All File Changes

v412_base to v413_preview (2021-03-22 to 2021-03-29) v413

• confs/asia.hg.conf
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    232a9a9a34d3910a3546a14e7f38c9d2bec1a100 Sun Mar 28 01:11:46 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 3, context: html, text, full: html, text
    232a9a9a34d3910a3546a14e7f38c9d2bec1a100 Sun Mar 28 01:11:46 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 7, context: html, text, full: html, text
    232a9a9a34d3910a3546a14e7f38c9d2bec1a100 Sun Mar 28 01:11:46 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    232a9a9a34d3910a3546a14e7f38c9d2bec1a100 Sun Mar 28 01:11:46 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 14, context: html, text, full: html, text
    2eca7c39811bd3a160a17f1d11b7250f872d5287 Wed Mar 24 09:25:41 2021 -0700
    change hgHubConnect to use the pipeline library to run hubCheck instead of popen() as popen is unsafe, refs #27274
• src/hg/hgTracks/config.c
  • lines changed 2, context: html, text, full: html, text
    42b30649ca62035147359f5569e78e52487f7089 Mon Mar 22 16:09:37 2021 -0700
    Force blue link on dialog (not sure why needed, sigh). refs #26385
• src/hg/hgTracks/recTrackSets.c
  • lines changed 3, context: html, text, full: html, text
    b63f5489c142c0dae20fabeeb30a1d43f3dcbf74 Tue Mar 23 10:38:03 2021 -0700
    Add medical disclaimer to Recommended Track Sets dialog, as per request from Ana. refs #25601
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    dd8d2773375a1e31bce66cb1bbc82ae44ef86bf8 Mon Mar 22 16:17:19 2021 -0700
    change wiggleWindow trackDb variable to maxWindowCoverage. Added doc. #27079
• src/hg/hgTracks/vcfTrack.c
  • lines changed 1, context: html, text, full: html, text
    d3f44a3071e0ffb35a5c984b326a03e5af2a3c75 Thu Mar 25 12:21:17 2021 -0700
    Fix missing call to hReplaceGbdb so wuhCor1 vcf tracks work on gbibs, refs #27172
• src/hg/htdocs/contacts.html
  • lines changed 7, context: html, text, full: html, text
    92ba162e4567b23ce5cb7dbde70c0fb9f6ba8ed9 Thu Mar 25 13:01:03 2021 -0700
    updating physical address
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 9, context: html, text, full: html, text
    dd8d2773375a1e31bce66cb1bbc82ae44ef86bf8 Mon Mar 22 16:17:19 2021 -0700
    change wiggleWindow trackDb variable to maxWindowCoverage. Added doc. #27079
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 7, context: html, text, full: html, text
    dd8d2773375a1e31bce66cb1bbc82ae44ef86bf8 Mon Mar 22 16:17:19 2021 -0700
    change wiggleWindow trackDb variable to maxWindowCoverage. Added doc. #27079
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 12, context: html, text, full: html, text
    dd8d2773375a1e31bce66cb1bbc82ae44ef86bf8 Mon Mar 22 16:17:19 2021 -0700
    change wiggleWindow trackDb variable to maxWindowCoverage. Added doc. #27079
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 1, context: html, text, full: html, text
    dc9c1c9f0f71751a02d7427ccae08e013fa7c224 Thu Mar 25 16:38:09 2021 -0700
    Fixing fat finger mistake in link, no RM.
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 7, context: html, text, full: html, text
    12c7c56154acd645d9a581752a9de2b2367dd9bd Tue Mar 23 13:49:08 2021 -0700
    Changing Help menu to say Contact Us instead of Mailing list and removing that from About Us dropdown refs #27213
  • lines changed 3, context: html, text, full: html, text
    1734b61ea9ea534a25c8754efacb96fdbc0ffc89 Tue Mar 23 14:02:01 2021 -0700
    Adding S in https for download server refs #27213
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    7ca00d20d2c5c137d78f47d364b4d5be09acfb15 Thu Mar 25 17:03:26 2021 -0700
    Stashing 2 tools and documenting others for refs #27278
  • lines changed 1, context: html, text, full: html, text
    1cfdf42a9451b42de426ec9f43fc34814f4b6a85 Thu Mar 25 17:18:26 2021 -0700
    Changing Utilities to Tools for Lou's suggestion refs #27278
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 2, context: html, text, full: html, text
    12c7c56154acd645d9a581752a9de2b2367dd9bd Tue Mar 23 13:49:08 2021 -0700
    Changing Help menu to say Contact Us instead of Mailing list and removing that from About Us dropdown refs #27213
  • lines changed 3, context: html, text, full: html, text
    1734b61ea9ea534a25c8754efacb96fdbc0ffc89 Tue Mar 23 14:02:01 2021 -0700
    Adding S in https for download server refs #27213
  • lines changed 17, context: html, text, full: html, text
    7ca00d20d2c5c137d78f47d364b4d5be09acfb15 Thu Mar 25 17:03:26 2021 -0700
    Stashing 2 tools and documenting others for refs #27278
  • lines changed 1, context: html, text, full: html, text
    1cfdf42a9451b42de426ec9f43fc34814f4b6a85 Thu Mar 25 17:18:26 2021 -0700
    Changing Utilities to Tools for Lou's suggestion refs #27278
• src/hg/htdocs/staff.html
  • lines changed 1, context: html, text, full: html, text
    7e78fe5c4f480aac560ba0846a6733ec05a3eb7a Mon Mar 22 15:17:46 2021 -0700
    Removing ChrisL from the ML (much overdue) no RM.
