All File Changes

v420_preview to v420_preview2 (2021-08-23 to 2021-08-30) v420

• confs/hgwdev.hg.conf
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    2a7fe39df4e11004d26a0c3be70a289118e55a97 Sun Aug 29 01:11:58 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgBlat/hgBlat.c
  • lines changed 6, context: html, text, full: html, text
    d8cf2d55439ec62a1f62be004713039331664798 Thu Aug 26 03:32:42 2021 -0700
    fixing hgBlat apache error log messages, refs #28051
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    eab7c9759c4a29064aab1143c2eb9d43a3050413 Thu Aug 26 12:44:56 2021 -0700
    Fixing typo: there is no webEndText, only webEnd.
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    db74f36bdb4f9546f9a9ff45ef8b012432962e87 Thu Aug 26 12:51:34 2021 -0700
    fixing dumb mistake that I made that broke the build, thanks to Angie who found this, refs #28051
  • lines changed 4, context: html, text, full: html, text
    4023e99edfbcb1e936b98326d9f99f1650541bbd Thu Aug 26 18:48:15 2021 -0700
    added ref to blat paper
• src/hg/hgGene/hgGene.c
  • lines changed 1, context: html, text, full: html, text
    9ec48c91786f9dfe13465405f11b98c2e7efe10c Wed Aug 25 14:53:25 2021 -0700
    take out text "Description and Page Index" from top of hgGene page
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 31, context: html, text, full: html, text
    68f95eec388eb3895787fc885fa01fe7ee3447ac Thu Aug 26 11:36:26 2021 -0700
    Recently usher started prepending node_ to numeric internal node names stored in the protobuf, so node names in usher outputs are now node_<number> instead of just <number>. However, the protobuf still has numeric names, so it may be necessary to strip the prefix when looking up bigTree nodes.
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    2aa99ff0ca7a50af99ba59a3e8a54d7a819e7808 Thu Aug 26 12:30:42 2021 -0700
    Yikes, I was forgetting to expand condensed nodes in the big tree when making custom track VCF for subtrees, resulting in some sequences not being found & having no alt alleles in VCF.
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    20ceda8601cb6eb3713512f9e945a61be9950e68 Fri Aug 27 12:49:23 2021 -0700
    Fix unhelpful error messages
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 8, context: html, text, full: html, text
    68f95eec388eb3895787fc885fa01fe7ee3447ac Thu Aug 26 11:36:26 2021 -0700
    Recently usher started prepending node_ to numeric internal node names stored in the protobuf, so node names in usher outputs are now node_<number> instead of just <number>. However, the protobuf still has numeric names, so it may be necessary to strip the prefix when looking up bigTree nodes.
  • lines changed 1, context: html, text, full: html, text
    2aa99ff0ca7a50af99ba59a3e8a54d7a819e7808 Thu Aug 26 12:30:42 2021 -0700
    Yikes, I was forgetting to expand condensed nodes in the big tree when making custom track VCF for subtrees, resulting in some sequences not being found & having no alt alleles in VCF.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 1, context: html, text, full: html, text
    b1470d6f462f975727df99a576b1b7ec72d05491 Fri Aug 27 12:44:36 2021 -0700
    Fix valgrind warning -- I didn't realize safencpy adds a null byte.
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 4, context: html, text, full: html, text
    68f95eec388eb3895787fc885fa01fe7ee3447ac Thu Aug 26 11:36:26 2021 -0700
    Recently usher started prepending node_ to numeric internal node names stored in the protobuf, so node names in usher outputs are now node_<number> instead of just <number>. However, the protobuf still has numeric names, so it may be necessary to strip the prefix when looking up bigTree nodes.
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 18, context: html, text, full: html, text
    2aa99ff0ca7a50af99ba59a3e8a54d7a819e7808 Thu Aug 26 12:30:42 2021 -0700
    Yikes, I was forgetting to expand condensed nodes in the big tree when making custom track VCF for subtrees, resulting in some sequences not being found & having no alt alleles in VCF.
  • lines changed 5, context: html, text, full: html, text
    baef96f3db3202daa9e254b029cbdac78a8f409e Fri Aug 27 12:46:08 2021 -0700
    Fix incorrect-freeing error introduced yesterday in 2aa99ff0.
• src/hg/hgTracks/hgTracks.c
  • lines changed 63, context: html, text, full: html, text
    a1525e0f14f76903c16d5ba788f7a9afcc8c5ed1 Fri Jun 4 04:56:39 2021 -0700
    adding folder icons to hgTracks main track list, refs #25035 code review: this is an experiment and initially should remain in the branch ui-track-icons, until merged on purpose into master.
