All File Changes

v354_preview2 to v354_base (2017-08-18 to 2017-08-28) v354

• src/hg/cirm/cdw/cdwWebBrowse/cdwHelp.html
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    329f35dbb1e2083df7b00ef73a12174828d01760 Fri Aug 25 16:49:08 2017 -0700
    removing Chris Eisenhart, adding Galt instead for contact info on cirm help page.
• src/hg/hgTracks/barChartTrack.c
  • lines changed 18, context: html, text, full: html, text
    86fdc2ac12ccfc5210455d4af0f499ffac0f2dbb Wed Aug 23 12:14:03 2017 -0700
    Fix graph height bug find by ChrisL, note 14. refs #19872
  • lines changed 33, context: html, text, full: html, text
    8b16df428363748e823cc2b5a646b33466524f65 Thu Aug 24 13:20:50 2017 -0700
    Extending maxHeight UI for barChart. refs #19872
  • lines changed 129, context: html, text, full: html, text
    bc948392618f037e666eeff707b087670e90c303 Thu Aug 24 14:17:35 2017 -0700
    Revert autoscale and maxHeight features (to commit 7d342854b5719897461428785269775c06727326). Waiting for after release of barchart tracks and hubs before adding back (with additional UI review). refs #19355
• src/hg/hgVai/hgVai.c
  • lines changed 5, context: html, text, full: html, text
    0ab5ce741156d73ef707d3db81d10007cc12589d Fri Aug 25 17:06:14 2017 -0700
    hgVai needs to make its own hgvsG terms for regulatory variants since they're not associated with a transcript. Thanks ChrisL for noticing they were missing! refs #19968
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 39, context: html, text, full: html, text
    f06568e8b9eba7bf420aab0b30e2918a41b176ce Fri Aug 25 15:31:09 2017 -0700
    News for new dbSNP 150 tracks, refs #19202
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    f06568e8b9eba7bf420aab0b30e2918a41b176ce Fri Aug 25 15:31:09 2017 -0700
    News for new dbSNP 150 tracks, refs #19202
• src/hg/inc/annoFormatVep.h
  • lines changed 3, context: html, text, full: html, text
    0ab5ce741156d73ef707d3db81d10007cc12589d Fri Aug 25 17:06:14 2017 -0700
    hgVai needs to make its own hgvsG terms for regulatory variants since they're not associated with a transcript. Thanks ChrisL for noticing they were missing! refs #19968
• src/hg/inc/barChartUi.h
  • lines changed 6, context: html, text, full: html, text
    8b16df428363748e823cc2b5a646b33466524f65 Thu Aug 24 13:20:50 2017 -0700
    Extending maxHeight UI for barChart. refs #19872
  • lines changed 19, context: html, text, full: html, text
    bc948392618f037e666eeff707b087670e90c303 Thu Aug 24 14:17:35 2017 -0700
    Revert autoscale and maxHeight features (to commit 7d342854b5719897461428785269775c06727326). Waiting for after release of barchart tracks and hubs before adding back (with additional UI review). refs #19355
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    6b9a6437044e4efd36158d81a7847ec6b0eac262 Mon Aug 28 10:05:26 2017 -0700
    New version number v354
• src/hg/js/utils.js
  • lines changed 16, context: html, text, full: html, text
    8b16df428363748e823cc2b5a646b33466524f65 Thu Aug 24 13:20:50 2017 -0700
    Extending maxHeight UI for barChart. refs #19872
  • lines changed 35, context: html, text, full: html, text
    bc948392618f037e666eeff707b087670e90c303 Thu Aug 24 14:17:35 2017 -0700
    Revert autoscale and maxHeight features (to commit 7d342854b5719897461428785269775c06727326). Waiting for after release of barchart tracks and hubs before adding back (with additional UI review). refs #19355
• src/hg/lib/annoFormatVep.c
  • lines changed 43, context: html, text, full: html, text
    0ab5ce741156d73ef707d3db81d10007cc12589d Fri Aug 25 17:06:14 2017 -0700
    hgVai needs to make its own hgvsG terms for regulatory variants since they're not associated with a transcript. Thanks ChrisL for noticing they were missing! refs #19968
• src/hg/lib/barChartUi.c
  • lines changed 2, context: html, text, full: html, text
    bf397954c17194c248df5bcacf1eecca545084b3 Wed Aug 23 12:16:22 2017 -0700
    Restore autoscale control, by request of ChrisL. refs #19872
  • lines changed 16, context: html, text, full: html, text
    8b16df428363748e823cc2b5a646b33466524f65 Thu Aug 24 13:20:50 2017 -0700
    Extending maxHeight UI for barChart. refs #19872
  • lines changed 86, context: html, text, full: html, text
    bc948392618f037e666eeff707b087670e90c303 Thu Aug 24 14:17:35 2017 -0700
    Revert autoscale and maxHeight features (to commit 7d342854b5719897461428785269775c06727326). Waiting for after release of barchart tracks and hubs before adding back (with additional UI review). refs #19355
• src/hg/lib/cartJson.c
  • lines changed 2, context: html, text, full: html, text
    4403e216c46d2f99eabd1f05e0e3c3531600b6ef Fri Aug 18 16:23:10 2017 -0700
    Remind the user which assembly is selected when we can't find a search term.
