, refs #28655
• src/hg/makeDb/doc/hg38/exomeProbesets.txt
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    f44d5b894cf549947ac06bf2203670b6c56b3c31 Fri Dec 17 09:21:39 2021 -0800
    adding exome probesets, refs #28655
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 18, context: html, text, full: html, text
    87069ba5e696cd3d4c10e0b528781e98a0c219e3 Sun Dec 19 20:57:52 2021 -0800
    primates moving to legacy no redmine
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 28, context: html, text, full: html, text
    10611d31b8d80eec5fe226d46bc1b97999069e69 Sun Dec 19 20:39:28 2021 -0800
    adding 18 new primate assemblies some older ones have moved to legacy no redmine
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes14.csh
  • lines changed 35, context: html, text, full: html, text
    4cba91d2140fe4cc6bb2748d9009201fbcae577d Tue Dec 14 12:46:17 2021 -0800
    update hg19 kgXref, kgAlias, the search index files, and the hgTracks bigBed with newer gene symbols
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV39.sh
  • lines changed 2, context: html, text, full: html, text
    b87243c823ae619a0f382db4236df99216f3f1e8 Mon Dec 13 10:38:39 2021 -0800
    some knownGene cleanup
• src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM28.sh
  • lines changed 11, context: html, text, full: html, text
    b87243c823ae619a0f382db4236df99216f3f1e8 Mon Dec 13 10:38:39 2021 -0800
    some knownGene cleanup
• src/hg/makeDb/trackDb/human/exomeProbesets.html
  • lines changed 6, context: html, text, full: html, text
    fba7b7cb89916e43814edb9409bc1d16e452ab06 Fri Dec 17 09:18:12 2021 -0800
    adding twist2 array, refs #28655
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    cd38b19d81e33b8698b91f880b9c7a3838afd7a8 Fri Dec 17 09:44:57 2021 -0800
    updating version number of twist track, refs #28655
• src/hg/makeDb/trackDb/human/hg19/exomeProbesets.ra
  • lines changed 9, context: html, text, full: html, text
    fba7b7cb89916e43814edb9409bc1d16e452ab06 Fri Dec 17 09:18:12 2021 -0800
    adding twist2 array, refs #28655
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    cd38b19d81e33b8698b91f880b9c7a3838afd7a8 Fri Dec 17 09:44:57 2021 -0800
    updating version number of twist track, refs #28655
  • lines changed 2, context: html, text, full: html, text
    339cedb5ce6937f04edc5538fff86b04aa6cff26 Fri Dec 17 14:43:55 2021 -0800
    Changing the Twist probeset default to be the new version from email by Twist refs #28655
  • lines changed 1, context: html, text, full: html, text
    c87036853b4f9dd3dc972cdb7a8adf11f8e37edc Fri Dec 17 18:31:40 2021 -0800
    Putting the Twist Comprehensive probeset track on as default per Twist request refs #28655
• src/hg/makeDb/trackDb/human/hg38/brainDevRegions.ra
  • lines changed 42, context: html, text, full: html, text
    db997308685e20958b6698106949c9681c1b607c Fri Dec 17 14:24:20 2021 -0800
    Adding brainDevRegions track.
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    ff980ca1294206936242b945c9835c066ffc3e8c Sun Dec 19 08:36:37 2021 -0800
    Changed a facet name from detailed_cell_type to cell_cluster
• src/hg/makeDb/trackDb/human/hg38/exomeProbesets.ra
  • lines changed 9, context: html, text, full: html, text
    fba7b7cb89916e43814edb9409bc1d16e452ab06 Fri Dec 17 09:18:12 2021 -0800
    adding twist2 array, refs #28655
  • lines changed 2, context: html, text, full: html, text
    cd38b19d81e33b8698b91f880b9c7a3838afd7a8 Fri Dec 17 09:44:57 2021 -0800
    updating version number of twist track, refs #28655
  • lines changed 3, context: html, text, full: html, text
    9d4bb725ccece1a7dcf120c05c782f5a449aa47e Fri Dec 17 11:12:04 2021 -0800
    In reviewing Twist track noticed mistmatched color on hg38 per html of track and hg19 refs #28655
  • lines changed 2, context: html, text, full: html, text
    339cedb5ce6937f04edc5538fff86b04aa6cff26 Fri Dec 17 14:43:55 2021 -0800
    Changing the Twist probeset default to be the new version from email by Twist refs #28655
  • lines changed 1, context: html, text, full: html, text
    c87036853b4f9dd3dc972cdb7a8adf11f8e37edc Fri Dec 17 18:31:40 2021 -0800
    Putting the Twist Comprehensive probeset track on as default per Twist request refs #28655
• src/hg/makeDb/trackDb/human/hg38/tabulaSapiens.ra
  • lines changed 2, context: html, text, full: html, text
    356667cb107c2bcf74f8031268a9ef426a94806b Mon Dec 13 14:56:25 2021 -0800
    Getting rid of some old huge commented out bar and color lists
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    2f068905be07e4d87c8e6e6624989397c3177730 Mon Dec 13 18:28:00 2021 -0800
    Setting maxWindowToDraw's of one million for the detailed single cell tracks.