  • lines changed 7, context: html, text, full: html, text
    90ea52575125dc10ccbdc96754b57025645f84f5 Mon Aug 9 05:25:06 2021 -0700
    For collection tracks, now using only the filled-out folder icon to simplify the display, suggested by Matt and Lou. refs #25035, The mouseover text shows the exact type.
  • lines changed 2, context: html, text, full: html, text
    b97034619937d4c0e440c014d7429687df69cf4f Mon Aug 9 05:38:05 2021 -0700
    using word container track instead of collection track in container track mouseover, refs #25035
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    c36618e1e842ee3cd84de927e963287868edead9 Wed Aug 25 02:16:31 2021 -0700
    Merge branch 'ui-track-icons'
  • lines changed 14, context: html, text, full: html, text
    871f2d654975f77385c1bccb62aa4d8f41f9f294 Fri Aug 27 05:18:24 2021 -0700
    Adding "search help" link to hgTracks, refs #15554
• src/hg/htdocs/contacts.html
  • lines changed 2, context: html, text, full: html, text
    c2e323af1cfff47a01e324fab96cfae2fb9a949f Mon Aug 30 09:13:00 2021 -0700
    add the redmine email widget to contacts.html
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 264, context: html, text, full: html, text
    6be65944defae5c9f1c9f8bb0b43b8e50337b6b9 Tue Aug 24 13:07:06 2021 -0700
    removed large duplicated text block from below the footer
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    a78324be2d472a1efd65f54b8006a3925e70ade7 Wed Aug 25 09:05:06 2021 -0700
    make goldenPath/help/hgGeneGraph.html executable
  • lines changed 12, context: html, text, full: html, text
    77bb0b172c197a780d719f1aba70a9a88173c4c8 Wed Aug 25 12:59:52 2021 -0700
    reusing the image to make a live link to the browser, so they can use it while they read the doc. pretties up the top of the page a bit, too
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 12, context: html, text, full: html, text
    2c91cdd0891e411d69bc5f0d0b920123e1c462eb Wed Aug 25 12:22:34 2021 -0700
    added link to gene graphs page and simplified organization a bit, grouping getting started items in a list
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    10bd71a94c73144171a338b7d21f055035b20594 Wed Aug 25 11:35:37 2021 -0700
    Fixing small typo discovered during NAR paper review (credit to Ann)
• src/hg/htdocs/redmineWidget.html
  • lines changed 27, context: html, text, full: html, text
    c2fe1cd77b01ebcd593c8dd8e2dfd2ee0eb62cc2 Tue Aug 24 16:06:45 2021 -0700
    adding redmineWidget
  • lines changed 4, context: html, text, full: html, text
    c2e323af1cfff47a01e324fab96cfae2fb9a949f Mon Aug 30 09:13:00 2021 -0700
    add the redmine email widget to contacts.html
• src/hg/htdocs/style/HGStyle.css
  • lines changed 6, context: html, text, full: html, text
    a1525e0f14f76903c16d5ba788f7a9afcc8c5ed1 Fri Jun 4 04:56:39 2021 -0700
    adding folder icons to hgTracks main track list, refs #25035 code review: this is an experiment and initially should remain in the branch ui-track-icons, until merged on purpose into master.
  • lines changed 6, context: html, text, full: html, text
    871f2d654975f77385c1bccb62aa4d8f41f9f294 Fri Aug 27 05:18:24 2021 -0700
    Adding "search help" link to hgTracks, refs #15554
• src/hg/htdocs/style/font-awesome.min.css
  • lines changed 4, context: html, text, full: html, text
    dc718bb73d346976671b0624730a38a30ffe8405 Wed Aug 25 12:00:00 2021 -0700
    adding missing font to css directory for icons, refs, refs #25035
• src/hg/htdocs/style/makefile
  • lines changed 2, context: html, text, full: html, text
    dc718bb73d346976671b0624730a38a30ffe8405 Wed Aug 25 12:00:00 2021 -0700
    adding missing font to css directory for icons, refs, refs #25035
• src/hg/htdocs/training/index.html
  • lines changed 19, context: html, text, full: html, text
    7735eee0e1b8400b1c9b5c31c467b2c820c14a11 Mon Aug 23 14:11:04 2021 -0700
    removing completed ESHG and removing invitation for F2F workshops for now
• src/hg/lib/bed5SourceVals.sql
  • lines changed 18, context: html, text, full: html, text
    e399f53ca6abf47c289eda845be502cb78e3f209 Fri Aug 27 23:49:56 2021 -0700
    Somebody had removed this file, but encode liftOvers for hg38 and hg19 patches still need it.