• src/hg/lib/cosmicNew.as
  • lines changed 3, context: html, text, full: html, text
    8661e8f2fc9a3dd45c75a4efe96c2cfa8676c958 Fri Aug 25 11:50:08 2017 -0700
    Documentation for the COSMIC track update, refs #19932
• src/hg/lib/hdb.c
  • lines changed 4, context: html, text, full: html, text
    237797ddf3c409a500449847bbdea1c47776ae44 Fri Aug 25 13:50:48 2017 -0700
    Count hashNumEntries only once instead of every time hRefSeqAccForChrom is called.
• src/hg/lib/hgFind.c
  • lines changed 2, context: html, text, full: html, text
    4403e216c46d2f99eabd1f05e0e3c3531600b6ef Fri Aug 18 16:23:10 2017 -0700
    Remind the user which assembly is selected when we can't find a search term.
• src/hg/lib/refSeqFuncElems.as
  • lines changed 19, context: html, text, full: html, text
    8661e8f2fc9a3dd45c75a4efe96c2cfa8676c958 Fri Aug 25 11:50:08 2017 -0700
    Documentation for the COSMIC track update, refs #19932
• src/hg/lib/tests/expected/hgvs/clinVarHgvs.txt
  • lines changed 4, context: html, text, full: html, text
    19c412b4ecb9bcc6c1816a0767be9666babe7e70 Fri Aug 25 10:14:50 2017 -0700
    Temporarily commenting out a test case due to ncbiRefSeqPsl being slightly different on hgwdev vs hgwbeta.
• src/hg/lib/tests/input/hgvs/clinVarHgvs.txt
  • lines changed 4, context: html, text, full: html, text
    19c412b4ecb9bcc6c1816a0767be9666babe7e70 Fri Aug 25 10:14:50 2017 -0700
    Temporarily commenting out a test case due to ncbiRefSeqPsl being slightly different on hgwdev vs hgwbeta.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 1, context: html, text, full: html, text
    8661e8f2fc9a3dd45c75a4efe96c2cfa8676c958 Fri Aug 25 11:50:08 2017 -0700
    Documentation for the COSMIC track update, refs #19932
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 1, context: html, text, full: html, text
    3dce4b046d6db0d965561eaa7cafa3d598a761ba Fri Aug 25 11:31:52 2017 -0700
    Updating refSeq func elems track to have mouse over labels, refs #19638
  • lines changed 1, context: html, text, full: html, text
    8661e8f2fc9a3dd45c75a4efe96c2cfa8676c958 Fri Aug 25 11:50:08 2017 -0700
    Documentation for the COSMIC track update, refs #19932
• src/hg/makeDb/doc/mm10.txt
  • lines changed 1, context: html, text, full: html, text
    3dce4b046d6db0d965561eaa7cafa3d598a761ba Fri Aug 25 11:31:52 2017 -0700
    Updating refSeq func elems track to have mouse over labels, refs #19638
• src/hg/makeDb/trackDb/augustusGene.html
  • lines changed 4, context: html, text, full: html, text
    c1be3b878064622c6ffbe4654e7381c49241ec64 Fri Aug 25 09:38:55 2017 -0700
    Updating redirected links on the augustus page, no redmine
• src/hg/makeDb/trackDb/blatFr1.html
  • lines changed 2, context: html, text, full: html, text
    3fcb588d0dfc1ef6bbc9b02cc57da1b04b854061 Fri Aug 25 11:03:29 2017 -0700
    Updating links found on the broken link report, no redmine
• src/hg/makeDb/trackDb/criGri/criGri1/crispr.html
  • lines changed 4, context: html, text, full: html, text
    53e7d25e55e63337ef4a78f50885a2e7e8e466e0 Thu Aug 24 14:46:10 2017 -0700
    Rewording a few sentences as per code review, CR#20013
• src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    2beb78816e018aa05a456042ce52fa32d2c61f2c Wed Aug 23 16:01:35 2017 -0700
    Removing the alpha,beta,public release tag now that the track is on the RR, CR #20013
• src/hg/makeDb/trackDb/geneid.html
  • lines changed 4, context: html, text, full: html, text
    3fcb588d0dfc1ef6bbc9b02cc57da1b04b854061 Fri Aug 25 11:03:29 2017 -0700
    Updating links found on the broken link report, no redmine
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    8661e8f2fc9a3dd45c75a4efe96c2cfa8676c958 Fri Aug 25 11:50:08 2017 -0700
    Documentation for the COSMIC track update, refs #19932
