All File Changes

v426_preview to v426_preview2 (2022-01-18 to 2022-01-24) v426

• confs/asia.hg.conf
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    e21917a837618b0cc6ccb3b5789ef0828b0d2880 Sun Jan 23 01:11:41 2022 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    e21917a837618b0cc6ccb3b5789ef0828b0d2880 Sun Jan 23 01:11:41 2022 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 7, context: html, text, full: html, text
    e21917a837618b0cc6ccb3b5789ef0828b0d2880 Sun Jan 23 01:11:41 2022 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 2, context: html, text, full: html, text
    e21917a837618b0cc6ccb3b5789ef0828b0d2880 Sun Jan 23 01:11:41 2022 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    e21917a837618b0cc6ccb3b5789ef0828b0d2880 Sun Jan 23 01:11:41 2022 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgCustom/hgCustom.c
  • lines changed 15, context: html, text, full: html, text
    0144c8f0636b4498055e67a1c772da68de25aeb7 Wed Jan 19 05:48:51 2022 -0800
    making it impossible for users to upload bigBed, bigWig or BAM files on hgCustom, refs #8155
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 9, context: html, text, full: html, text
    a555f913f8ea500e670e38d03a365ea7c1426fa9 Wed Jan 19 17:32:57 2022 -0800
    Documenting liftOver file size limit part A of refs #28765
• src/hg/hgPcr/hgPcr.c
  • lines changed 1, context: html, text, full: html, text
    2968c22e9a0e002863a920d5a60ad93df5cb48a7 Tue Jan 18 18:22:28 2022 -0800
    Updating the hgPcr example video link, refs #28779
• src/hg/hgTables/bigBed.c
  • lines changed 8, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgTables/bigWig.c
  • lines changed 5, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgTracks/chainTrack.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    4b36474ffce6a684ab848e918363c678f635da66 Wed Jan 19 18:30:07 2022 -0800
    Removing the word assembly from hgTracks title refs #28788
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    4c4e222e61f00468072b481e7f7139bf5d3fc0f9 Fri Jan 21 01:38:16 2022 -0800
    removing the year from a few assemblies on the hgTracks label, refs #28788
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgTracks/vcfTrack.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 4, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/barChartClick.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/bigBedClick.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/bigDbSnpClick.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/bigRmskClick.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/clinvarSubLolly.c
  • lines changed 3, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/encodeClick.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/hgc.c
  • lines changed 8, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/lrgClick.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/mafClick.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/transMapClick.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/hgc/wiggleClick.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/htdocs/FAQ/FAQmaillist.html
  • lines changed 1, context: html, text, full: html, text
    eba63a257169375d0edb44dd5d823cb998894960 Tue Jan 11 13:11:46 2022 -0800
    Code Review changes ref #28741
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    eba63a257169375d0edb44dd5d823cb998894960 Tue Jan 11 13:11:46 2022 -0800
    Code Review changes ref #28741
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 50, context: html, text, full: html, text
    ac303f8bb9baf25d201ad8530d4560fa3175fcd9 Wed Jan 19 16:31:45 2022 -0800
    Adding documentation about configuring SSL web server certs for use with openssl and the UCSC Genome Browser. refs #28792
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 8, context: html, text, full: html, text
    a555f913f8ea500e670e38d03a365ea7c1426fa9 Wed Jan 19 17:32:57 2022 -0800
    Documenting liftOver file size limit part A of refs #28765
• src/hg/htdocs/goldenPath/labs.html
  • lines changed 1, context: html, text, full: html, text
    83566c956c485a71a0439a5d745593a0ee53bf83 Tue Jan 18 15:02:00 2022 -0800
    Updating a link to RIKEN found by 404 cronjob search of static pages, no RM
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 3, context: html, text, full: html, text
    27e9e95868aa092f167c553c4f075e54071ae977 Thu Jan 20 11:49:34 2022 -0800
    Adding PMCID for 2022 update paper now that it is available.