  • lines changed 1, context: html, text, full: html, text
    4ee8be3a646653395a336b28cb365fb8bc6dd16c Sat Aug 28 00:21:24 2021 -0700
    oops. fixed.
• src/hg/lib/lrg.c
  • lines changed 20, context: html, text, full: html, text
    5aa96722c0548d51c76a430c576d1e7823c30ef7 Wed Aug 25 11:32:44 2021 -0700
    Get double sided gaps supported in building of LRG track, refs #24672
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    7110f5219b9ea255b4c8c4d2ef2be4b3bed4195a Tue Aug 24 12:32:39 2021 -0700
    added a word to filter statement on hgTracks, items filtered out
• src/hg/lib/variantProjector.c
  • lines changed 4, context: html, text, full: html, text
    755406e622ce53a7ec5be4c5210f783084d9dd0e Fri Aug 27 12:39:45 2021 -0700
    Fix valgrind warning (although the value from a bad read of [ix+1] wouldn't have been used).
• src/hg/makeDb/doc/hg19.txt
  • lines changed 7, context: html, text, full: html, text
    081663b13c9af5d19bbfb7260715a0d7bed17fd5 Fri Aug 27 16:27:09 2021 -0700
    Updating makedoc with symlinks refs #28027
• src/hg/makeDb/doc/hg38/jaspar.txt
  • lines changed 7, context: html, text, full: html, text
    081663b13c9af5d19bbfb7260715a0d7bed17fd5 Fri Aug 27 16:27:09 2021 -0700
    Updating makedoc with symlinks refs #28027
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV38.sh
  • lines changed 1, context: html, text, full: html, text
    ea9b4c160de0350d5441efc6739cd3c304a12878 Tue Aug 24 16:05:54 2021 -0700
    starting on hg38 Gencode V38
• src/hg/makeDb/doc/ucscGenes/mm39.gencodeVM27.sh
  • lines changed 743, context: html, text, full: html, text
    4ef472a0cd3441f7b6f490c8651b9975c5946830 Mon Aug 23 15:15:54 2021 -0700
    polishing up the VM27 release of knownGene
• src/hg/makeDb/trackDb/human/caddSuper.html
  • lines changed 3, context: html, text, full: html, text
    798895d6438939c52afe7850553ea1b2916a3350 Tue Aug 24 09:06:30 2021 -0700
    Feedback from CR refs #28026
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    59c5f45a1b1d3a94b3b618dc4b307157bd343566 Fri Aug 27 13:51:21 2021 -0700
    Modifying description page and removing pennantIcon refs #27061
• src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra
  • lines changed 10, context: html, text, full: html, text
    9a541f705e5a5d5f5dd290a71412a3e92a013f72 Thu Aug 26 15:44:52 2021 -0700
    Added html setting to .ra file so that tracks would inherit top-level description page. refs #28059
• src/hg/makeDb/trackDb/human/hg38/ileumWang.html
  • lines changed 7, context: html, text, full: html, text
    33f2627eb960453f83c128bb4557394700b7e17e Wed Aug 25 09:29:23 2021 -0700
    Deleted a sentence.
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
  • lines changed 51, context: html, text, full: html, text
    ea9b4c160de0350d5441efc6739cd3c304a12878 Tue Aug 24 16:05:54 2021 -0700
    starting on hg38 Gencode V38
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    72eb33d9c6bc89f4a35e00efd6978c898e963e8a Wed Aug 25 16:37:15 2021 -0700
    added knownGeneV38 and a supertrack with knownGeneV36
• src/hg/makeDb/trackDb/human/hg38/oldKnownGene.ra
  • lines changed 33, context: html, text, full: html, text
    c39cf7dd8ede5ad6f5dc1bc19e392d1c1b61248c Wed Aug 25 16:38:39 2021 -0700
    add knownGene archive super track
• src/hg/makeDb/trackDb/human/hg38/placentaVentoTormo.ra
  • lines changed 2, context: html, text, full: html, text
    e56832fdb8e0f2aad367e7288722c899d2ed3676 Thu Aug 26 15:47:38 2021 -0700
    Changed cell type labels. refs #26967
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    72eb33d9c6bc89f4a35e00efd6978c898e963e8a Wed Aug 25 16:37:15 2021 -0700
    added knownGeneV38 and a supertrack with knownGeneV36
• src/hg/makeDb/trackDb/human/jaspar.html
  • lines changed 114, context: html, text, full: html, text
    c13042f97958c80572df64988506484749ff46af Mon Aug 23 15:30:41 2021 -0700
    Final Dev staging for JASPAR tracks refs #27061