  • lines changed 24, context: html, text, full: html, text
    f7c5b6aae97e26587098ed01fde5d9bccd92fb9b Fri Aug 25 15:23:03 2017 -0700
    Ordering variation tracks, new snp150, refs #19202
  • lines changed 1, context: html, text, full: html, text
    a85a9c06c4807afd914ec4eb47dcb3646bc8416a Mon Aug 28 08:54:43 2017 -0700
    Updating Cosmic V81 track type from a bigBed8 to a bigBed4, refs #20048
• src/hg/makeDb/trackDb/human/hg38/barCharts.ra
  • lines changed 2, context: html, text, full: html, text
    c54d49e381445c5cd1371cb52bd5622ebde2eb5e Thu Aug 24 15:40:06 2017 -0700
    Adding a maxItems limit for the tcga tracks, refs #19155
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    7be4eafa4c0e02c8e54e93f9bbaf40c09736461d Thu Aug 24 16:54:40 2017 -0700
    Adding the beta release tag, refs #19155
  • lines changed 1, context: html, text, full: html, text
    d260bb93662c0b186f06e15b4d3768ff088039b0 Fri Aug 25 16:30:45 2017 -0700
    Adding a maxItems limit to prevent issues when switching between 'full', 'pack', etc. refs #19350
• src/hg/makeDb/trackDb/human/hg38/tcgaExpr.html
  • lines changed 1, context: html, text, full: html, text
    42f9d14e7e73d38f6c160d7fb383675fe05d0059 Wed Aug 23 08:59:39 2017 -0700
    Adding an apostrophe to tissues. refs #19155
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    61bdb5b78a5f8afeb9e6c453f43486a9b2453607 Wed Aug 23 09:26:07 2017 -0700
    Making the HTML page conform to our guidelines, refs #19155
  • lines changed 8, context: html, text, full: html, text
    4beeeb3a936414b2424ed330df7c0caf96823d3f Wed Aug 23 09:34:54 2017 -0700
    Fixing capitalization issue with 'GTEX'. Rewording a sentence. Italicizing our tool names. refs #19155
  • lines changed 7, context: html, text, full: html, text
    79b9db77a7470efcb4e48bf026883c3ad4492182 Wed Aug 23 09:53:53 2017 -0700
    Adding target='_blank' to a couple links. Refs #19155
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    53f905275d3a104851b2006c709622586c0c8fba Wed Aug 23 10:23:54 2017 -0700
    Adding a missing paragraph tag, refs #19155
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    7743ee95093647b34540ee8bf844e9198b64f3b7 Wed Aug 23 10:29:10 2017 -0700
    Fixing the barchar image. refs #19155
  • lines changed 1, context: html, text, full: html, text
    dbd2b91fc6476240779971c45f42fbef4d4e8ed0 Wed Aug 23 10:55:19 2017 -0700
    Replacing a comma with a semicolon. refs #19155
  • lines changed 5, context: html, text, full: html, text
    9b9312dd2f3f81e2a6a120f7c1436192842bd6e6 Fri Aug 25 11:41:38 2017 -0700
    Removing the <p> tag to recombine two paragraphs to match the styling on the GTEx tracks, refs #19155
• src/hg/makeDb/trackDb/human/hg38/tcgaGeneExpr.html
  • lines changed 12, context: html, text, full: html, text
    68cb4ee59f3003202887b53f048f040ce6d1b4c8 Wed Aug 23 10:03:56 2017 -0700
    Adding target='_blank' to a few links. refs #19155
  • lines changed 38, context: html, text, full: html, text
    8aac04034cafcf051e4b737235702cfc2f63529f Wed Aug 23 10:17:41 2017 -0700
    Making this html page conform to our HTML guidelines, refs #19155
  • lines changed 4, context: html, text, full: html, text
    8e451222034b582283200a243a1719b467f873ab Wed Aug 23 10:36:30 2017 -0700
    Fixing the barchart image on the Gene Expression html page, refs #19155
  • lines changed 10, context: html, text, full: html, text
    6b02a27bd312559b5da88edebbb1a3a91df4131d Wed Aug 23 10:53:28 2017 -0700
    Fixing a capitalization issue with 'GTEX'. Rewording a few sentences. Italicizing our tools. refs #19155
  • lines changed 6, context: html, text, full: html, text
    9b9312dd2f3f81e2a6a120f7c1436192842bd6e6 Fri Aug 25 11:41:38 2017 -0700
