All File Changes

v408_preview to v408_preview2 (2020-11-23 to 2020-11-30) v408

• src/hg/hgPhyloPlace/phyloPlace.c
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    ac23b2beea95c281450dcbbaa40b2a03c2f8d141 Wed Nov 25 12:09:48 2020 -0800
    Add 'view subtree in Nextstrain' button to each subtree section in results (user request).
• src/hg/hgTracks/config.c
  • lines changed 30, context: html, text, full: html, text
    d9ed8e1065858b02349060ebbb8fc4c99ed010ee Sat Nov 28 11:41:43 2020 -0800
    finalizing font work (dropping some fonts and fiddling with the visibility of the style menu.
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    4a8271aa2e533ae8acf003c35456c63665d563b4 Sat Nov 28 12:57:26 2020 -0800
    oops... wasn't working correctly for "Normal" choices
• src/hg/hgTracks/lolly.h
  • lines changed 1, context: html, text, full: html, text
    33bb159f2fc8bc12bd68418424b0504dd1dd3bf8 Fri Nov 27 14:14:01 2020 -0800
    fix the drawing of lollipops in multi-region
• src/hg/hgTracks/lollyTrack.c
  • lines changed 83, context: html, text, full: html, text
    33bb159f2fc8bc12bd68418424b0504dd1dd3bf8 Fri Nov 27 14:14:01 2020 -0800
    fix the drawing of lollipops in multi-region
• src/hg/hgTracks/wigTrack.c
  • lines changed 4, context: html, text, full: html, text
    95a26c9ef09eae3c8d6290eb92712a4c7f31d9c6 Tue Nov 24 12:20:03 2020 -0800
    prepare for future with different track types and different item data structures refs #21980
• src/hg/hgc/hgc.c
  • lines changed 78, context: html, text, full: html, text
    513ff234094b883276ecb289fd9839792e2ddb20 Tue Nov 3 16:39:53 2020 -0800
    First cut of custom table on hgc, no styling
• src/hg/htdocs/training/index.html
  • lines changed 16, context: html, text, full: html, text
    bdf9adbfcffa53518c3fbcf1af20e480126342e7 Tue Nov 24 14:36:36 2020 -0800
    dropped genetic counselors workshop. adding ucla in january
• src/hg/js/hgTracks.js
  • lines changed 41, context: html, text, full: html, text
    95a26c9ef09eae3c8d6290eb92712a4c7f31d9c6 Tue Nov 24 12:20:03 2020 -0800
    prepare for future with different track types and different item data structures refs #21980
• src/hg/lib/barChartUi.c
  • lines changed 1, context: html, text, full: html, text
    981eeffeb0f237ff33ad262e1eff2c280b1da3ab Wed Nov 25 09:37:25 2020 -0800
    Fix from ChrisLee code review, thanks! refs #22075
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 63, context: html, text, full: html, text
    e57a5ccb480ec2763fb049b88bec3f8012c70993 Tue Nov 24 08:35:08 2020 -0800
    gnomAD v3.1 ready for QA, refs #26449
• src/hg/makeDb/trackDb/chicken/bgiSnp.html
  • lines changed 2, context: html, text, full: html, text
    041918f9fb9dfa0f7f0453bf6d6f512f84ef1a63 Mon Nov 30 09:28:16 2020 -0800
    Updating redirected links for galGal3 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    041918f9fb9dfa0f7f0453bf6d6f512f84ef1a63 Mon Nov 30 09:28:16 2020 -0800
    Updating redirected links for galGal3 found by the uiLinks cronjob, no Redmine.
• src/hg/makeDb/trackDb/human/clinvar.html
  • lines changed 13, context: html, text, full: html, text
    7dafa70b5044ac9e08701b53c15bc750a4e98089 Tue Nov 24 14:30:01 2020 -0800
    Improving readability of the clinVar desc page, and adding a target blank to external link refs #26330
• src/hg/makeDb/trackDb/human/hg19/trackDb.100way.ra
  • lines changed 1, context: html, text, full: html, text
    e3f25c2d9122b8b1cb5ecfc764e54b0e3e67af4b Wed Nov 25 14:16:14 2020 -0800
    Changing Default tracks as directed by Jim refs #25525
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 3, context: html, text, full: html, text
    513ff234094b883276ecb289fd9839792e2ddb20 Tue Nov 3 16:39:53 2020 -0800
    First cut of custom table on hgc, no styling
• src/hg/makeDb/trackDb/human/hg38/defaultPriority.ra
  • lines changed 1, context: html, text, full: html, text
    e3f25c2d9122b8b1cb5ecfc764e54b0e3e67af4b Wed Nov 25 14:16:14 2020 -0800
    Changing Default tracks as directed by Jim refs #25525
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 26, context: html, text, full: html, text
    e57a5ccb480ec2763fb049b88bec3f8012c70993 Tue Nov 24 08:35:08 2020 -0800
    gnomAD v3.1 ready for QA, refs #26449
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    ce4471a047ac2ff82d0384c4b55607f8181bb151 Tue Nov 24 11:50:09 2020 -0800
    Add population freq table to gnomAD v3.1 update, refs #26449
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
  • lines changed 2, context: html, text, full: html, text
    e3f25c2d9122b8b1cb5ecfc764e54b0e3e67af4b Wed Nov 25 14:16:14 2020 -0800
    Changing Default tracks as directed by Jim refs #25525
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 1, context: html, text, full: html, text
    6e07a263965b82266fd19ec57d95e9a6a7a836db Tue Nov 24 14:19:02 2020 -0800
    Shortening the short label so it fits in franklin display refs #26330
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    4f5780587f2f64d2d734f10153d0b0b0f4f56308 Wed Nov 25 10:30:40 2020 -0800