• src/hg/inc/chromAlias.h
  • lines changed 5, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/lib/chainNetDbLoad.c
  • lines changed 3, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/lib/chromAlias.c
  • lines changed 69, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/lib/customFactory.c
  • lines changed 3, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/lib/hgHgvs.c
  • lines changed 2, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/hg/lib/hui.c
  • lines changed 8, context: html, text, full: html, text
    19de5d37d6012bd61b9c5a57fbc524581c7a1987 Tue Jan 18 15:25:13 2022 -0800
    adding support for speciesLabels to hgTrackUi
• src/hg/makeDb/doc/assemblyEquivalence/update.2022-01-18.txt
  • lines changed 391, context: html, text, full: html, text
    1834a2b061d8583ee144f1adf0d0ce3c58166d93 Tue Jan 18 16:02:05 2022 -0800
    updated to Ensembl v105 and now including all bacteria, virus, fungi, everything no redmine
• src/hg/makeDb/gnomad/gnomadVcfBedToBigBed
  • lines changed 28, context: html, text, full: html, text
    89422546b1bfadf27a115ae774571a5f57a916d8 Tue Jan 18 14:37:33 2022 -0800
    Re-do the v2.1.1 (hg19) and v3.1.1 (hg38) versions of the gnomad tracks after a user found we were incorrectly pre-filtering intergenic variants from the whole genome data sets, refs #28666
• src/hg/makeDb/schema/all.joiner
  • lines changed 70, context: html, text, full: html, text
    635ca2890b6308aec5bf2536060bd9c220dc5e25 Wed Jan 19 10:41:31 2022 -0800
    fix up V39 HTML, and (finally) remove all the *ToKg* rules in all.joiner
• src/hg/makeDb/trackDb/crisprAll.html
  • lines changed 2, context: html, text, full: html, text
    b788a707887a79434941ee37b1c5f5c496995c70 Thu Jan 20 07:14:25 2022 -0800
    added definition of CFD score
• src/hg/makeDb/trackDb/human/hg19/gnomadExomesGenomes.html
  • lines changed 17, context: html, text, full: html, text
    89422546b1bfadf27a115ae774571a5f57a916d8 Tue Jan 18 14:37:33 2022 -0800
    Re-do the v2.1.1 (hg19) and v3.1.1 (hg38) versions of the gnomad tracks after a user found we were incorrectly pre-filtering intergenic variants from the whole genome data sets, refs #28666
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.alpha.ra
  • lines changed 944, context: html, text, full: html, text
    68445ecc745425fca75838ac73d23076c19bd532 Thu Jan 20 12:42:51 2022 -0800
    Updating trackDb to reflect new gnomAd data and settings for refs #28666
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 5, context: html, text, full: html, text
    68445ecc745425fca75838ac73d23076c19bd532 Thu Jan 20 12:42:51 2022 -0800
    Updating trackDb to reflect new gnomAd data and settings for refs #28666
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    68445ecc745425fca75838ac73d23076c19bd532 Thu Jan 20 12:42:51 2022 -0800
    Updating trackDb to reflect new gnomAd data and settings for refs #28666
• src/hg/makeDb/trackDb/human/hg38/gnomadV3_1_1.html
  • lines changed 8, context: html, text, full: html, text
    89422546b1bfadf27a115ae774571a5f57a916d8 Tue Jan 18 14:37:33 2022 -0800
    Re-do the v2.1.1 (hg19) and v3.1.1 (hg38) versions of the gnomad tracks after a user found we were incorrectly pre-filtering intergenic variants from the whole genome data sets, refs #28666
  • lines changed 4, context: html, text, full: html, text
    68445ecc745425fca75838ac73d23076c19bd532 Thu Jan 20 12:42:51 2022 -0800
    Updating trackDb to reflect new gnomAd data and settings for refs #28666
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 6, context: html, text, full: html, text
    77205f9f98cea502c7a5e3a72a49829214f9bc8e Tue Jan 18 16:36:16 2022 -0800
    update knownGene.alpha.ra to use GENCODE V39
• src/hg/makeDb/trackDb/human/hg38/knownGeneArchive.ra
  • lines changed 34, context: html, text, full: html, text
    3d92184650492b66c5ead4d4b2dbd63028b596cc Wed Jan 19 11:03:29 2022 -0800
    add V38 to knownGeneArchive
• src/hg/makeDb/trackDb/human/hg38/knownGeneV39.html
  • lines changed 140, context: html, text, full: html, text