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    70da2a9339eeaf6a9441b198ce4fcb2ab198622f Wed Dec 15 08:20:49 2021 -0800
    Bumping max window on full details barcharts from 1M to 2M.
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    c005deeec758b8922d72dbe1985e4f4d065cf3bb Wed Dec 15 09:19:08 2021 -0800
    Bumping up max window size since barchart drawer/mapbox maker can handle it now.
  • lines changed 35, context: html, text, full: html, text
    0fce19e6095612f58c15f77fa50400876c963365 Fri Dec 17 16:53:21 2021 -0800
    Improving short and long labels. Removing some unneeded subtracks.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    db997308685e20958b6698106949c9681c1b607c Fri Dec 17 14:24:20 2021 -0800
    Adding brainDevRegions track.
• src/hg/makeDb/trackDb/mouse/mm10/tabulaMurisSenis.ra
  • lines changed 2, context: html, text, full: html, text
    2f068905be07e4d87c8e6e6624989397c3177730 Mon Dec 13 18:28:00 2021 -0800
    Setting maxWindowToDraw's of one million for the detailed single cell tracks.
  • lines changed 2, context: html, text, full: html, text
    70da2a9339eeaf6a9441b198ce4fcb2ab198622f Wed Dec 15 08:20:49 2021 -0800
    Bumping max window on full details barcharts from 1M to 2M.
  • lines changed 2, context: html, text, full: html, text
    c005deeec758b8922d72dbe1985e4f4d065cf3bb Wed Dec 15 09:19:08 2021 -0800
    Bumping up max window size since barchart drawer/mapbox maker can handle it now.
  • lines changed 116, context: html, text, full: html, text
    c4640a1f9cd94203c06b75c17485d34f57f8333d Fri Dec 17 16:54:43 2021 -0800
    Removing all but usual and full tracks. Merging 10x and FACS into same supertrack. Improving short and some long labels.
• src/hg/makeDb/trackDb/uniprot.ra
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    8bd374ecb63b76ee98d212810ca13d6ccec0e45e Mon Dec 20 05:48:20 2021 -0800
    small uniprot tdb change, refs #28560
• src/hg/pslCDnaFilter/cDnaAligns.c
  • lines changed 23, context: html, text, full: html, text
    54805fea0022a5d8d26ce1eadc2ac470a0b564ef Fri Dec 17 18:53:31 2021 -0800
    Pass through PSLs without modification when -repsAsMatch is used. This allows for doing repeat cotent analysis even filtering.
• src/hg/pslCDnaFilter/cDnaAligns.h
  • lines changed 4, context: html, text, full: html, text
    54805fea0022a5d8d26ce1eadc2ac470a0b564ef Fri Dec 17 18:53:31 2021 -0800
    Pass through PSLs without modification when -repsAsMatch is used. This allows for doing repeat cotent analysis even filtering.
• src/hg/pslCDnaFilter/cDnaReader.c
  • lines changed 8, context: html, text, full: html, text
    54805fea0022a5d8d26ce1eadc2ac470a0b564ef Fri Dec 17 18:53:31 2021 -0800
    Pass through PSLs without modification when -repsAsMatch is used. This allows for doing repeat cotent analysis even filtering.
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • lines changed 3, context: html, text, full: html, text
    54805fea0022a5d8d26ce1eadc2ac470a0b564ef Fri Dec 17 18:53:31 2021 -0800
    Pass through PSLs without modification when -repsAsMatch is used. This allows for doing repeat cotent analysis even filtering.
• src/hg/pslCDnaFilter/tests/expected/repsAsMatchTest/keep.psl
  • lines changed 8, context: html, text, full: html, text
    54805fea0022a5d8d26ce1eadc2ac470a0b564ef Fri Dec 17 18:53:31 2021 -0800
    Pass through PSLs without modification when -repsAsMatch is used. This allows for doing repeat cotent analysis even filtering.
