All File Changes

v479_preview2 to v479_base (2025-03-10 to 2025-03-17) v479

• src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c
  • lines changed 2, context: html, text, full: html, text
    45eed0b682bf7a4aab1234a5f97cc700bb0f88c3 Wed Mar 12 14:57:03 2025 -0700
    Adding rds and h5ad as formats OK to ignore in cdw validtion steps
• src/hg/hgHubConnect/hooks/hooklib.c
  • lines changed 3, context: html, text, full: html, text
    7a48ee92468a7bb4f778372c37ee2d43186681ff Wed Mar 12 15:24:09 2025 -0700
    Changes from code review, refs #35318
• src/hg/hgHubConnect/trackHubWizard.c
  • lines changed 4, context: html, text, full: html, text
    7a48ee92468a7bb4f778372c37ee2d43186681ff Wed Mar 12 15:24:09 2025 -0700
    Changes from code review, refs #35318
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 4, context: html, text, full: html, text
    5340ada259767114db7bdd6100946b9c7cd4b84a Wed Mar 12 16:12:55 2025 -0700
    Adding <BR> tags for the displayed links and changing the order of View and Download conversion links, refs #20666
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 15, context: html, text, full: html, text
    8023a86c18c4eecf838f9e40abfe963627cee967 Wed Mar 12 13:22:03 2025 -0700
    Make warning about extra file(s) from usher appear only on hgwdev*/genome-test, and account for a file that for some reason gets a slightly different name on the RR. refs #35363
• src/hg/hgTracks/heatmap.c
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    ac21738f7d300c547f394228e274f8f161c49a88 Mon Mar 17 08:32:53 2025 -0700
    Minor change to permit re-use of derived heatmap structures, refs #35320
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 4, context: html, text, full: html, text
    ef86e1ae8596e109c4a217c1f8747d92551630ce Wed Mar 12 10:28:24 2025 -0700
    Fixing typos found in code review, refs #35360
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    05d4d7daf863400e820ccc217118ffddc52cc86c Fri Mar 14 16:18:00 2025 -0700
    Announcing the denovo-db track for hg19, refs #28790
• src/hg/htdocs/indexNews.html
  • lines changed 14, context: html, text, full: html, text
    05d4d7daf863400e820ccc217118ffddc52cc86c Fri Mar 14 16:18:00 2025 -0700
    Announcing the denovo-db track for hg19, refs #28790
• src/hg/inc/versionInfo.h
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    864846249d1323e9d51366ea37d6b3684b0abc9b Mon Mar 17 11:05:17 2025 -0700
    New version number v479
• src/hg/lib/bigGenePredRefSeq.as
  • lines changed 25, context: html, text, full: html, text
    7e56337aaaae09a348dd7393fef23300d3404212 Tue Mar 11 15:32:39 2025 -0700
    custom description comments on fields for NCBI RefSeq track refs #34704
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    bbf871ec1996725a16659ea37063d411dbc1b272 Wed Mar 12 13:28:03 2025 -0700
    adding brief description refs #34704
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    18c4cc4b3f046023c7904d77bae9dde6f43d9544 Sat Mar 15 09:59:39 2025 -0700
    stop limiting number of species groups in MAFs to 20. Now we're limited at 1000
• src/hg/lib/trackHub.c
  • lines changed 16, context: html, text, full: html, text
    ae32a4a8f4fc23c2696f618a97f28a2360c3f038 Tue Mar 11 15:53:30 2025 -0700
    ongoing work on quickLift. Deal correctly with views
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 3, context: html, text, full: html, text
    51678035cb4dbce2addaaaa3f7a5289f9cb7598e Sun Mar 16 01:03:44 2025 -0700
    adding 3 bacteria per user request refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    51678035cb4dbce2addaaaa3f7a5289f9cb7598e Sun Mar 16 01:03:44 2025 -0700
    adding 3 bacteria per user request refs #29545
• src/hg/makeDb/doc/hg19.txt
  • lines changed 34, context: html, text, full: html, text
    9432efd3c178a06d46745d02e019c2267b27e620 Thu Mar 13 14:12:34 2025 -0700
    Adding the makedoc steps that Megna used to create the track, refs #28790
• src/hg/makeDb/doc/hg38/gnomad.txt
  • lines changed 41, context: html, text, full: html, text
    2313e3d71f8d98d0166357c1970ba487ba820ef1 Thu Mar 13 13:39:43 2025 -0700
    Updating the gnomAD SV v4.1 track by adding a filter to show only the PASS variants and updating the mouseOver per Anna's request, refs #35295
• src/hg/makeDb/doc/hg38/pseudogenes.txt
  • lines changed 118, context: html, text, full: html, text
    e42db081e12ceb2019b78b9b29e7838b908c74f9 Thu Mar 13 12:31:40 2025 -0700
    adding pseudogene makedoc
• src/hg/makeDb/scripts/wigColorByColors/makeWigColorByRevelCadd.py
  • lines changed 3, context: html, text, full: html, text
    8c8275d8b2ff5fc093f351b811b93068866ed1f3 Fri Mar 14 17:04:10 2025 -0700
    Fixing the revel values, I accidentally makde the wrong boundaries in my first pass, refs #35352
• src/hg/makeDb/trackDb/human/hg19/denovoDb.html
  • lines changed 69, context: html, text, full: html, text
    f51f75cd54a6c91df3b555bd625d69859fcf1b5d Wed Mar 12 17:00:07 2025 -0700
    initial commit of the denovo-db track. Created by Megna Chalamala during her internship with the Genome Browser, refs #28790
  • lines changed 11, context: html, text, full: html, text
    037716fe1767d85858afd7af5e175ea67b8a1c36 Thu Mar 13 13:21:45 2025 -0700
