All File Changes

v433_preview2 to v433_base (2022-06-20 to 2022-06-27) v433

• src/hg/bedIntersect/bedIntersect.c
  • lines changed 2, context: html, text, full: html, text
    85b15e64af21551227c0c052b3dcbb65a54225ef Fri Jun 24 15:07:55 2022 -0700
    allow binKeeper to work with chr sizes up to 2Gb refs #29545
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    845dfcdd54bdf5cbda67a70b7b3946f2892104ea Fri Jun 24 08:25:12 2022 -0700
    changing copy icon as per QA, refs #29583
• src/hg/hgSession/hgSession.c
  • lines changed 2, context: html, text, full: html, text
    313f7e73df24f4593df8f3009890893f4abcd47e Thu Jun 23 04:55:32 2022 -0700
    changing copy button text after QA feedback, refs #29586
• src/hg/hgTracks/bamTrack.c
  • lines changed 1, context: html, text, full: html, text
    50461aa0137fb4d85bcb2566e441f1b582594401 Wed Jun 22 20:37:43 2022 -0700
    Removing calls to baseColorDrawCleanup.
• src/hg/hgTracks/cds.c
  • lines changed 76, context: html, text, full: html, text
    2b789d0cc2a1f7c5d287820c20d2039a77a16009 Wed Jun 22 20:45:03 2022 -0700
    Removing baseColorDrawCleanup. Adding "2bit" type to baseColorUseSequence trackDb setting. Adding otherTwoBitUrl tag to trackDb. Enabling psl and bitPsl to use "baseColorDrawCLeanup 2bit" and "otherTwoBitUrl someTwoBitUrl.2bit" combination to get differing bases to be hilit in red and displaying bases when zoomed in to base level.
  • lines changed 1, context: html, text, full: html, text
    1728b2a32c308745358df39a8f25c1a8e8cbfad9 Thu Jun 23 13:39:00 2022 -0700
    Oops, fixing a NULL check I missed that was leading to crashs. #29585
• src/hg/hgTracks/cds.h
  • lines changed 4, context: html, text, full: html, text
    2b789d0cc2a1f7c5d287820c20d2039a77a16009 Wed Jun 22 20:45:03 2022 -0700
    Removing baseColorDrawCleanup. Adding "2bit" type to baseColorUseSequence trackDb setting. Adding otherTwoBitUrl tag to trackDb. Enabling psl and bitPsl to use "baseColorDrawCLeanup 2bit" and "otherTwoBitUrl someTwoBitUrl.2bit" combination to get differing bases to be hilit in red and displaying bases when zoomed in to base level.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    ca03872563e0ec57aef2d4214d9ac1361b0cbb86 Wed Jun 22 20:46:11 2022 -0700
    Removing call to baseColorDrawCleanup()
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 17, context: html, text, full: html, text
    abd6ac195970e8c6893bf204d9ecb940b5a0fa49 Mon Jun 20 13:43:53 2022 -0700
    Improving #RIGHT_CLICK_NAV section of hgTracksHelp.html, no RM
  • lines changed 2, context: html, text, full: html, text
    b2adcaf126fb465a23da4d7e2b5379c04c8ecd61 Mon Jun 20 14:06:59 2022 -0700
    Making new right-click image a link, without disconnecting custom tracks/hubs, no RM
• src/hg/htdocs/goldenPath/help/hic.html
  • lines changed 5, context: html, text, full: html, text
    6ecc9ffc2466edde7f943ad7456a969bde280127 Thu Jun 23 06:09:46 2022 -0700
    Adding an image for Hi-C on the hic.html page after MLQ, refs #29620
  • lines changed 7, context: html, text, full: html, text
    fce7add7dd785f2a73b56bdbbb9a3f8ed7269132 Fri Jun 24 07:08:37 2022 -0700
    Adding a link to the hic Track Config page at the top of hic.html, and existing hicDrawModes.png img refs #29620
• src/hg/htdocs/goldenPath/help/trix.html
  • lines changed 19, context: html, text, full: html, text
    a729a9e1d69997979c922c69f1cfb0f55cd5fe98 Sat Jun 25 07:49:13 2022 -0700
    Expanding an example on trix.html, no RM
  • lines changed 6, context: html, text, full: html, text
    d139f387c9952df1f43550ae1a418b843dd5ecb3 Sun Jun 26 07:52:53 2022 -0700
    Adding doc of -maxWordLength=N option for ixIxx to trix.html
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 19, context: html, text, full: html, text
    ac8ff435df0013484aee3fbdc6e8bf1840dd6944 Mon Jun 27 07:35:11 2022 -0700
    Adding a news item about logo=on dynseq bigWig feature, no RM
• src/hg/htdocs/images/hic_image.png
  • lines changed 0, context: html, text, full: html, text
    65cf1d1857c499b53a39a0124ddd6b63512c8017 Thu Jun 23 06:06:33 2022 -0700
    Adding an image for Hi-C on the hic.html page after MLQ, refs #29620
• src/hg/htdocs/images/right_click_example.png
  • lines changed 0, context: html, text, full: html, text
    745a6cd8f7ccfb04c907efecd45e4f2c40b1d972 Mon Jun 20 13:21:40 2022 -0700
    Adding an image for right_click #RIGHT_CLICK_NAV section of hgTracksHelp.html
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    ac8ff435df0013484aee3fbdc6e8bf1840dd6944 Mon Jun 27 07:35:11 2022 -0700
    Adding a news item about logo=on dynseq bigWig feature, no RM
• src/hg/htdocs/staff.html
  • lines changed 5, context: html, text, full: html, text