• src/hg/utils/otto/clinGen/makeDosage.sh
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    4d496ac9b43b29987257f6e38b90a03b300922d8 Thu Dec 16 13:17:07 2021 -0800
    Updating name for what files we check on clinGen, refs ChrisL
• src/hg/utils/otto/knownGene/buildCgap.sh
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    b87243c823ae619a0f382db4236df99216f3f1e8 Mon Dec 13 10:38:39 2021 -0800
    some knownGene cleanup
• src/hg/utils/otto/knownGene/buildCore.sh
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    b87243c823ae619a0f382db4236df99216f3f1e8 Mon Dec 13 10:38:39 2021 -0800
    some knownGene cleanup
• src/hg/utils/otto/knownGene/buildKnown.sh
  • lines changed 5, context: html, text, full: html, text
    b87243c823ae619a0f382db4236df99216f3f1e8 Mon Dec 13 10:38:39 2021 -0800
    some knownGene cleanup
• src/hg/utils/otto/knownGene/buildTo.sh
  • lines changed 8, context: html, text, full: html, text
    b87243c823ae619a0f382db4236df99216f3f1e8 Mon Dec 13 10:38:39 2021 -0800
    some knownGene cleanup
• src/hg/utils/otto/orphanet/checkOrphanet.sh
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    947ae9b56eab34e9e2fbc1bfa26d65a7bb8b0cd8 Mon Dec 13 14:45:05 2021 -0800
    Fixing up some of the validation for orphanet, missing negative and getting proper file count. Spoke to Chris about changes.
• src/hg/utils/otto/uniprot-wuhCor1/doUpdate.sh
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    edca5ab88e578d32cfcfd9551e5cc257272f36ef Mon Dec 13 16:11:20 2021 -0800
    Adding the wuhCor1 unirprot otto to the tree. Refs Max.
• src/inc/common.h
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    7a9ec1f838c6a2546278075ffe575fc950ef0b45 Tue Dec 14 20:58:27 2021 -0800
    Addng slName sorting function that ignores case and sorts numbers.
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    eb09b58ec1c838bc315f37322872369200ffe7b9 Sun Dec 19 08:37:56 2021 -0800
    Added uglyt function, like uglyTime, but without the html formatting, so can use it in command line utilities.
• src/inc/fieldedTable.h
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    d3f9b9ecf2a6d30bd8f97566f72e5650982c308d Mon Dec 13 15:22:03 2021 -0800
    Adding hgTracks display of merged bar charts.
• src/inc/vMatrix.h
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    a8c1fc078328e6589cce6dda9090b85e66e77332 Sun Dec 19 08:47:46 2021 -0800
    Making tsvMatrix a private structure.
• src/lib/common.c
  • lines changed 9, context: html, text, full: html, text
    7a9ec1f838c6a2546278075ffe575fc950ef0b45 Tue Dec 14 20:58:27 2021 -0800
    Addng slName sorting function that ignores case and sorts numbers.
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    eb09b58ec1c838bc315f37322872369200ffe7b9 Sun Dec 19 08:37:56 2021 -0800
    Added uglyt function, like uglyTime, but without the html formatting, so can use it in command line utilities.
• src/lib/fieldedTable.c
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    d3f9b9ecf2a6d30bd8f97566f72e5650982c308d Mon Dec 13 15:22:03 2021 -0800
    Adding hgTracks display of merged bar charts.
• src/lib/https.c
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    a67fd2ae15993a7cf5129a53ab1fa193c318bf80 Tue Dec 14 14:05:17 2021 -0800
    Fixing compatibility with openssl 1.1 by removing obsolete ctx->current_cert in https.c, refs #28639
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    01c79192840e6a0ce909b3b75741a0aed8d119f0 Fri Dec 17 03:07:16 2021 -0800
    Add support for a wildcard in httpsCertCheckDomainExceptions. A few are reported in the logs with one low-level wildcard, and it is easy to do and efficient to allow just one asterisk wildcard substitution on one lowest-level subdomain. refs #28657
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    a5c6ed5242b41ecb22dd1dfff89776346de34832 Fri Dec 17 17:03:00 2021 -0800
    Adding a few sites found in logs on RR, euro, asia official mirrors.
• src/lib/memalloc.c
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    5fe279baa642eaee9b0f292a6a171dcbac1cf350 Thu Dec 16 00:30:55 2021 -0800
    Fixing annoying message in needMem when user passes a signed int that has overflowed. Recent example came in liftOver question from user when they were running on a 3GB file.
• src/lib/strex.c
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    14f04b894268dfdf9a94c8123df088e54683fa2c Fri Dec 17 16:48:33 2021 -0800
    Fixing tidy() function in strex.