  • lines changed 1, context: html, text, full: html, text
    533b40bdb41c73a9fd5416b2df8133133c603e69 Mon Mar 22 16:39:51 2021 -0700
    Updating ucsc instead of soe email address, no RM.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    42b30649ca62035147359f5569e78e52487f7089 Mon Mar 22 16:09:37 2021 -0700
    Force blue link on dialog (not sure why needed, sigh). refs #26385
• src/hg/htdocs/util.html
  • lines changed 34, context: html, text, full: html, text
    7ca00d20d2c5c137d78f47d364b4d5be09acfb15 Thu Mar 25 17:03:26 2021 -0700
    Stashing 2 tools and documenting others for refs #27278
• src/hg/lib/googleAnalytics.c
  • lines changed 1, context: html, text, full: html, text
    c148ffe7330990f162157aa435888c6f0d71a193 Wed Mar 24 04:59:41 2021 -0700
    fixing small bug in outlink tracking, refs #21916
  • lines changed 3, context: html, text, full: html, text
    92286f5dde77067218d7c7fcbf8bb4674516b0c6 Thu Mar 25 04:37:29 2021 -0700
    cosmetic outlink tracking change, refs #21916
• src/hg/makeDb/trackDb/bonobo/panPan3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.chainNet.ra
  • lines changed 2, context: html, text, full: html, text
    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/chimp/panTro6/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/cow/bosTau9/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/dog/canFam5/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/dolphin/turTru2/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/galVar/galVar1/trackDb.chainNet.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/gorilla/gorGor6/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.chainNet.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.chainNet.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/horse/equCab3/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/human/caddAlpha.ra
  • lines changed 2, context: html, text, full: html, text
    dd8d2773375a1e31bce66cb1bbc82ae44ef86bf8 Mon Mar 22 16:17:19 2021 -0700
    change wiggleWindow trackDb variable to maxWindowCoverage. Added doc. #27079
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    17c14c5488572ca799d345a9257c84a5f845b51c Wed Mar 24 17:16:31 2021 -0700
    Updating the dataVersion for the sno/miRNA update, refs #27017
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    f31502b39cdfaa4a728c976d43b61be684c42677 Tue Mar 23 14:30:09 2021 -0700
    Code review typo fix refs #27259
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    154d14eb3ec7ed21fc299824a1fd942c52534f50 Wed Mar 24 06:56:01 2021 -0700
    adding covidHct track, no redmine yet
• src/hg/makeDb/trackDb/lamprey/petMar3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/makefile
  • lines changed 4, context: html, text, full: html, text
    2403d57e2315713ed10bcc3007947bd8ffe9d2d3 Mon Mar 22 14:39:34 2021 -0700
    remove trackDbCache directory after build
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/opossum/monDom5/trackDb.chainNet.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/pangolin/manPen1/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/pika/ochPri3/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/rat/rn6/trackDb.chainNet.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/rhesus/rheMac10/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/seal/neoSch1/trackDb.chainNet.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/sheep/oviAri4/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/shrew/sorAra2/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/tagTypes.tab
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    dd8d2773375a1e31bce66cb1bbc82ae44ef86bf8 Mon Mar 22 16:17:19 2021 -0700
    change wiggleWindow trackDb variable to maxWindowCoverage. Added doc. #27079
• src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.chainNet.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/tenrec/echTel2/trackDb.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/treeShrew/tupBel1/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.uniprot.ra
  • lines changed 63, context: html, text, full: html, text
    cfdb96ef270bc819770e953a3bb2a8be4304a203 Tue Mar 23 10:55:13 2021 -0700
    Adding 4 uniprot tracks previously hidden, refs #27252
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    456843d0d594caf408d5a7cd40aa7d76c2ba5d3a Tue Mar 23 13:57:24 2021 -0700
    Updating file paths to corrected name, refs #27252
• src/hg/makeDb/trackDb/xenTro/xenTro9/trackDb.chainNet.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.chainNet.ra
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    5cdbeec66940a828267ebe5ff146f272116ab4bb Tue Mar 23 12:18:19 2021 -0700
    Changed the databases shortLabel name display for mm10 and hg19, refs #26815
• src/utils/qa/weeklybld/buildEnv.csh
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    1ec6ecb0fb3c0a4bc5fc705dac923a3ed2826e16 Mon Mar 29 10:06:37 2021 -0700
    v413 preview1, refs #27172

• lines changed: 337
• files changed: 67