    e98a6b7a08e89f8ba5f792b31d8b8ba819dd4f59 Wed Jun 22 07:05:35 2022 -0700
    Retiring Ann to project alumni on staff.html, no RM
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    f9e5a987858f88f2f3ce5fdca8a14e5f52065d9a Mon Jun 27 10:09:02 2022 -0700
    New version number v433
• src/hg/js/hgHubConnect.js
  • lines changed 1, context: html, text, full: html, text
    cb1a90324212bef926a2d1523121b5543feead82 Mon Jun 27 06:20:32 2022 -0700
    changing alert box text for hgHubConnect, refs #29583
• src/hg/js/utils.js
  • lines changed 1, context: html, text, full: html, text
    313f7e73df24f4593df8f3009890893f4abcd47e Thu Jun 23 04:55:32 2022 -0700
    changing copy button text after QA feedback, refs #29586
• src/hg/lib/chromBins.c
  • lines changed 6, context: html, text, full: html, text
    80265657aadfc44b510d03b44d8858cae0dfbda7 Sun Jun 26 16:26:24 2022 -0700
    can use the largest integer for the maximum chrom size for chrom sizes up to 2^31 - 1 no redmine
• src/hg/makeDb/doc/asmHubs/commonNames.pl
  • lines changed 42, context: html, text, full: html, text
    6d83c1f80eed30361f2c3a7d4c1282f48592b839 Wed Jun 22 15:50:38 2022 -0700
    util script to find common name string given an asmId refs #29545
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 107, context: html, text, full: html, text
    9b1060e344334eac530cc21bb44751afd070ee98 Tue Jun 21 12:47:23 2022 -0700
    catch up update as of 23 May 2022 refs #29545
• src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv
  • lines changed 4, context: html, text, full: html, text
    efa46520962635449236b8948ea35205971a5257 Thu Jun 23 09:52:52 2022 -0700
    GenArk update adding four genomes refs #29545
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 23, context: html, text, full: html, text
    8c9a790644615898527e7828e459d72163b1fcbd Wed Jun 22 15:21:20 2022 -0700
    adding 16 new genomes for update refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 29, context: html, text, full: html, text
    189562588fbfacd463e0e121743ca0464d8b1d6f Fri Jun 24 12:30:40 2022 -0700
    GenArk update addgin 29 new genomes refs #29545
• src/hg/makeDb/doc/hs1/initial.txt
  • lines changed 44, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 82, context: html, text, full: html, text
    cd81f57acca462c86f554b229889fd76664ce5e8 Fri Jun 24 11:06:34 2022 -0700
    GenArk update three failing refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    ef5883930d5d1e990327dc673b23a67c060903fd Thu Jun 23 09:55:08 2022 -0700
    completed GenArk update refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 12, context: html, text, full: html, text
    2365f128025272b7ebff9c96b161e1215a5047c1 Fri Jun 24 11:46:27 2022 -0700
    GenArk update adding 11 genomes refs #29545
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    69758abc00f4e443b73add19b655d5df9a818567 Tue Jun 21 13:06:01 2022 -0700
    catch up update as of 23 May 2022 refs #29545
• src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    96c8a6f205736b81782282a73b25d15463e3ae04 Thu Jun 23 15:05:06 2022 -0700
    GenArk update add three vertebrates refs #29545
• src/hg/makeDb/trackDb/human/constraintSuper.html
  • lines changed 6, context: html, text, full: html, text
    d10f51c182d74b4984da9b1eb5914d11872454d9 Wed Jun 22 04:49:06 2022 -0700
    Adding Ana's suggested improvements for HMC docs page, refs #29153
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.assembly.html
  • lines changed 33, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.augustus.html
  • lines changed 106, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.catLiftOffGenesV1.html
  • lines changed 104, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.censat.html
  • lines changed 34, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.chainNet.html
  • lines changed 183, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.clinVar20220313.html
  • lines changed 14, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.cpgIslands.html
  • lines changed 78, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.dbSNP155.html
  • lines changed 14, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.description.html
  • lines changed 131, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.encode.html
  • lines changed 41, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.gc5Base.html
  • lines changed 21, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.gwasSNPs2022-03-08.html
  • lines changed 14, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.hgCactus.html
  • lines changed 44, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.hgLiftOver.html
  • lines changed 245, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.hgUnique.html