    6123cee6c76c2cc2f143a385a1947a735f178e35 Tue Jan 18 15:26:53 2022 -0800
    Adding html for GENCODE V39
  • lines changed 10, context: html, text, full: html, text
    635ca2890b6308aec5bf2536060bd9c220dc5e25 Wed Jan 19 10:41:31 2022 -0800
    fix up V39 HTML, and (finally) remove all the *ToKg* rules in all.joiner
• src/hg/makeDb/trackDb/virus/wuhCor1/articV4_1.html
  • lines changed 6, context: html, text, full: html, text
    6b3101b9186d98972f0eeed84536d83ba2a3d4bd Tue Jan 18 17:15:51 2022 -0800
    fixing minor typo and format for CR refs #28777
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    21ec4227aa96abba7f519d50611164f41c1d2435 Tue Jan 18 10:50:31 2022 -0800
    add chainCleaner and pslSortAcc to utilities build
• src/hg/mouseStuff/makefile
  • lines changed 1, context: html, text, full: html, text
    21ec4227aa96abba7f519d50611164f41c1d2435 Tue Jan 18 10:50:31 2022 -0800
    add chainCleaner and pslSortAcc to utilities build
• src/hg/utils/phyloTrees/findScores.pl
  • lines changed 46, context: html, text, full: html, text
    db83fe93e41c16a07ce4c30d316ed77eee3a849c Wed Jan 19 13:35:36 2022 -0800
    now working OK with assembly hub as targetDb refs #28757
• src/inc/bbiFile.h
  • lines changed 4, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/inc/bigBed.h
  • lines changed 3, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/inc/bigWig.h
  • lines changed 3, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/lib/bbiRead.c
  • lines changed 60, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/lib/bigBed.c
  • lines changed 7, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/lib/bwgQuery.c
  • lines changed 7, context: html, text, full: html, text
    54406b80d5d435970989acff7b22dd6146c6b411 Sat Jan 22 15:24:59 2022 -0800
    adding chrom alias support to big files
• src/utils/chromToUcsc/chromToUcsc
  • lines changed 16, context: html, text, full: html, text
    dc808927b55b21c72db0cd528f76624fcba339dd Mon Jan 24 05:15:33 2022 -0800
    adding igv-style chrom alias support to chromToUcsc, refs #28722
• src/utils/chromToUcsc/tests/GCF_002742125.1.chromAlias.txt
  • lines changed 2, context: html, text, full: html, text
    dc808927b55b21c72db0cd528f76624fcba339dd Mon Jan 24 05:15:33 2022 -0800
    adding igv-style chrom alias support to chromToUcsc, refs #28722
• src/utils/chromToUcsc/tests/expected/genark.bed
  • lines changed 1, context: html, text, full: html, text
    dc808927b55b21c72db0cd528f76624fcba339dd Mon Jan 24 05:15:33 2022 -0800
    adding igv-style chrom alias support to chromToUcsc, refs #28722
• src/utils/chromToUcsc/tests/expected/genark.err
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    dc808927b55b21c72db0cd528f76624fcba339dd Mon Jan 24 05:15:33 2022 -0800
    adding igv-style chrom alias support to chromToUcsc, refs #28722
• src/utils/chromToUcsc/tests/in/genark.bed
  • lines changed 1, context: html, text, full: html, text
    dc808927b55b21c72db0cd528f76624fcba339dd Mon Jan 24 05:15:33 2022 -0800
    adding igv-style chrom alias support to chromToUcsc, refs #28722
• src/utils/chromToUcsc/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    dc808927b55b21c72db0cd528f76624fcba339dd Mon Jan 24 05:15:33 2022 -0800
    adding igv-style chrom alias support to chromToUcsc, refs #28722
• src/utils/chromToUcsc/tests/out/genark.bed
  • lines changed 1, context: html, text, full: html, text
    dc808927b55b21c72db0cd528f76624fcba339dd Mon Jan 24 05:15:33 2022 -0800
    adding igv-style chrom alias support to chromToUcsc, refs #28722
• src/utils/chromToUcsc/tests/out/genark.err
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    dc808927b55b21c72db0cd528f76624fcba339dd Mon Jan 24 05:15:33 2022 -0800
    adding igv-style chrom alias support to chromToUcsc, refs #28722
• src/utils/qa/weeklybld/buildEnv.csh
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    8a395717bcf58d15a41f4c1116f86358a3494ff5 Mon Jan 24 10:14:20 2022 -0800
    v426 preview2, refs #TICKETID

• lines changed: 2096
• files changed: 75