    Removing the <p> tag to recombine two paragraphs to match the styling on the GTEx tracks, refs #19155
• src/hg/makeDb/trackDb/human/hg38/tcgaTranscExpr.html
  • lines changed 12, context: html, text, full: html, text
    e090a5710a29dd83f910a6a61c519c691796ec1a Wed Aug 23 11:23:59 2017 -0700
    Adding target='_blank' to a few links. refs #19155
  • lines changed 31, context: html, text, full: html, text
    f5e8e08b0d0083e33fdd001c25b2c8603d8c940c Wed Aug 23 11:37:04 2017 -0700
    Making this HTML page conform to our guidelines, refs #19155
  • lines changed 16, context: html, text, full: html, text
    215df0a1711faf5de7cc884dcb6b4a4f5d5443e2 Wed Aug 23 12:05:19 2017 -0700
    Fixing a captialization issue with 'GTEX'. Rewording a few sentences. Italicizing our tool names. refs #19155
  • lines changed 6, context: html, text, full: html, text
    9b9312dd2f3f81e2a6a120f7c1436192842bd6e6 Fri Aug 25 11:41:38 2017 -0700
    Removing the <p> tag to recombine two paragraphs to match the styling on the GTEx tracks, refs #19155
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    3dce4b046d6db0d965561eaa7cafa3d598a761ba Fri Aug 25 11:31:52 2017 -0700
    Updating refSeq func elems track to have mouse over labels, refs #19638
  • lines changed 47, context: html, text, full: html, text
    f7c5b6aae97e26587098ed01fde5d9bccd92fb9b Fri Aug 25 15:23:03 2017 -0700
    Ordering variation tracks, new snp150, refs #19202
• src/hg/makeDb/trackDb/human/snp150.shared.html
  • lines changed 5, context: html, text, full: html, text
    e3ec64173c4e66e2a75ebcfb3a78e770f4d8f6cf Thu Aug 24 12:42:01 2017 -0700
    Adding details about snp coloring, refs #19202
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 46, context: html, text, full: html, text
    f7c5b6aae97e26587098ed01fde5d9bccd92fb9b Fri Aug 25 15:23:03 2017 -0700
    Ordering variation tracks, new snp150, refs #19202
• src/hg/makeDb/trackDb/miRNA.html
  • lines changed 11, context: html, text, full: html, text
    3fcb588d0dfc1ef6bbc9b02cc57da1b04b854061 Fri Aug 25 11:03:29 2017 -0700
    Updating links found on the broken link report, no redmine
• src/hg/makeDb/trackDb/microsat.html
  • lines changed 3, context: html, text, full: html, text
    3fcb588d0dfc1ef6bbc9b02cc57da1b04b854061 Fri Aug 25 11:03:29 2017 -0700
    Updating links found on the broken link report, no redmine
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    3dce4b046d6db0d965561eaa7cafa3d598a761ba Fri Aug 25 11:31:52 2017 -0700
    Updating refSeq func elems track to have mouse over labels, refs #19638
• src/hg/makeDb/trackDb/phastConsElements.html
  • lines changed 9, context: html, text, full: html, text
    3fcb588d0dfc1ef6bbc9b02cc57da1b04b854061 Fri Aug 25 11:03:29 2017 -0700
    Updating links found on the broken link report, no redmine
• src/hg/makeDb/trackDb/rnaCluster.html
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    3fcb588d0dfc1ef6bbc9b02cc57da1b04b854061 Fri Aug 25 11:03:29 2017 -0700
    Updating links found on the broken link report, no redmine
• src/hg/makeDb/trackDb/simpleRepeat.html
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    3fcb588d0dfc1ef6bbc9b02cc57da1b04b854061 Fri Aug 25 11:03:29 2017 -0700
    Updating links found on the broken link report, no redmine
• src/hg/makeDb/trackDb/twinscan.html
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    3fcb588d0dfc1ef6bbc9b02cc57da1b04b854061 Fri Aug 25 11:03:29 2017 -0700
    Updating links found on the broken link report, no redmine
• src/hg/makeDb/trackDb/worm/ce2/axtNetCb1.html
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    a1ff095e828d2e29eae8f49aad3ccb538a7b01bc Fri Aug 25 11:08:44 2017 -0700
    Updating links found on the broken links report that are specific to ce2, no redmine