  • lines changed 45, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.liftJkAll.html
  • lines changed 6, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.microsatellites.html
  • lines changed 31, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.proseq.html
  • lines changed 57, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.rdnaModel.html
  • lines changed 10, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.refSeqComposite.html
  • lines changed 186, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.repeatMasker.html
  • lines changed 149, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.rnaseq.html
  • lines changed 68, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.sedefSegDups.html
  • lines changed 43, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.sgdpCopyNumber.html
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    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.simpleRepeat.html
  • lines changed 48, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.t2tRepeatMasker.html
  • lines changed 153, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.tanDups.html
  • lines changed 101, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.windowMasker.html
  • lines changed 34, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/html/GCA_009914755.4_T2T-CHM13v2.0.xenoRefGene.html
  • lines changed 88, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/human/hs1/liftJkAll.ra
  • lines changed 54, context: html, text, full: html, text
    e32ecd59b34531455b424a6f0249353fe5ec4262 Fri Jun 24 10:54:16 2022 -0700
    fix problem with geneType in knownGene bigGenePred file
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 6132, context: html, text, full: html, text
    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
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    52269827f6e4219781da466967850ca0011d1445 Fri Jun 24 10:55:37 2022 -0700
    oops... add jkLiftAll
• src/hg/makeDb/trackDb/makefile
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    e37c8b2581aa25f3deb43db2f54642cfc53abeff Thu Jun 23 13:29:46 2022 -0700
    create hs1 hub
• src/hg/makeDb/trackDb/maybeBuildHub
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    eb977447c35d01a2aa61f7ff47a1de0ed477b6cf Fri Jun 24 09:51:46 2022 -0700
    check to make sure database exists before accessing it
• src/hg/makeDb/trackDb/tagTypes.tab
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    5f4d3d1d62d21db2e0ca873be3d0b4779166c1f5 Wed Jun 22 20:36:35 2022 -0700
    Adding otherTwoBitUrl tag.
• src/hg/makeDb/trackDb/virus/wuhCor1/resist.html
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    afc7eee26cc29ad47254e2d72a5bd459509ef260 Tue Jun 21 12:51:36 2022 -0700
    Slight word changes for resist track refs #28889
• src/hg/mouseStuff/mafToPsl/mafToPsl.c
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    4e346bd64d3157d7add9043b93ebf124cdbed1be Thu Jun 23 14:43:07 2022 -0700
    Prevent SEGV caused by trying to convert components with no sequence, e.g. from 'e' lines with double-sided insertion. refs #29636
• src/hg/oneShot/refGraphTest/makefile
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    95df32e007a5dbe0e8bfe718fbb46f970e045050 Wed Jun 15 14:25:04 2022 -0700
    Some experimental work that has let me know where the alt-haplotypes land on the main chromosomes.
• src/hg/oneShot/refGraphTest/refGraphTest.c
  • lines changed 268, context: html, text, full: html, text
    95df32e007a5dbe0e8bfe718fbb46f970e045050 Wed Jun 15 14:25:04 2022 -0700
    Some experimental work that has let me know where the alt-haplotypes land on the main chromosomes.
• src/hg/oneShot/testLiftRechainer/makefile
  • lines changed 3, context: html, text, full: html, text
    29f88e9827e33081a9e4c4db1c6dcca6542f7ccd Sun Jun 19 22:29:39 2022 -0700
    First cut of next generation liftOver chain maker. This one is meant to handle swapping in alternate haplotypes properly, even when, as is the case with the HLA locus in the t2t, more than one alt is moved. Still needs lots of testing and polishing, but finishes and makes something semi-plausable on t2t's chr6 going against hg38's chr6 + alts.
• src/hg/oneShot/testLiftRechainer/testLiftRechainer.c
  • lines changed 455, context: html, text, full: html, text
    29f88e9827e33081a9e4c4db1c6dcca6542f7ccd Sun Jun 19 22:29:39 2022 -0700
    First cut of next generation liftOver chain maker. This one is meant to handle swapping in alternate haplotypes properly, even when, as is the case with the HLA locus in the t2t, more than one alt is moved. Still needs lots of testing and polishing, but finishes and makes something semi-plausable on t2t's chr6 going against hg38's chr6 + alts.