    Updating the long/shortLabels for the denovo-db tracks. Adding a note about the Simons Simplex Collection to the track description page. Adding contact information about the SSC dataset. refs #28790
  • lines changed 3, context: html, text, full: html, text
    1ef2c27ca71759262ecd3ac1a415660aaa9d93a8 Fri Mar 14 15:31:50 2025 -0700
    Adding a link to the Simons Simplex Collection page. Adding the additional mouseover information to the track description page, refs #28790
• src/hg/makeDb/trackDb/human/hg19/denovoDb.ra
  • lines changed 31, context: html, text, full: html, text
    f51f75cd54a6c91df3b555bd625d69859fcf1b5d Wed Mar 12 17:00:07 2025 -0700
    initial commit of the denovo-db track. Created by Megna Chalamala during her internship with the Genome Browser, refs #28790
  • lines changed 8, context: html, text, full: html, text
    037716fe1767d85858afd7af5e175ea67b8a1c36 Thu Mar 13 13:21:45 2025 -0700
    Updating the long/shortLabels for the denovo-db tracks. Adding a note about the Simons Simplex Collection to the track description page. Adding contact information about the SSC dataset. refs #28790
  • lines changed 2, context: html, text, full: html, text
    1b1e34e450c583d3f0dc540ccf680a1e1b11fb44 Thu Mar 13 13:27:01 2025 -0700
    Adding 'from denovo-db' to the longLabel, refs #28790
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    0048454edea05f9e23c1cf9d3994d49214031854 Thu Mar 13 15:10:36 2025 -0700
    Adding the transcript ID to the mouseover, refs #28790
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    f51f75cd54a6c91df3b555bd625d69859fcf1b5d Wed Mar 12 17:00:07 2025 -0700
    initial commit of the denovo-db track. Created by Megna Chalamala during her internship with the Genome Browser, refs #28790
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 3, context: html, text, full: html, text
    2313e3d71f8d98d0166357c1970ba487ba820ef1 Thu Mar 13 13:39:43 2025 -0700
    Updating the gnomAD SV v4.1 track by adding a filter to show only the PASS variants and updating the mouseOver per Anna's request, refs #35295
• src/hg/makeDb/trackDb/human/hg38/gnomadSv.html
  • lines changed 8, context: html, text, full: html, text
    c04d5a3f4a410b489dc90670d2a72737bcaf67b9 Fri Mar 14 14:24:18 2025 -0700
    Adding a note about the quality filter to show only the PASS variants, refs #35295
• src/hg/makeDb/trackDb/human/revel.html
  • lines changed 3, context: html, text, full: html, text
    95d62eaffe46026207539ae1d1e815c1c83779ff Fri Mar 14 17:24:32 2025 -0700
    Fixing the revel values, I accidentally makde the wrong boundaries in my first pass, refs #35352
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 22, context: html, text, full: html, text
    7039e0813fcb8d36a43b3b115b47781ea20488b4 Tue Mar 11 10:02:10 2025 -0700
    Fix frameshift filter setting for dbSnp153 (SO term encoded as 865 not 0865) and dbSnp155 (different SO term: 1589 frameshift_variant instead of 865 frameshift). refs #35344
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 3, context: html, text, full: html, text
    27f8305f94133580996568a3209e5d61bcf5054f Wed Mar 12 14:27:15 2025 -0700
    correct URL for the RefSeq name2 outlink refs #32704
• src/hg/utils/automation/doNcbiRefSeq.pl
  • lines changed 6, context: html, text, full: html, text
    30502ec213047397912c79d846c92ad726af87e6 Tue Mar 11 15:35:07 2025 -0700
    custom description comments on fields for NCBI RefSeq track refs #34704
• src/hg/utils/automation/updateName2.pl
  • lines changed 83, context: html, text, full: html, text
    0f1c9a391299747bdac544ce016ddbf291ca75c7 Wed Mar 12 13:38:03 2025 -0700
    adding parent relation and description column refs #32704
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    864846249d1323e9d51366ea37d6b3684b0abc9b Mon Mar 17 11:05:17 2025 -0700
    New version number v479
• src/utils/qa/checkHTTPS
  • lines changed 2, context: html, text, full: html, text
    d4d9714e4340bf73498fa248644f6f5e9549f60c Tue Mar 11 17:53:10 2025 -0700
    Updating the cron since the ',' is causing issues, No RM
• src/utils/qa/check_Tables_Metadata.py
  • lines changed 160, context: html, text, full: html, text
    2aa31eacd21082add302adf39d080e47ebc01598 Sun Mar 16 15:37:10 2025 -0700
    Adding a new script to replace the checkSyncAndMetaDataAll cron. The python script compares hg38, hg19, mm39, and mm10 tables and metadata tables for hgw1 and hgwbeta discrepancies, refs #35172
• src/utils/qa/makefile
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    c0db81ddad85fa9f45a0155a42c16584cc5424df Sun Mar 16 15:48:14 2025 -0700
    Adding a new script to replace the checkSyncAndMetaDataAll cron, refs #35172
• src/utils/qa/qaTestScript.py
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    3f1e0d4cf01c8a0b0b00ad2421577d3883ec6e86 Sun Mar 16 16:50:05 2025 -0700
    Updating the script so it can locate the updated 'View conversions' link, refs #20666
• src/utils/qa/weeklybld/buildEnv.csh
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    90d90c4d12bbd407e89ff6a357788dee21e155e3 Mon Mar 17 11:03:22 2025 -0700
    v479 final build, refs #35332

• lines changed: 748
• files changed: 41