• src/hg/makeDb/trackDb/worm/ce2/blastzCb1.html
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    a1ff095e828d2e29eae8f49aad3ccb538a7b01bc Fri Aug 25 11:08:44 2017 -0700
    Updating links found on the broken links report that are specific to ce2, no redmine
• src/hg/makeDb/trackDb/worm/ce2/c_briggsae_pwMaf.html
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    a1ff095e828d2e29eae8f49aad3ccb538a7b01bc Fri Aug 25 11:08:44 2017 -0700
    Updating links found on the broken links report that are specific to ce2, no redmine
• src/hg/makeDb/trackDb/worm/ce2/chainCb1.html
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    a1ff095e828d2e29eae8f49aad3ccb538a7b01bc Fri Aug 25 11:08:44 2017 -0700
    Updating links found on the broken links report that are specific to ce2, no redmine
• src/hg/makeDb/trackDb/worm/ce2/netCb1.html
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    a1ff095e828d2e29eae8f49aad3ccb538a7b01bc Fri Aug 25 11:08:44 2017 -0700
    Updating links found on the broken links report that are specific to ce2, no redmine
• src/hg/makeDb/trackDb/worm/ce2/picTar.html
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    30c4730ea9c3e38988d5dd836515ec3fc37e6ff6 Fri Aug 25 09:34:04 2017 -0700
    Updating links for ce2 from the broken link report, no redmine
• src/hg/makeDb/trackDb/worm/ce2/wabaCbr.html
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    a1ff095e828d2e29eae8f49aad3ccb538a7b01bc Fri Aug 25 11:08:44 2017 -0700
    Updating links found on the broken links report that are specific to ce2, no redmine
• src/hg/makeDb/trackDb/worm/chainSelf.html
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    a1ff095e828d2e29eae8f49aad3ccb538a7b01bc Fri Aug 25 11:08:44 2017 -0700
    Updating links found on the broken links report that are specific to ce2, no redmine
• src/hg/makeDb/trackDb/worm/est.html
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    30c4730ea9c3e38988d5dd836515ec3fc37e6ff6 Fri Aug 25 09:34:04 2017 -0700
    Updating links for ce2 from the broken link report, no redmine
• src/hg/makeDb/trackDb/worm/intronEst.html
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    30c4730ea9c3e38988d5dd836515ec3fc37e6ff6 Fri Aug 25 09:34:04 2017 -0700
    Updating links for ce2 from the broken link report, no redmine
• src/hg/makeDb/trackDb/worm/mrna.html
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    30c4730ea9c3e38988d5dd836515ec3fc37e6ff6 Fri Aug 25 09:34:04 2017 -0700
    Updating links for ce2 from the broken link report, no redmine
• src/hg/makeDb/trackDb/worm/refGene.html
  • lines changed 7, context: html, text, full: html, text
    30c4730ea9c3e38988d5dd836515ec3fc37e6ff6 Fri Aug 25 09:34:04 2017 -0700
    Updating links for ce2 from the broken link report, no redmine
• src/hg/makeDb/trackDb/xenoRefGene.html
  • lines changed 9, context: html, text, full: html, text
    3fcb588d0dfc1ef6bbc9b02cc57da1b04b854061 Fri Aug 25 11:03:29 2017 -0700
    Updating links found on the broken link report, no redmine
• src/hg/utils/automation/cosmicToBed
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    04e70b617f917af875ac1e884702c30a06571a5b Wed Aug 23 16:00:55 2017 -0700
    Changing COSMIC to a bed8+ track to get the mouse over labels working, refs #19799
• src/lib/cosmicNew.as
  • lines changed 44, context: html, text, full: html, text
    04e70b617f917af875ac1e884702c30a06571a5b Wed Aug 23 16:00:55 2017 -0700
    Changing COSMIC to a bed8+ track to get the mouse over labels working, refs #19799
• src/utils/qa/weeklybld/buildEnv.csh
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    3cee39250b117b9dee7fc7b6ae3fd8d4f4e228b1 Mon Aug 28 10:04:30 2017 -0700
    v354 final build

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• files changed: 83