    Enabling hideEmptySubtracks on non mm* or hg* assemblies refs #25784
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    4f5780587f2f64d2d734f10153d0b0b0f4f56308 Wed Nov 25 10:30:40 2020 -0800
    Enabling hideEmptySubtracks on non mm* or hg* assemblies refs #25784
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    513ff234094b883276ecb289fd9839792e2ddb20 Tue Nov 3 16:39:53 2020 -0800
    First cut of custom table on hgc, no styling
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
  • lines changed 1, context: html, text, full: html, text
    4f5780587f2f64d2d734f10153d0b0b0f4f56308 Wed Nov 25 10:30:40 2020 -0800
    Enabling hideEmptySubtracks on non mm* or hg* assemblies refs #25784
• src/hg/makeDb/trackDb/virus/wuhCor1/escape.html
  • lines changed 38, context: html, text, full: html, text
    2471fc00f22e5a9e7e97e32deeb1fc71ac634952 Tue Nov 24 03:28:27 2020 -0800
    docs page for escape wuhCor1 track, refs #26497
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    1ca89a1fb2e0d21201b0463713af4ac0b5d81535 Mon Nov 23 16:18:31 2020 -0800
    Staging the S protein track on hgwbeta, refs #26564
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    9dbb4f0453af2704aa63509c6761738fd4708f9a Tue Nov 24 10:51:35 2020 -0800
    Removing release tags now that the S protein track is ready to be pushed to the RR, refs #26564
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    eac2c7dbea55bd5bf31f6a0a24ca8a6812be9e30 Mon Nov 16 14:15:40 2020 -0800
    Adding release tags for sarsCov2Phylo{,Pub} update. Also adding 'All' subtracks to sarsCov2PhyloPub (all public sequences, not just the subset in both GISAID and public). refs #26530
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    681a44a6baf8c2c897d4bf3f91d976e4de78c5b8 Wed Nov 25 09:24:12 2020 -0800
    Oops, typo in path.
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    a0a7b39c0da592f97d0b31be2fa8d3e2da698b24 Wed Nov 25 15:48:32 2020 -0800
    Adding noScoreFilter to track which doesn't have scores #26497
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    5b3504c5929dc752869a65ff3134f27b4b666cc6 Wed Nov 25 15:57:33 2020 -0800
    Adding pennantIcon line #26497
• src/hg/utils/automation/asmHubChromAlias.pl
  • lines changed 2, context: html, text, full: html, text
    03456e3b8643743836b3c76c667ddd8ed6d4af82 Thu Nov 26 22:26:55 2020 -0800
    fixup chromAlias build for NCBI named assemblies and have duplicates refs #24396
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    0a7c7349c6768dfdd3433781d087a44cfe03cd74 Sun Nov 29 00:48:48 2020 -0800
    correctly doing chromAlias for refSeq not UCSC names with duplicates refs #24396
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 2, context: html, text, full: html, text
    03456e3b8643743836b3c76c667ddd8ed6d4af82 Thu Nov 26 22:26:55 2020 -0800
    fixup chromAlias build for NCBI named assemblies and have duplicates refs #24396
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    0a7c7349c6768dfdd3433781d087a44cfe03cd74 Sun Nov 29 00:48:48 2020 -0800
    correctly doing chromAlias for refSeq not UCSC names with duplicates refs #24396
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    4e32052e618df259f0c0d77434641db7793e41d1 Sun Nov 29 23:24:26 2020 -0800
    correctly remove duplicate sequences from NCBI rm.out refs #24396
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 22, context: html, text, full: html, text
    4e32052e618df259f0c0d77434641db7793e41d1 Sun Nov 29 23:24:26 2020 -0800
    correctly remove duplicate sequences from NCBI rm.out refs #24396
• src/hg/utils/automation/parseLrgXml.pl
  • lines changed 8, context: html, text, full: html, text
    e01ec3b3db24748aeb0797ca4807d9a2c427d71d Wed Nov 25 10:27:06 2020 -0800
    Make parseLrgXml.sh have an optional argument pointing to where the downloaded xml lives so we don't have to duplicate files for multiple assemblies, refs #17877
• src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
  • lines changed 1, context: html, text, full: html, text
    81672aadf156d034a3fd95a1fd76c258070da064 Tue Nov 24 14:06:45 2020 -0800
    Increase tolerance for BioSample IDs not found. (Checked some on the NCBI website... just not found.)
• src/hg/utils/otto/sarscov2phylo/publicCredits.sh
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    81672aadf156d034a3fd95a1fd76c258070da064 Tue Nov 24 14:06:45 2020 -0800
    Increase tolerance for BioSample IDs not found. (Checked some on the NCBI website... just not found.)
• src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c
  • lines changed 7, context: html, text, full: html, text
    23a71fbe15337ff7a46ff9ab889bfed88f6849f6 Sun Nov 29 10:17:54 2020 -0800
    vcfRenameAndPrune: prevent safecpy overflow in rare case by leaking a little memory.
• src/lib/freeType.c
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    e5ac5a7d220b37c0c4303e2594050e94fd7ca665 Mon Nov 23 10:13:37 2020 -0800
    do a better job of catching errors in font handling

• lines changed: 655
• files changed: 43