  • lines changed 24, context: html, text, full: html, text
    c9941d5c3c0198fea692d72db7fa44a711858598 Mon Jun 20 13:51:30 2022 -0700
    Fixing off by one bug in traceback
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    6c0adf59ef794e2a107de7cbf638041158dc406e Mon Jun 20 17:35:31 2022 -0700
    Fixed crash bug. Improved status reporting. Removed some debugging statements.
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    6557cfc305545ee5c43930fb7548b3310061c2d6 Wed Jun 22 20:32:53 2022 -0700
    First full genome functioning build of dynamic programming version to pick best chains to use for liftOver purposes out of a a pairwise genome alignment to allow best liftovers from query to target maximizing coverage of target while minimizing coverage of query. An improvement over the greedy algorithm used in netChain/chainNetSubset.
• src/hg/ratStuff/mafCounts/mafCounts.c
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    b7f5213aa30a1a6f58773601b5c7f0885e909264 Fri Jun 24 13:08:18 2022 -0700
    explicating the function of this code in response to code review
• src/hg/txGraph/txgToAgx/txgToAgx.c
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    45a43477fb72105c168c76e551407e7a68eeabdd Sat Jun 25 11:46:46 2022 -0700
    change commas in source table entries to underbars to prevent confustion in comma-separated list
• src/hg/utils/automation/HgAutomate.pm
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    b67e9a30432634d4134d356a1b7160efaf6facc9 Wed Jun 22 11:37:24 2022 -0700
    nomore newdev no redmine
• src/hg/utils/automation/doAssemblyHub.pl
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    2b2a19a35ceb667d2c0659ff422a980e7e1e22c1 Thu Jun 23 13:23:49 2022 -0700
    correctly sizing numbers in allGaps refs #29545
• src/hg/utils/genePredToBigGenePred/genePredToBigGenePred.c
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    e32ecd59b34531455b424a6f0249353fe5ec4262 Fri Jun 24 10:54:16 2022 -0700
    fix problem with geneType in knownGene bigGenePred file
• src/hg/utils/otto/knownGene/buildCore.sh
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    e32ecd59b34531455b424a6f0249353fe5ec4262 Fri Jun 24 10:54:16 2022 -0700
    fix problem with geneType in knownGene bigGenePred file
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    26f1c3fc24fd6b4a1f5376cf609726d5c551c08f Fri Jun 17 12:06:21 2022 -0700
    Added lineages BA.1.15.3, BD.1, BA.1.23, BA.1.24, BA.2.2.1, BA.2.3.{5-18}, BA.2.9.{3-4}, BG.1, BA.2.12.2, BA.2.{46-73}, BA.2.56.1, BA.4.1.{1-2}, BA.5.{1-3,5}, BA.5.2.1, BF.1, BA.5.3.{1-2}, BE.1, XZ, XA{A-H} -- pango-designation v1.10. Renamed 5 proposed labels that were designated, added 2 proposed labels, added BA.2.3.16_alt and BA.2.13_revs labels for split branches due to artefacts; labels will need to be tweaked when making lineageTree.pb.
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    986b0aedc124961eefdb62ae9af7b690591cdb60 Wed Jun 22 15:24:23 2022 -0700
    Added labels BA.2.3.9_rev241 and BA.2.3.9_rev10198 to include branches split off by reversions. Added BG.2 - pango-designation v1.11.
• src/inc/localmem.h
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    345e4ee67a3c7afb41be7899635259f8745fefe3 Sat Jun 18 06:31:46 2022 -0700
    Adding lmSlRef function.
• src/inc/rangeTree.h
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    31857342d47d49372089fe3b5aa802932313f3ef Sat Jun 18 06:30:38 2022 -0700
    Fixed bug in rangeTreeAddToCoverageDepth. Added parallel rangeTreeAddToCoverageList.
• src/inc/srcVersion.h
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    f9e5a987858f88f2f3ce5fdca8a14e5f52065d9a Mon Jun 27 10:09:02 2022 -0700
    New version number v433
• src/lib/localmem.c
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    345e4ee67a3c7afb41be7899635259f8745fefe3 Sat Jun 18 06:31:46 2022 -0700
    Adding lmSlRef function.
• src/lib/rangeTree.c
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    31857342d47d49372089fe3b5aa802932313f3ef Sat Jun 18 06:30:38 2022 -0700
    Fixed bug in rangeTreeAddToCoverageDepth. Added parallel rangeTreeAddToCoverageList.
• src/utils/bedInvert.pl
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    8c084018dedc1241e5220ad9b80f83e957368890 Fri Jun 24 15:27:06 2022 -0700
    handle case of empty input file no redmine
• src/utils/qa/weeklybld/buildEnv.csh
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    7f218abca571a580a8a64572b8afce01987bdf3b Mon Jun 27 10:08:04 2022 -0700
    v433 final build, refs #29585

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