All File Changes

v442_preview2 to v442_base (2023-01-03 to 2023-01-09) v442

• confs/hgwdev.hg.conf
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    d5835cfe4a6ed89c4d4c5710f376cd05b95cbfeb Sun Jan 8 01:11:24 2023 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 2, context: html, text, full: html, text
    29553f7e87a2e1f8f2113b596d311ad924008924 Thu Jan 5 14:47:39 2023 -0800
    Editing note regarding SNPs on hgLiftover, refs #30426
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 1, context: html, text, full: html, text
    e69775942159246bf5aa3aea511f793e1e331b45 Tue Jan 3 12:43:22 2023 -0800
    Telling R to use 6 characters when converting integers into hex for RGB strings, refs #30426
• src/hg/hgc/hgcData/gtexColorsV4.R
  • lines changed 2, context: html, text, full: html, text
    e69775942159246bf5aa3aea511f793e1e331b45 Tue Jan 3 12:43:22 2023 -0800
    Telling R to use 6 characters when converting integers into hex for RGB strings, refs #30426
• src/hg/hgc/hgcData/gtexColorsV8.R
  • lines changed 2, context: html, text, full: html, text
    e69775942159246bf5aa3aea511f793e1e331b45 Tue Jan 3 12:43:22 2023 -0800
    Telling R to use 6 characters when converting integers into hex for RGB strings, refs #30426
• src/hg/htdocs/goldenPath/trackDescriptions/bigRmskTrackDesc.html
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    d658c2606ff722c12f893fef705f614ccd8483bb Thu Jan 5 11:28:06 2023 -0800
    Fixing 404 link for the Static Page Cronjob 2022-12-15, no RM
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    657ff9bb0c3e403f010c0de7848e6baf12fb2c4e Mon Jan 9 10:14:47 2023 -0800
    New version number v442
• src/hg/js/autocomplete.js
  • lines changed 7, context: html, text, full: html, text
    4abc3ccae28a9c56849029b9ad8c791da1efff0e Mon Jan 9 04:53:29 2023 -0800
    adding small text in autocommplete on hgTracks to indicate that enter or go trigger a full text search, refs #30449
• src/hg/js/hgSearch.js
  • lines changed 1, context: html, text, full: html, text
    a8979eb50f2e97813bbbe9282a2bdebe827d81ac Tue Jan 3 15:24:14 2023 -0800
    Work around 'error' message when searching. Previously, just typing in a term that we can't find is considered an error and we throw up a confusing alert message. Now we work around that specific error message and just let the search UI handle saying no results, refs #30419
• src/hg/js/utils.js
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    538c55556505945753bdb3e6ecbd804f858d3219 Fri Jan 6 11:09:03 2023 -0800
    Fix typo in position regex, refs #30415
• src/hg/lib/variantProjector.c
  • lines changed 7, context: html, text, full: html, text
    43722932e2326cad75a374cc87eeca7a3cf62fc9 Thu Jan 5 16:25:52 2023 -0800
    Make hgVai not crash on some problematic variants. When the cds start site of a transcript overlapping a variant is undefined, we can still annotate the variant as a coding variant, just not the standard frameshift,missense,etc. Related, prevent crashing when certain required structures are NULL, refs #29262
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 3, context: html, text, full: html, text
    ee980ed88db33f4dcde0edca82add49988f5d096 Sat Jan 7 17:09:41 2023 -0800
    adding GCA_024364735.1_CEBAR_Bro_1.0 Chinese key per user request and now have GRCh38.p13 and p14 refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    ee980ed88db33f4dcde0edca82add49988f5d096 Sat Jan 7 17:09:41 2023 -0800
    adding GCA_024364735.1_CEBAR_Bro_1.0 Chinese key per user request and now have GRCh38.p13 and p14 refs #29545
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 4, context: html, text, full: html, text
    6e5da16253fd64e1db11c82b4c55ea244b0270e3 Fri Jan 6 15:38:35 2023 -0800
    Tweaking default human visibilities, refs #30373
• src/hg/makeDb/trackDb/human/hg38/wgEncodeReg.ra
  • lines changed 2, context: html, text, full: html, text
    6e5da16253fd64e1db11c82b4c55ea244b0270e3 Fri Jan 6 15:38:35 2023 -0800
    Tweaking default human visibilities, refs #30373
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra
  • lines changed 1, context: html, text, full: html, text
    6e5da16253fd64e1db11c82b4c55ea244b0270e3 Fri Jan 6 15:38:35 2023 -0800
    Tweaking default human visibilities, refs #30373
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    6e5da16253fd64e1db11c82b4c55ea244b0270e3 Fri Jan 6 15:38:35 2023 -0800
    Tweaking default human visibilities, refs #30373
• src/hg/utils/automation/asmHubRepeatMasker.sh
  • lines changed 4, context: html, text, full: html, text
    83aa49897ba111a554ff5b92659c868ca47ead0b Tue Jan 3 17:16:01 2023 -0800
    correct use of new and improved rmToTrackHub.pl script no redmine
• src/hg/utils/automation/faToHub.sh
  • lines changed 194, context: html, text, full: html, text
    57d6df521aa11c79fa5e6d3f37f35804b3720a28 Thu Jan 5 12:32:08 2023 -0800
    beginning of a script that can convert a fasta file into an assembly hub no redmine
  • lines changed 74, context: html, text, full: html, text
    38942a57b41e68d9432452fa40e9bbae5a9f8085 Thu Jan 5 16:32:57 2023 -0800
    now with appropriate symlinks for bbi and ixIxx files and template description pages for tracks and hub documentation no redmine
  • lines changed 25, context: html, text, full: html, text
    fe1290a83aa62636e7f26092751571e016818493 Thu Jan 5 16:59:10 2023 -0800
    correct NCBI Nucleotide database outlink and now with gap track no redmine
• src/hg/utils/otto/otto.crontab
  • lines changed 1, context: html, text, full: html, text
    b0830c92d6fe1abb3637c4f517ffbda06401223d Tue Jan 3 12:08:02 2023 -0800
    Reducing frequency of a cron, no RM
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    657ff9bb0c3e403f010c0de7848e6baf12fb2c4e Mon Jan 9 10:14:47 2023 -0800
    New version number v442
• src/utils/fastqToFa/fastqToFa.c
  • lines changed 1, context: html, text, full: html, text
    cfe02faff12c12a4e09ee5dd50729c804f98a92f Sun Jan 8 19:19:18 2023 -0800
    increase fixed buffer size to handle ONT RNA-Seq minimap BAMs
• src/utils/qa/searchedTermsCron.py
  • lines changed 1, context: html, text, full: html, text
    ca9f657a88b60c888dcc72d1ed8eb7a652ddbf2b Sat Jan 7 13:37:17 2023 -0800
    Code review change for the method to create a directory, refs #30442
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    d533e27be3e715730536e4bc712c354f312d1ff3 Mon Jan 9 10:13:08 2023 -0800
    v442 final build, refs #30409

• lines changed: 344
• files changed: 26