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    baedcfa9b0bf1ff6516c0a733b53e4c7009b3beb Wed Aug 25 13:52:12 2021 -0700
    Committing minor viewing modification to jaspar track refs #27061
  • lines changed 26, context: html, text, full: html, text
    59c5f45a1b1d3a94b3b618dc4b307157bd343566 Fri Aug 27 13:51:21 2021 -0700
    Modifying description page and removing pennantIcon refs #27061
  • lines changed 66, context: html, text, full: html, text
    8f0fb6c4a07a0eff3650e49b3a7ad2808f644bc7 Fri Aug 27 17:40:45 2021 -0700
    Format and text changes for CR refs #28027
• src/hg/makeDb/trackDb/human/jaspar.ra
  • lines changed 9, context: html, text, full: html, text
    c13042f97958c80572df64988506484749ff46af Mon Aug 23 15:30:41 2021 -0700
    Final Dev staging for JASPAR tracks refs #27061
  • lines changed 4, context: html, text, full: html, text
    baedcfa9b0bf1ff6516c0a733b53e4c7009b3beb Wed Aug 25 13:52:12 2021 -0700
    Committing minor viewing modification to jaspar track refs #27061
  • lines changed 4, context: html, text, full: html, text
    8f0fb6c4a07a0eff3650e49b3a7ad2808f644bc7 Fri Aug 27 17:40:45 2021 -0700
    Format and text changes for CR refs #28027
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 10, context: html, text, full: html, text
    5aa96722c0548d51c76a430c576d1e7823c30ef7 Wed Aug 25 11:32:44 2021 -0700
    Get double sided gaps supported in building of LRG track, refs #24672
• src/hg/makeDb/trackDb/relatedTracks.ra
  • lines changed 13, context: html, text, full: html, text
    321076d3ad24bb8074379a301d980e58f6765af2 Mon Aug 23 10:46:19 2021 -0700
    Fixing unpaired line error for Max and Chris, No RM
• src/hg/utils/automation/parseLrgXml.pl
  • lines changed 60, context: html, text, full: html, text
    5aa96722c0548d51c76a430c576d1e7823c30ef7 Wed Aug 25 11:32:44 2021 -0700
    Get double sided gaps supported in building of LRG track, refs #24672
• src/hg/utils/otto/knownGene/ReadMe.txt
  • lines changed 4, context: html, text, full: html, text
    4ef472a0cd3441f7b6f490c8651b9975c5946830 Mon Aug 23 15:15:54 2021 -0700
    polishing up the VM27 release of knownGene
• src/hg/utils/otto/knownGene/buildEnv.sh
  • lines changed 49, context: html, text, full: html, text
    ea9b4c160de0350d5441efc6739cd3c304a12878 Tue Aug 24 16:05:54 2021 -0700
    starting on hg38 Gencode V38
• src/hg/utils/otto/knownGene/buildKnown.sh
  • lines changed 1, context: html, text, full: html, text
    4ef472a0cd3441f7b6f490c8651b9975c5946830 Mon Aug 23 15:15:54 2021 -0700
    polishing up the VM27 release of knownGene
• src/hg/utils/otto/knownGene/copyFilesToAssembly.sh
  • lines changed 6, context: html, text, full: html, text
    4ef472a0cd3441f7b6f490c8651b9975c5946830 Mon Aug 23 15:15:54 2021 -0700
    polishing up the VM27 release of knownGene
• src/hg/utils/otto/knownGene/sample.buildEnv.sh
  • lines changed 49, context: html, text, full: html, text
    ea9b4c160de0350d5441efc6739cd3c304a12878 Tue Aug 24 16:05:54 2021 -0700
    starting on hg38 Gencode V38
• src/hg/utils/otto/lrg/buildLrg.sh
  • lines changed 9, context: html, text, full: html, text
    5aa96722c0548d51c76a430c576d1e7823c30ef7 Wed Aug 25 11:32:44 2021 -0700
    Get double sided gaps supported in building of LRG track, refs #24672
• src/utils/bamToPsl/bamToPsl.c
  • lines changed 5, context: html, text, full: html, text
    1a98c031559edae71e6272570a671c8a107c81a1 Thu Aug 26 01:34:44 2021 -0700
    small change to bamToPsl.c docs, refs #28044
• src/utils/hubPublicMail
  • lines changed 16, context: html, text, full: html, text
    3bfceef9b449d5a09134333d4762bbf146e6f805 Fri Aug 27 02:49:30 2021 -0700
    fixing hubPublicEmail script, refs #27779
• src/utils/qa/weeklybld/buildEnv.csh
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    aeec54d3ed99b3310d571d13558163e9a850f38e Mon Aug 30 10:05:38 2021 -0700
    v420 preview2, refs #28041

• lines changed: 1963
• files changed: 70