• src/lib/vMatrix.c
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    a8c1fc078328e6589cce6dda9090b85e66e77332 Sun Dec 19 08:47:46 2021 -0800
    Making tsvMatrix a private structure.
• src/tabFile/tabToTabDir/tests/expected/a_strex_test.tsv
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    14f04b894268dfdf9a94c8123df088e54683fa2c Fri Dec 17 16:48:33 2021 -0800
    Fixing tidy() function in strex.
• src/utils/makefile
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    6811d1e191fbec5ad2685c6232e86f287609acb1 Sun Dec 19 08:51:08 2021 -0800
    Adding matrixClusterColumns and matrixNormalize to the make chain.
• src/utils/matrixClusterColumns/matrixClusterColumns.c
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    78488aa1acc150f98398d66f8bbf87e93ec889ee Tue Dec 14 21:00:13 2021 -0800
    Making this sort the same nice way the browser faceted tables do.
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    2671b4753566a83d798087c6432159336ba90a40 Sat Dec 18 11:04:43 2021 -0800
    Microoptimization in writing out zeros sped it up 10%. Refactoring a code snippet into a function for possible reuse.
• src/utils/matrixNormalize/matrixNormalize.c
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    68882077fc47d554bfb5284949c52cc871ca8903 Sat Dec 18 09:50:50 2021 -0800
    Added special case for zero during printing out of matrix cause it's so common and fprintf(f, %g, 0.0) is rather slower than fputs(0, f);
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    cc7c832d77253b88358ece4b128ceafd6bf8d5c4 Sat Dec 18 11:58:42 2021 -0800
    Multithreading to speed things up a bit in column mode.
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    06a9b44cb029413d7d7b27367230bf5b5b0dd006 Sat Dec 18 12:03:00 2021 -0800
    Put in the usual optimization to print zero faster for a 5% speedup.
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    ebfdcc9a044d15c0bd9c4355b2c92ff3d6f95024 Sun Dec 19 08:50:12 2021 -0800
    Parallelizing memMatrixToTsv and moving it to a library. Parallelizing column normalizing.
• src/utils/matrixNormalize/tests/colLength.out
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    ff980ca1294206936242b945c9835c066ffc3e8c Sun Dec 19 08:36:37 2021 -0800
    Changed a facet name from detailed_cell_type to cell_cluster
• src/utils/matrixNormalize/tests/colSum.out
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    ff980ca1294206936242b945c9835c066ffc3e8c Sun Dec 19 08:36:37 2021 -0800
    Changed a facet name from detailed_cell_type to cell_cluster
• src/utils/matrixNormalize/tests/expected/colLength.out
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    ff980ca1294206936242b945c9835c066ffc3e8c Sun Dec 19 08:36:37 2021 -0800
    Changed a facet name from detailed_cell_type to cell_cluster
• src/utils/matrixNormalize/tests/expected/colSum.out
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    ff980ca1294206936242b945c9835c066ffc3e8c Sun Dec 19 08:36:37 2021 -0800
    Changed a facet name from detailed_cell_type to cell_cluster
• src/utils/matrixNormalize/tests/expected/rowLength.out
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    ff980ca1294206936242b945c9835c066ffc3e8c Sun Dec 19 08:36:37 2021 -0800
    Changed a facet name from detailed_cell_type to cell_cluster
• src/utils/matrixNormalize/tests/expected/rowSum.out
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    ff980ca1294206936242b945c9835c066ffc3e8c Sun Dec 19 08:36:37 2021 -0800
    Changed a facet name from detailed_cell_type to cell_cluster
• src/utils/matrixNormalize/tests/makefile
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    30c104443327d6c2c7beaf0e9d508bf2f123f15c Sun Dec 19 08:52:58 2021 -0800
    Adding basic tests to test chain.
• src/utils/matrixNormalize/tests/rowLength.out
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    ff980ca1294206936242b945c9835c066ffc3e8c Sun Dec 19 08:36:37 2021 -0800
    Changed a facet name from detailed_cell_type to cell_cluster
• src/utils/matrixNormalize/tests/rowSum.out
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    ff980ca1294206936242b945c9835c066ffc3e8c Sun Dec 19 08:36:37 2021 -0800
    Changed a facet name from detailed_cell_type to cell_cluster
• src/utils/qa/weeklybld/buildEnv.csh
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    86c0ae01a623e119c5fde1409507ab190ce5cd2f Mon Dec 20 10:59:54 2021 -0800
    v425 preview2, refs #28625
• src/utils/qa/whoMadeIt.csh
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    b18eb27f3dd7e5470ab93353fb179730ce1eb75e Tue Dec 14 15:21:30 2021 -0800
    fixed file name per hiram suggestion

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